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Cortex 2 Manual

1. 1 TopHead Rectify QuickID Rectify Create Template Template RB Marker ID Exchange Linear Cubic RB Virtual Calc Smooth Make Delete Copy Cut Cut 2 L_Head Unnamed Template ID Rectify Rectify Join Join Join Join VMs Unnamed Unnamed Outside alls endl MarkerSets New Add Quick Prop DaveBody DaveFace eai m Eea Right Click Menu TopSpne 7 RShoulder In 3 D Display IE m m 10 ShoulderOttset 3D Display Show Properties 11 RBicep Subject 12 RElbow 7 Markers 7 Cameras 13 RWrist 14 RPinky 7 Links 7 Camera Ra 14 RPInky_ F 15 RThumb MarkerSet Names v Cam Field Of View 16 LShoulder Marker Numbers vi Foa 17 LBicep Marker Names Volume 18 LElbow Trados Reference Video 19 List 20 LPinky Camera Coverage Motion Trails elme Virtual Markers iew 22 Midback Force Vectors Camera Coverage ene Sala Scele 1 mm Minimum Number of Cameras raat caer ne 24 RootOffset Keep Centered pant Denn Of Field moiy Only Skin cates Aas Skeleton Axes Auto Rotate 27 BLHip Trajectories Forces Relative Viewing 28 FRHip Num Frames Behind J Forceplate Numbers O Perspective View 29 FLHip 30 RThigh Num Frames Ahead C Backcale O Orthographic View 31 Rknee Motion Trails Model Pose RAnkle Mariari 33 RHeel SF Links KinTools RT Display Options 34 RMidfoot Segment Center of Mass 35 RToe 7 Skeleton i x Linear Velocity eA x
2. Measurement for Y Up X Right mm Measurements for Z Up Y Right mm X Y Z X Y Z 1 0 0 0 1 0 0 0 2 50 0 0 2 0 50 0 3 200 0 0 3 0 200 0 4 0 150 0 4 0 0 150 0 0 0 50 0 0 mm 200 0 0 mm 3 Note This L Frame can be oriented vertically or horizontally If this is oriented on the floor horizontally you must make the proper adjustments to the tables above Index Numerics 10 Camera Setup Typical 3 7 12 Camera Setup Typical 3 7 14 Camera Setup Typical 3 8 16 Camera Setup Two Tier 3 4 Typical 3 8 2 Markers 9 15 2 Panes Top Bottom 4 62 28 Camera 3 Tier Setup 3 4 2D Display 4 15 4 61 4 67 options 4 67 pop up menu 4 67 3 Markers 9 15 3 Point Average Filter 8 9 32 Camera Setup Typical 3 9 3D Display Tab 4 30 3D View options 4 64 pop up menu 4 64 4 Panes Layout 4 61 5 Point Average Filter 8 9 6 Camera Setup Typical 3 6 8 Camera Setup Typical 3 6 Accuracy 9 24 Add MarkerSet 4 10 Adjusting Thresholds 5 12 Aiming Cameras 6 9 All Camera Types 4 25 All Markers Radial Button 8 14 All On Button 6 11 Amplitude Zoom 4 83 AMTI Force Plates Calibration Matrix C 7 forcepla cal C 2 Using C 7 AMTI Gain Setting C 7 AMTI or Bertec Force Plates B 4 Cortex 2 1 Reference Manual Analog Acquisition Rate 5 16 B 11 Analog ASCII Row Column E 11 Analog Channel Names Replace 4 44 analog data files opening F 6 Analog data graphs 4 15 An
3. m Mtracking Events Connect To Cameras Disconnect Use Raw Files Settings oT crs 1 0 J a J aron J 1 I 2 3 sil 5 I g 564 Frames 120 FPS SXUp Unitsimm Analog 600 00H2 Pose ID in Message Center New Subject Button Reset IDs Button Recommended Procedure Get a Range of Motion Trial and Make a Template Updating the Template also updates the Model Pose so before clicking the Update Template button you should again get your new person into something close to the Pose position The changes can be saved in your capture file if you want After you Update the Template the template is then re sized to the new person s limb lengths and marker placements Note that the changes in the lengths as recorded in the range of motion trial is still saved so that you will not need to do another range of motion The new template should work well for many sizes and marker adjustments using the same marker set 1 Create your own library capture file for the marker set This library contains your markers set with the template created from your range of motion capture files and your Pose ID 2 When creating the library capture file start with the range of motion capture type file in the neutral position facing X arms down feet slightly apart to show all the markers That would be frame 1 to make the Pose ID easy to find When you create the Template for your library file you would have
4. Screw Screw Terminal Cortex Setup Terminal Cortex Setup Channel Name Channel Name 1 CH 1 49 CH 21 2 CH9 50 CH 29 3 AI GND 51 Al GND 4 CH2 52 CH 22 5 CH 10 53 CH 30 6 Al GND 54 Al GND 7 CH3 55 CH 23 8 CH 11 56 CH 31 9 Al GND 57 Al GND 10 CH 4 58 CH 24 11 CH 12 59 CH 32 12 AI GND 60 Al GND 13 NOT USED 61 NOT USED 14 Al GROUND 62 Al GND 15 NOT USED 63 NOT USED 16 NOT USED 64 NOT USED 17 CH5 65 NOT USED 18 CH 13 66 NOT USED 19 Al GND 67 NOT USED 20 CH 6 68 NOT USED 21 CH 14 69 NOT USED 22 Al GND 70 NOT USED 23 CH7 71 NOT USED 24 CH 15 72 NOT USED 25 Al GND 73 PFI O 26 CH8 74 PFI 1 27 CH 16 75 PFI 2 28 NOT USED 76 PFI 3 29 NOT USED 77 PFI 4 30 Al GND 78 PFI 5 31 NOT USED 79 PFI 6 32 NOT USED 80 PFI 7 4 7 kQ Resistor amp A D Sync Cable amp Jumper Cable 33 CH 17 81 PFI8 34 CH 25 82 D GND 35 Al GND 83 PFI9 36 CH 18 84 D GND 37 CH 26 85 PFI 10 38 AI GND 86 D GND 39 CH 19 87 PFI 11 40 CH 27 88 D GND 41 Al GND 89 PFI 12 42 CH 20 90 D GND A D Sync Ground amp Jumper Cable 43 CH 28 91 PFI 13 44 Al GND 92 D GND 45 NOT USED 93 PFI 14 46 Al GND 94 D GND 47 NOT USED 95 PFI 15 48 Al GND 96 5 V 4 7 KQ Resistor A Jumper Cable is required if multiple NI USB 6259 units are being used together gt 64 channels B 12 Appendix C Force Plate Configuration Forceplate cal File Setup General Information Force Plate File Data Force Plate Scaling
5. Cortex 2 1 Reference Manual Appendix I Useful Blank Forms Human Body Outline Front Project Date Appendix I Useful Blank Forms Cortex 2 1 Reference Manual Human Body Outline Side Project Date Cortex 2 1 Reference Manual Appendix I Useful Blank Forms Human Body Outline Back Project Cate Appendix I Useful Blank Forms Cortex 2 1 Reference Manual CLF 200 Small Calibration L Frame 200 mm 0 150 0 mm ieg MolonAnal Setup Instructions 1 Open the Calibration Settings Window Tools gt Calibration Setup 2 In the Calibration Frame tab enter all the information into the text boxes or use the CLF 200 Calibration Presets if present 3 In the Lenses Orientation tab flag each camera as either Normal or Alternate Alternate should be selected if the camera is below the horizontal line from marker 1 to marker 3 see below and aiming up 4 Mount the Small Calibration L Frame in a vertical position e g against a wall on a stand or horizontal flat position 5 Remove or cover the L Frame prior to starting your motion capture session 6 If you make your own L Frame it must be set to a right hand coordinate system with markers 1 2 and 3 on the horizontal line and marker 4 on the vertical line Also marker 2 must be between 1 4 to 1 3 of the distance between markers 1 and 3 Calibration Settings for Vertical Positioning
6. Here you can specify the size of your capture volume The measurement units are the same as the specified calibration units see Calibration Frame This can be used to provide visual feedback in the 3d display It does not affect the tracked data in any manner Note In the Plugins gt X panel the Delete Outside Volume feature will delete any marker data outside of the capture volume Note The Volume display is used as a visual aid when aiming the cameras in real time during setup 4 19 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Calibration Tab gt Other Figure 4 16 Calibration gt Other Settings Tab Fle Structure Tracking Cameras Playback 3D Display Post Process Tools Misc d Params Plugins Calibration Frame Lenses Orientation Capture Volume Other Unconstrained followthrough iterations Extra wand processing iterations 0 Include wand metric refinement in calibration Origin Offset Applied at L Frame Calibration Time Property X Translation Y Translation Z Translation Unconstrained Follow Through Iterations This relaxes the wand length constraint and executes additional measure ment iterations These relaxed iterations are the equivalent of doing con secutive Refine Calibrations using the want data Include wand metric refinement in calibration This expl
7. Edit Help Marker Options IV Stream Marker Data Marker Representation Spheres Locators Scaling Option Scale C Inverse Scale Marker Scale Factor fi 0000 Marker Cloud Name Scott Get EVaRT Marker Cloud s Skeleton Options IV Stream Skeleton Data Scaling Option Scale C Inverse Scale Skeleton Scale Factor fi 0000 Skeleton Name s far EVaRT Skeletons gt I Drive skeleton s using only rotational data I Assume HTR Bones in Scene Get EVaRT Skeleton s Send Selected Skeleton s ta EVaRT EVaRT Host Computer EagleHost Connect to Host Start Streaming Note Only selected skeletons will be driven when connecting and streaming Apply Close Apply and Close Cortex 2 1 Reference Manual Chapter 1 Introduction OrthoTrak OrthoTrak is a completely integrated full body gait analysis package de signed for use in clinical and research studies of human locomotion The system provides state of the art software designed to be used by clinicians in orthopaedics neurology and physical therapy or for any person inter ested in assessing locomotor abilities of humans The system provides e quantification of 3D body segmental and joint motions e analysis of the forces occurring in locomotion e records of neuromuscular function through electromyography Intended Use OrthoTrak is designed primarily for analyzing a walking motion over level ground but
8. 5 U_S lt Empty gt Glu amp lt Emotw gt en 100 m celeton aa 200 PURE OOE Se es ee UALTA RLA YALE VALSA PLAANE Ae ALA 300 400 50 600 700 800 900 0 2 CCC Cee Cole 921 Frames 120 FPS Z Up Units mm Analog 600 00 Hz Menu Bar File Menu File gt Load Capture Post Process Dashboard The Menu Bar selects the primary items for Cortex functionality These include file management layout control data views tools and help The following is a list of the basic operations that can be performed on Setup and Capture Files All of these items are accessible from the File menu Prompts the user to select a Capture for loading into Post Processing All MarkerSets and data files associated with the capture are loaded A pre 4 3 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual view of what files will be loaded is visible on the right hand side of the di alog Below the preview is a check box which allows the Setup File to be loaded optionally Figure 4 3 Load Capture Dialog Load Capture Look in jo Golf Swing with Temper OQ 2 fa My Recent Documents E Desktop 9 My Documents My Computer L o UMET Filename ears wing_2 cap v Places Files of type Capture files cap 7 Cancel 21x Preview Setup SetupWithE vents cal Analog Data RawFiles GolfSwing_2 Go
9. ccccccceceeceeseeeeeeeeeees A 7 Appendix B Analog Input Hardware and Software ETIO a aaa acm aetna B 1 Installing NIDAQ Software on an Cortex Computer ceeee B 3 Analog Signal Naming Conventions cccceceeeeeeceeeeeeseeeeeeeeaes B 4 32 Channel 16 Bit NI USB 6218 Configuration cccceceees B 5 NI USB 6259 Analog Channel Connections ccccccseeereeeeees B 11 Cortex 2 1 Reference Manual Appendix C Force Plate Configuration Forceplate cal File Setup General Mioma C 1 Force Plate File Data reinen eaae aE Eaa C 4 Force Plate Scaling Factor X Width and Y Length 0 ee C 6 Using AMTI and Bertec Force Plates cccccceccecceeeeeeeeeeeeeeeeeees C 7 Using Kistler Foree PIKES a icincisiwiesiainnieinimmmauniiinianaien C 10 Appendix D SDK Software Developers Kit SDK oa Bente eee ner er eee one oer eee ere a EEE D 1 SDK Programming Example Write your own Streaming Plugin D 1 Appendix E Import and Export File Formats WENE W a a ee ee ee ERC eRe aE er I oe MEE mee E 1 FAG WGA 1 EEE A AAA A AEE E E esa A E 2 PRJ Legacy Cortex Project File wssscissisierinevedisvessacatsecsaninivarnisencvees E 3 TRO Taek ROW C OUI sorei ra E 3 HTR Heirarchical Translations amp Rotations cccccccseseeeeeeeeees E 6 ANC Analog ASCII Row Column cccccccceeescceeessseeeeeeeneeeees E 11 TS Time Series Files from the Cortex Analysis
10. t Save As Group Save Selected As Group Select at Unselect an Select Al Unselect a Clear a Installation The Fusion Object Loader plugin is part of the standard Cortex software installation It uses a Dynamic Link Library Fusion dll file which Cor tex uses as an additional resource This file is installed into the C Pro gram Files Motion Analysis Cortex2 Release2 X X Plugins folder Any Cortex plugin dll placed in this folder will automatically be recog nized and used by Cortex 7 4 Cortex 2 0 Reference Manual Chapter 7 Motion Capture Tab Using the Fusion Object Loader Note When initially installed the Fusion Object Loader control is found in the Plugins tab of the Cortex interface As an option you can move the plu gin to another tab if it better fits the way you use it For example you may wish to move the Fusion Control panel to the Motion Capture tab since that is where it is typically used To move the Fusion control panel to a new tab select the Tools gt Set tings gt Plugin tab From there you can choose from the list of available tabs The Title bar of the Fusion Object Loader displays the number of objects that can be loaded into your version of Cortex in parenthesis On the left there is a set of radio buttons to select the type of file from which you wish to load objects including cap Cortex capture files prop Cor tex pr
11. Fractions of the whole Center of Mass Radius of Gyration Segment Mass yi z x K z Pelvis 01117 05 0 551 0 615 0 587 R Thigh 0 1416 0 329 0 329 0 149 LThigh 0 1416 0 329 0 329 0 149 R Shank 0 0433 0 251 0 246 0 102 LShank 0 0433 0 251 0 246 0 102 R Foot 0 0137 0 257 0 245 0 124 L Foot 0 0137 J 0 257 0 245 0 124 Torso 0 3229 0 294 0 342 0 233 Head 0 0694 0 362 0 376 0 312 R Upper rm 0 0271 0 285 0 269 0 158 L Upper m 0 0271 0 285 0 269 0 158 Segment Sum 1 Normalize Load Calculate Kinetics 10 20 30 1 1 Tr T T T T mT prrrerrrrrprere T T rrr 40 50 60 70 80 90 100 110 120 ar 0 15 Calculate _ ae connec E Lee b 6 Calculate 151 Frames 60 FPS 2 Up Unitsimm Analog 960 00 Hz The Mass Model Editor shows in tabular format how the mass is distrib uted throughout the segments of the current skeleton model For more information refer to the KinTools RT User s Manual 4 50 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt BioFeedTrak Event Editor The Event Editor Dialog is used to edit Event and Cycle definitions The Event Editor form consists of two main components the Events Area and the Scripts Area The Events Area is used for adding removing editing Event and Cycle definitions The Scripts Area is used to view the status of the scripts that are used by the Events Events
12. MattPickup1 tre Import_MattPickup1 cal Import_MattPickup1 cap MattSwant tre Import_MattSwant cal Import_MattSwanl cap MattRun tre Import_MattRunt cal Import_MattRunl cap Status Log File Exporting 4 8 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface File gt Load Capture Prompts the user to select a capture for which portions will be loaded into Live Live Mode The MarkerSets and raw files are loaded for re recording A preview of what files will be loaded is visible on the right hand side of the dialog Below the preview is a check box which allows the Setup File to be loaded optionally This can be useful for re tracking pre recorded Cap tures from raw data VC files Figure 4 8 Load Capture Live Dialog M Preview Look in Golf Swing with Temper z O P gt a Setup Setup WithE vents cal fe YC Data My Recort RawFiles GolfSwing_2 GolfSwing_2 vc1 Documents B Analog Data a RawFiles GolfSwing_2 GolfSwing_2 anb E E Video Data RawFiles GolfSwing_2 GolfSwing_2 avi Dekio Audio Data Timecode CyberGlove Data E MarkerSets My Documents Body mars Club mars er a My Computer EL CS My Network File name Gors wing_2 cap X Places Files of type Capture files cap Cancel T Load Setup SetusWith ves cat File gt Load Setup Prompts the user to select a Setup File cal from which a Se
13. Figure E 3 An Example of a HTR Version 1 File Header FileType htr DataType HTRS FileVersion 1 integer NumSegments 20 integer NumFrames 196 integer DataFrameRate 30 integer EulerRotationOrder XYZ CalibrationUnits mm RotationUnits Degrees Header keywords are followed by a single value single word string Hierarchical translations followed by rotations and Scale one word string one word string one word string HHHHHHH HH OH GlobalAxisofGravity Y character X or Y or Z BoneLengthAxis Y ScaleFactor 1 0000 SegmentNames amp Hierarchy CHILD PARENT LowerTorso GLOBAL UpperTorso LowerTorso LCollarBone UpperTorso RCollarBone UpperTorso LUpArm LCollarBone RUpArm RCollarBone LLowArm LUpArm RLOwArm RUpArm LHand iLOwArm RHand RLowArm LPelvis LowerTorso RPelvis LowerTorso LThigh LPelvis RThigh RPelvis LLowLeg LThigh RLowLeg RThigh LFoot iLowLeg RFoot RLOwLeg Neck UpperTorso Head Neck BasePosition SegmentName Tx Ty AF Rx Ry Rz BoneLength LowerTorso238 320832923 726971241 2948288 8069650 0000002 422863 141 720766 UpperTorso0 000000141 7207660 000000 9 396187 0 112582 0 4 226674324 970754 LCollarBoneO 000000324 9707540 000000 8 9120410 520925 117 992062155 689602 RCollarBoneO 000000324 9707540 000000 7 516124 0 516778118 838556127 553756 LUpArm 0 000000155 6896020 000000 11 284636 3 556895 24 261557 273 483757 RUpArm 0 000000127 5537560 000000 12 990029 2 960321 24 2508
14. GolfSwing_1 cap 4 72 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface The concept behind the Join Virtual and the Virtual Marker definitions are the same and are much more stable and more useful than the classic Rigid Body data filling mechanisms The reason is that you get to choose two sets of three markers in decreasing importance that determine the re placement data These three markers are 1 the Origin Marker 2 the Long Axis Y Marker 3 the Plane XY Marker The two sets of virtual marker definitions allow you to continue generat ing virtual marker data if one of the definition markers is not being tracked For the Join Virtual function to work properly you will need a minimum of three different support markers among the six spots to fill If you are in Streaming mode from cameras or VC files the first definition set is used If you are in Post Process mode you may choose which defi nition set works best Figure 4 58 Virtual Marker Definitions Streaming vs Post Processing Virtual Marker Definitions Three Marker Value O Three Marker Ratio O Two Marker Value O Two Marker Ratio O Emr Enter Name of Virtual Marker Origin Marker Long Axis Marker Plane Marker KenterHead 5 M_F_Head 3 M_B_Head 4 M_R_head Snap to this Marker optional Long Axis mm Plane mm 0 00 Perpendicular mm SS Calculate Virtual Markers New V Marker Definition Delete V Marker
15. Note Positioning Aiming Cameras Not all of the cameras need to see the L Frame Configurations with only 1 2 of the cameras seeing the L Frame work very well provided there is sufficient overlap in the wand data In the Calibrate panel under the Calibration tab check Camera Aiming and then press Run The cameras that see four individually defined mark ers will instantly adjust to their approximate positions in Cortex as in Figure 6 7 If a camera does not see all four markers or sees more than four markers it will be displayed at the origin facing down as in Figure 6 7 This camera will not have a seed calibration which is acceptable Refer to Extending the Seed Calibration on page 6 20 If the camera is not seeing all of the points first try one or more of the following steps 1 Adjust the threshold to see four centroids Insert Masks to eliminate stray data points 3 Move the camera position so that it sees four defined markers In Fig ure 6 7 a poorly positioned camera will be shown as a camera situ ated at the origin 4 If one camera is seen in the exact opposite position in the room the orientation up down must be changed in the Lenses tab in the Cali bration Settings menu This usually occurs when cameras are tilted more than 90 or mounted upside down Figure 6 7 Poorly Positioned Camera 4 Results in a Non Seeded Camera Camera 4 Ble rots Yew Tous Help Dapatent Dere 1010de Fa Saip
16. These parameters only affect Post Process s Boot Strap rectification algorithm This is the non template non rigid body rectify Identifying Parameters Linkage Stretch Parameters To Reconsider std dev Max Acceptable std dev Linkage Stretch Parameters To Reconsider std dev If a link stretches more than the set amount the path is snipped into two paths where the link stretches too much This happens if markers come to gether and pull apart and the identity is not correct when they pull apart The software may not see it right away but after a few frames the linkage for the wrongly named markers get too long and the path is cut The big ger the number the more the link is allowed to stretch before it is cut Smaller means fewer errors more cuts Larger means more stretching is allowed before the cuts It is measured in multiples of the standard devia tion of the linkage length to make it accommodate linkages that normally change a lot head to shoulder and linkages that do not change much el bow to wrist Linkage Stretch Parameters Max Acceptable std dev If there is a missing marker and there is an Un named marker within this distance of known linkages the Un named marker is accepted as a Named marker 4 40 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Settings gt This provides a custom function to set where the Plugins tab will reside Plu
17. e Above Calculation Floor All pixels above the Greyscale Calcula tion Floor setting are rendered in greyscale based on the brightness of the pixel All other pixels are rendered black e Above Threshold All pixels above the camera Threshold setting are rendered in greyscale based on the brightness of the pixel All other pixels are rendered black e Topographic Currently undefined e Binary All pixels above the Greyscale Calculation Floor setting are rendered pure white while all other pixels are rendered black e Saturated Pixels Only fully saturated pixels are rendered e Unprocessed tThe raw greyscale image is rendered Greyscale Calculation Floor raw sensor values This is a parameter to the camera s on board centroid calculation algo rithm Any pixels below this value will not be used when performing cen troid calculations The units for this setting are raw camera sensor values Greyscale Calculation Margin pixels This is a parameter to the camera s on board centroid calculation algo rithm The first step in the camera s image processing algorithm is to find a region of the greyscale image that a centroid exists in The camera then calculates the centroid within that region This setting adds an extra mar gin around the camera s calculated region of interest causing more pixels to be included in the calculation Asymmetry Limit pixels This is a parameter to the camera s on
18. 3 Load a Capture with tracks that are identified Only identified tracks are refined Unnamed marker data is not affected 4 Select X Panel gt Refine Tracks The message appears as shown in Figure 10 4 Figure 10 4 Retracking Identified TRB Data Message This will retrack the identified trb data using the loaded raw data files 5 Select OK 6 Select File gt Save Capture if you want to save the results 10 3 Chapter 10 Plugins Tab Cortex 2 1 Reference Manual Global Marker Data Adjustments Model Adjustment Delete Artificial Data Load Another Tracks File The Global Marker Data Adjustment section allows the user to modify the tracks data by translating rotating and or scaling the data This is an op eration that applies to all marker data over all the tracks It s especially handy for converting the overall orientation of the data such as from a Z up coordinate system to a Y up coordinate system The Model Adjustment section allows the user to update the Calcium Solver model pose data and the template model pose data simultaneously this is the data displayed when the Show Model Pose flag is on The marker data in the model pose is used for two different operations as a starting pose for the template when doing a New Subject operation and as the matching base pose for the skeleton in the Calcium Solver model Doing both adjustments at once is important to maintaining the integrity of
19. Figure 9 6 Marker Parameters Cortex Jodi cal Led Twe Current Directory c Program Files Matic v C Browse Exe Markers Treeview E Jodi Markers 41 M_BL_Head M_FR_head Markerset M_BR_Head x M_RShoulder M_RBicep M_RElbow M_RForeArm M_Rinsidevvrist M_ROutsideVYrist M_RHand M_FL_Head Color E i0 Optional False Ms aa Skeleton Ke Calculate fs Loade 8240 Frames 60 FPS p Units imm pe 9 14 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab Tree View gt VMarkers Virtual Markers Virtual Marker Definitions Virtual markers are markers that get their position from a combination of the position of two or three actual markers in the motion capture data Typically a virtual marker is used to generate the actual joint center posi tion of the performer or subject being motion captured This is neces sary since the actual markers lie on the outside of the performer Joint center markers are desirable for use with analytical and skeleton recon struction tools There are two methods for defining Virtual Markers VM 1 2 Marker Two markers are used to define a line in space A new vir tual marker can be calculated anywhere on this line 2 3 Marker Three markers are used to define a plane in space A new virtual marker can be calculated anywhere in space relative to the ori gin of this plane The placement of the virtual marker a
20. Figure 8 10 The Curve After an Application of the 5 Point Average Filter The type of smoothing you choose depends on your needs and how much and in what way you want to change your data It is perfectly reasonable to make successive applications of the filter s to affect the data in various ways The number of possible combinations are extremely high so some experimentation will be necessary to find the right one for you 8 9 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Unnamed Markers Note Unnamed markers are defined as unidentified markers that are either real or not real Some unnamed markers represent good data yet were uniden tified during a motion capture session Others are called ghost markers and should be deleted Ghost markers can also be removed from future data captures by going to the Tracking panel in Motion Capture and set ting the Min Cameras to Use minimum number of cameras to use to 3 Caution should be taken here as this process may also eliminate good data 8 10 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Post Process Tool Strip Figure 8 11 Post Process Tool Strip Cortex SetupWithtyents cal GollSwing_1 cap Cuman Drectay C Progam Fiee Motun Analyen CatenZ S ampkee GotS wang wih Brot eed rah Biore System Calbration Motion Capture Post Process Modal Edir Plugins Presentation Markers segments zi e o A 4 a N
21. zero based index Use the value as the volume control swSoundPlay 440 Value End Sub 4 53 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tools gt BioFeedTrak Event Timeline The BioFeedTrak Event Time Line Dialog is used to display and edit which frames an event occurs on These can be automatically detected and manually set changed Form Controls Event Type Event Name Event Frame Displays the information about the currently selected event The Event Frame up down can be used to change the frame number for the event Snap To Move the selected event to the current frame Auto Discover All Clears all event frames and does an automatic discovery over all frames for all events Clear All Clears all event frames Buttons These buttons add the corresponding event on the current frame Editor Opens the Event Editor Refresh Forces the popup to refresh itself Time Line Visualization The timeline displays events as vertical lines and cycles as a transparent fill between events The selected event is rendered extra thick Mouse Controls Controlling the Current Frame Left Click to select Left click and drag to scrub Selecting an Event Ctrl Left Click is used to select an event Modifying Event Frames To move an event select it continue holding Ctrl Left Click and drag it A frame can also be moved one frame at a time by selecting it then Ctrl Shift Left Click o
22. All cameras or the Selected cameras based on the setting of the Edit These Cameras radio button at the bottom of the Cameras tab Threshold The camera threshold is used to determine what pixels should be included in the edge detection algorithms that take place on the Motion Analysis cameras Any pixels below this threshold will be considered back ground noise and be ignored 4 25 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Brightness The brightness setting determines how bright to set the camera ring light This is specified as a percentage of the maximum brightness for the ring light Min Horizontal Lines per Marker This is the minimum number horizontal scan lines required for a group of pixels to be considered a marker in the camera s 2D view Note This is the per camera setting and is only used if the Use Per Camera Settings box is checked in the Settings gt Tracking tab If these settings are not being used the slider will be disabled Max Horizontal Lines per Marker This is the maximum number horizontal scan lines allowed for a group of pixels to be considered a marker in the camera s 2D view Note This is the per camera setting and is only used if the Use Per Camera Settings box is checked in the Settings gt Tracking tab If these settings are not being used the slider will be disabled Settings for Raptor Cameras Only Figure 4 20 Raptor Spe
23. Motion Analysis Corporation Software License Agreement Terms and Conditions Definitions The following terms are defined for the purpose of this Agreement as follows a Designated System means the specified computer system described on the facing of this agreement which Licensee has purchased from the Licensor b Licensed Program means the software program described on the facing page of this Agreement in object code form only any updates subsequently provided by License all permitted copies made by Licensee and all basic or related materials pertinent to such programs License Under a license granted under this Agreement License is authorized on a non exclusive basis to use the Licensed Program on the Designated System License shall refrain from taking any action such as reverse assembly or reverse compilation to derive a source code equivalent of the Licensed Program A license shall be valid until terminated under this Agreement The license fee is part of the purchase price of the Designated System Title The original and any copies of the Licensed Program in whole or in part which are made by Licensee are the property of Licensor Copies With each license Licensee may make one 1 copy of the Licensed Program in object code form only for use by Licensee with the Designated System for backup or archive purposes Licensee agrees to maintain records of each copy of the Licensed Program and the serial number o
24. Rigid Body Rectify and Template Rectify assume that all the current marker identifications are correct They are intended for continuing the identification process without undoing previous work Rigid Body Rectify is a tool that could be considered a stand alone tool It does not use anything from the marker set definition at all When the tool is activated 1 The three or more selected markers are dynamically turned into a Rigid Body definition and measured 2 The previous frame and the current frame are then used to predict the next frame 3 Identify the frame This stops when less than three markers of the original selected markers is identified If one or more markers are already correctly identified then that can help prevent errors This has been used to identify the entire body 1 Select ALL the markers minus the obscured ones The starting frame must be identified manually Press Rigid Body Rectify Go forward to the frame where the misidentification occurred Make unnamed Repeat steps 2 through 5 ea a a Data within the selected frames including endpoints will be copied and available for Paste Cut or copied XYZ marker data will be inserted into the data set begin ning with the current frame 8 18 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Rigid Body Join Fe a Rectify Functions What They Do and When To Use Them The rigid body join feature has been c
25. g a i Cick Alore ChitCick Togge A bak MOR Oi VTevvrsi ae B 1d QuckID Rectily Cese Tengiste Template Marker ID Exchange Cubic Vrtud Cak Smooth Make Rectly Delete Cut Ct Search PP 21m L Hesa Tempio 10 Ractfy kin kin Ms Unnamed Urnamod Unnamed Outside Settings EO v O Vee SALamo QuickID Rectify Create Template Template Marker ID Exchange Cubic Virtual Calc Smooth Make Rectify Delete Cut Cut Search PP Template ID Rectify Join Join VMs Unnamed Unnamed Unnamed Outside Settings All of the Identifying tools are accessible using hot keys panel buttons and right mouse menu items on the 3D View and XYZ Graphs Note You can rearrange add and delete the icons by right clicking on the Post Process Tool Strip To move the icon to a different location on the Tool Strip press the Alt Left Mouse button and drag it to the new location The Tool Strip order is remembered the next time Cortex is launched al lowing for user customizing and convenience Also any of these func tions can be stored and accessed under Hot Keys Default Icons The following are the default icons as set by the initial installation of the Cortex software Quick ID Identifies the selected marker identifying all markers one by one accord ing to the list It will normally select with auto incrementation auto incre ment The user identifies the markers in the MarkerSet list one marker at a time from the top of the list The marker list will a
26. s data line This action will deselect all other markers leaving only the display of the Target Marker Other important view options that are general in nature are described here These options can only be accessed as XYZ Graphs right mouse pop up menu items e Auto Scale dynamically scales the display to accommodate data in the visible frame range e Uniform Scale the display such that X Y and Z conform to a uniform range e Show Residuals and Cameras shows residuals and cameras along with XYZ data 8 4 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Joining Gaps in Data Filters Join functions are not always confined to selected frames as a conve niencer For example if you select only one frame in a gap of marker data tools intended to fill that gap will seek out appropriate endpoints to that gap store all necessary data in an undo buffer and effect a repair to that gap without requiring you to tediously hand select the appropriate endpoints The smooth function smooths data within the selected frames with a But terworth Filter algorithm This is a low pass high block two pass 4th order zero phase shift filter This data can be spikes created by frames in which a marker has experienced an acceleration greater than or equal to a selected value or gaps missing data Manually selecting frames is done by dragging the mouse in the XYZ Graphs with the middle mouse button pressed Low and High Se
27. 1 Linearly transform the data to be filtered so that the first and last points are zero 0 2 Double the number of points to be filtered The data goes into the middle 2 4 3 4 3 Mirror image the first half of the data into the first quarter of the expanded points 4 Mirror image the second half of the data into the fourth quarter of the expanded points 5 Finally run the two pass fourth order filtering and then restore the data through the inverse transform done in step 1 8 8 Cortex 2 1 Reference Manual Chapter 8 Post Processing Tab 3 Point Average and 5 Point Average Filters Two other filters the 3 Point Average and the 5 Point Average filter are provided as an alternative to the Butterworth filter In some circumstances particularly with facial data these can provide better results The 3 Point Average smooths the data by taking a data point on either side of a given original data point and averaging their values into the original one to cre ate a new data value for that sample This filter provides a moderate amount of smoothing as shown below Figure 8 9 The Curve After an Application of the 3 Point Average Filter The 5 Point Average filter works just like the 3 Point Average filter except that it uses 2 data points on either side of the original data point to pro duce a new value Since the width of the filter is wider the results are more aggressive which creates more smoothing as seen here
28. 1 Load a Capture into Post Processing 2 Select Data Views gt Analog Graphs 3 In the Analog Graphs display right click and select the Shift the Data option 4 In the Visible Channels dialog select only the channels you want shifted typically the EMG data 5 In the Shift the Data dialog select the Selected Channels option 6 Set the value for the Shift the data this number of samples This can be calculated by the following formula of samples to shift Analog Sample Rate x Time Delay For an analog sampling rate of 1200 samples second and a time delay of 15 ms 15 x 10 seconds the calculation would be of samples to shift 1200 samples sec x 15 x 10 sec 18 samples 1 To input this frame shift correctly enter the number as negative value 18 Negative values indicate a shift to the left decreasing the delay pos itive numbers indicate a shift to the right increasing the delay 2 To change the entered value from red to black press Enter 3 Click on Apply When it prompts you with Would you like to re write the analog file select Yes Figure 5 9 Shift the Analog Data Dialog Box Shift the Analog Data All Channels Selected Channels Shift the data this number of samples 18 Apply 5 15 Chapter 5 System Tab Cortex 2 1 Reference Manual Maximum Analog Acquisition Rate Terminal Configuration RSE Referenced Single Ended NRSE Non
29. 10 5 V 4 7 KQ Resistor 42 5 V Not Used 11 D GND A D Sync Ground amp Jumper Cable 43 D GND Not Used 12 AO 0 Not Used 44 NC Not Used 13 AO 1 Not Used 45 NC Not Used 14 AO GND Not Used 46 Al GND Not Used 15 CH 1 47 CH 17 16 CH9 48 CH 25 17 CH2 49 CH 18 18 CH 10 50 CH 26 19 CH3 51 CH 19 20 CH 11 52 CH 27 21 CH 4 53 CH 20 22 CH 12 54 CH 28 23 Al SENSE Not Used 55 Al GND Not Used 24 CH5 56 CH 21 25 CH 13 57 CH 29 26 CH 6 58 CH 22 27 CH 14 59 CH 30 28 Al GND Not Used 60 Al GND Not Used 29 CH7 61 CH 23 30 CH 15 62 CH 31 31 CH 8 63 CH 24 32 CH 16 64 CH 32 Note A Jumper Cable is required if multiple NI USB 6218 units are being used together gt 32 channels Note NI Numbering starts at Channel 0 where Cortex channel numbering starts at 1 For example AI 0 corresponds to Cortex Channel 1 B 10 Cortex 2 1 Reference Manual Appendix B Analog Input Hardware and Software Maximum Analog Acquisition Rate When measuring 64 or more channels with 16 bit resolution the maxi mum analog rate is determined by one of the following considerations 1 The maximum throughput of the National Instruments NI A D product 2 The video sample rate multiplied by 255 The NI USB 6218 A D unit which is often supplied with Motion Analy sis systems has a maximum throughput of 250 000 samples sec per unit So two units with 64 channels would have the ability to collect up to 500 000 samples sec
30. 100 GByte hard drive IDE or SCSI USB 2 0 Ports x3 Internal CD RW drive 1 Gigabit Ethernet Network Interface Card NIC quantity dependent on the following options e Connecting to camera network e Connecting to Internet e Streaming to SDK or plugins 104 key keyboard Three button mouse The program requires a middle mouse button for zooming and selecting in several of the graphical panes 200 GByte hard drive IDE or SCSI USB 2 0 Ports x4 Internal CD DVD RW Two Separate Gigabit Ethernet Network Interface Cards NIC quantity dependent on the following options e Connecting to camera network e Connecting to Internet e Streaming to SDK or plugins 104 key keyboard Three button mouse The program requires a middle mouse button for zooming and selecting in several of the graphical panes IEEE 1394 standard Firewire for Reference Video option IEEE 1394 standard Firewire for Reference Video option Hardware Using Raptor Eagle and Hawk Digital Cameras Using Falcon Cameras Middle Mouse Button Cortex will perform best on a dual processor host computer with an OpenGL graphics card This is used for all Motion Analysis camera types The Raptor Eagle and Hawk digital camera motion capture system in cludes a set of digital cameras with ring lights LAN power cables and a power hub and ethernet switch Cortex does not support collecting data with analog camera systems Fal con
31. 3 25 Chapter 3 Camera Setup Cortex 2 1 Reference Manual The Ping command should return a message similar but not exactly the same as follows Pinging 10 1 1 201 with 32 bytes of data Reply from 10 1 1 bytes 32 time 20ms TTL 128 Reply from 10 1 1 bytes 32 time 20ms TTL 128 Reply from 10 1 1 bytes 32 time 20ms TTL 128 Reply from 10 1 1 bytes 32 time 20ms TTL 128 Ping Statistics for 10 1 1 201 Packets Sent 4 Received 4 Lost 0 0 loss Approximate Round trip times in milliseconds Minimum 0ms Maximum 242ms Average 128ms If you are getting a message that says Pinging 10 1 1 201 with 32 bytes of data Request timed out Request timed out Request timed out Request timed out Ping Statistics for 10 1 1 201 Packets Sent 4 Received 0 Lost 4 100 loss Approximate Round trip times in milliseconds Minimum 0ms Maximum 0ms Average 0ms Then the camera is not responding to Ping requests 6 This last step involves trying to determine if there is a camera cable or connection that may be causing the system to not identify the cam eras The best way to do this is to unplug all of the cameras from the EagleHub and then individually plug each camera in do not connect any other camera cables to the hub It does not matter which RJ45 port you connect the Ethernet switch The same applies to the power connector The only other connection going into the EagleHub is the cable coming from the
32. 3 Degrees of Freedom A single marker can have a maximum Translation of 3 Degrees of Freedom XY amp Z Translations in X Y and Z over time Translation Two Markers 5 Degrees of Freedom X Y amp Z Side to side 3 Markers 6 Degrees of Freedom Translation Rotation about the bone axis X Y amp Z i u xi Side to side 9 17 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual Figure 9 10 Examples of Hinge Joints Knee Modified Hinge Joint Secondary Rotation about the bone of the lower leg Limited to a few degrees Note No Rotation about the bone axis at the knee Secondary Rotation about the bone axis of the lower fe A Primary Rotation Flexion Extension Note Hinge Joint assumed only to flex and extend no other rotations Elbow Hinge Joint Ankle Modified Hinge Joint Primary Rotation Flexion Extension Secondary Rotation Inversion Eversion 9 18 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab Calculating Virtual Calculate virtual marker trajectories based on the Virtual Marker defini Marker Tracks tions in the current MarkerSet Virtual Markers are cleared when you track any new data Track and edit your trials before calculating the Virtual Marker Tracks 1 Open the Virtual Markers Definitions form by clicking the V Marker Definitions button in Model Edit or by selecting Tools gt Virtual Marker Definitions in the Menu Bar 2
33. Camera Setup Note Control Points e The calibration L frame is oriented correctly in the room when you collect the calibration trial The position of the calibration L frame determines the orientation of your calibration The International Society of Biomechanics ISB has officially adopted the convention that the Y axis should point up This has the advantage that in both 2D and 3D studies the Y axis is up However many studies and software packages use the Z up coordinate system favored by mathe maticians Once a reference frame has been selected you must provide a number of calibration markers with known locations which can be used for control purposes hence these calibration markers are known as control points The control points serve much the same purpose as the simple scale widely used for two dimensional studies they are in fact a three di mensional yardstick representing the X Y and Z dimensions Motion Analysis offers a calibration L frame with four retro reflective spheres The relative position of the spheres have been accurately mea sured and they define the origin and direction of the Global Coordinate System used in the motion measurements See Chapter 6 Calibration Tab for more details Placing the Calibration L Frame Mark the floor area with tape where the motion is to take place e Set Marker 1 of the calibration L frame at the desired origin of the capture volume e If the orientation of t
34. Either way it is 250 000 32 channels or about 7500 samples sec per channel with all channels collecting data If you cut down to 16 channels you can have 15 000 samples sec per channel You can also connect up to 6 devices and use only 16 channels from each device For increased speed use the faster USB 6259 A D unit from NI This unit is 32 channels 16 bits same as USB 6218 but has a throughput of 1 25 Million samples sec or 5 times greater than the throughput of the USB 6218 The video sample rate multiplied by 255 limitation comes into play mainly if a slow mocap video rate e g 60 Hz is being used The max an alog rate in this case is 15 300 60 X 255 Under normal conditions cus tomers using higher analog rates would also be using higher mocap video rates With a mocap video rate of 200 Hz the max analog setting is 200 multiplied by 255 or 51 000 Hz Note that you can do this with the USB 6218 with fewer channels turned on 250 000 51 000 4 9 or 4 chan nels NI USB 6259 Analog Channel Connections The following table Table B 3 provides the analog channel connections and master camera clocking for the NI USB 6259 as interfaced in the Cortex software Appendix B Analog Input Hardware and Software Cortex 2 1 Reference Manual Table B 3 Analog Input Channel Connections and Master Camera Clocking NI USB 6259
35. F_Head 6 TopSpine 7 RShoulder 14 RPinky 415 RThumb 16 LShoulder 17 LBicep 18 LElbow 19 LWrist 20 LPinky 21 LThumb 22 Midback 23 LowBiack 24 RootOftset 26 BRHip 27 BLHip 28 FRHip 29 FLHip 30 RThigh 31 RKnee 32 RAnkle 33 RHeel 34 RMidtoot 35 RToe 136 LThigh 1 u4 2 u2 3 jus 4 U_4 lt Empty gt 5 U_5 lt Empty gt 6 U_6 lt Empty gt 7 U_7 lt Empty gt _8 U_8 Empty aln a Emna Click AllNone Ctri Click Toggle Click AllNone Ctri Click Toggle A IS k E3 C Skeleton iia ines Le amor JL JL eS aed LP 00 00 00 01 Calculate 1080 Frames 60 FPS Y Up Unitsimm a ae cS NONE Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Calibration Files Calseed vcX Calwand vcX TrialN cal Note The following are the types of calibration files generated in your selected capture folder Calseed vexX files one for each camera get written when you press the Calibrate button in the Calibration with L Frame box and when you are connected to the cameras If you are not connected to the cameras you can use the Disconnect Use Raw Files item and select the Calseed vc1 or Calseed cap file to re process the Calseed files This is a kind of simu lated realtime mode that allows you go back and process the Calseed files and evaluate your data files When you press the Calibrate button in the Calibrat
36. Fill out the Virtual Marker Definitions form for the desired markers 3 Click Calculate to calculate the virtual marker positions Virtual Marker For notes and examples on how to use Virtual Markers there are two Notes and valuable sources Examples 1 Video tutorials from the Cortex Help gt Tutorials menu The first of this set of three tutorials shows how to set up and use Vir tual Markers To see this you will need to install the full Samples and Tutorials from the Cortex installation CD or FTP site 2 KinTools RT User s Manual 9 19 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual i gt electing any of the links in the Treeview allows you to make changes to Tree View Selecting any of the links in the T llows y ke chang Links the links in the current capture file The link property values that can be changed include the following Right click can only delete Index Displays the link number in the order the link appears in the list of links for the capture This is not editable Marker1 Allows you to select and edit which marker is the first end point of the link definition To edit click on the property and select from the drop down menu Marker2 Allows you to select and edit which marker is the 2nd of two end point of the link definition To edit click on the property and select from the drop down menu Color Displays and edits the color associated to the link in the 3D View To change the color c
37. Head 4 R Shoulder 5 R Oftset 6 Elbo 1 154 37 0 7 Reist 8 L Shoulder 10 L Wrist 1 RASIS 12 LASIS 13 V Sacral f 14 R Thigh 15 R Knee 16 R Shank 17 R Ankle 19 R Toe Click AllNone Ctri Click Toggle 1 U_1 lt Empty gt 2 U_2 lt Empty gt 3 U_3 lt Empty gt 4 U_4 lt Empty gt v v VMs 10 20 v 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 18 Skeleton 1 ir 7 Kinetics Selected B 1 4 ri 181 181 00 00 00 01 Visible E ble bes Calculate 48 Loaded Capture C Program Files Motion Analysis Cortex2 Samples SIMM OrthoTrak Helen Hayes Marker Set Walki c 181 Frames 60 FPS 2 Up Units mm Analog 1200 00 Hz im Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual Collada Skin and The following example will show both the Collada skin and the scene Scene Example 1 In Cortex Use the Browse button in the upper right corner to open the C Program Files Motion Analysis Cortex2 Samples Three Person Collada Dance Triplets_1 cap file 2 Right click in the 3D Display and select Unshow Linkages Show Skin Show Scene 3 Click Play Press the 9 Hot key for the Graphics Only view toggle without the menu items This procedure will produce a subject with a skeleton and skin as shown in Figure 9 4 Figure 9 4 Collada Skin and Collada Scene 9 8 Cortex 2 1 Reference Manual Chapter
38. It also supports the replay and tracking of previously recorded data with a simulation of real time from the raw VC camera files To help you distinguish between the two modes Real Time and Post Pro cess the dashboard and the floor color changes Figure 4 56 Real Time Dashboard Configure Motion Capture Connect to Cameras Reset IDs using Current Frame Time Code the Template r ee Game es j a E C Skeleton GolfSwing_1 cap v 00 00 03 044 A1 on E I 2 I 3 I 4 I 5 j 8 I 7 8 J 23 Stopped 9d4 Frames 120 FPS z Up Unitsimm Analog 600 00 Hz Events Camera Buitons New Subject FIFO Slider Join Virtual Check Template Cortex The Real Time Dashboard camera buttons inform you of the following Dashboard Camera Button Colors Green Light green Yellow Light yellow White Dark grey Camera is completely calibrated Camera is completely calibrated and is selected Camera has undergone seed calibration but not wand calibration Camera has undergone seed calibration and is selected Camera is not calibrated Camera is inactive A right mouse click on the camera number will enable and disable that camera Note Camera 1 must remain enabled when you collect data to make sure you have a selectable VC1 file 4 71 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tracking I
39. LBHD LFHD HEDO HEDP HEDA HEDL F 30 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module clavicle_l L Clavicle scapula_I L Scapula L Scapula Top L Scapula Bottom L Angulus Acromialis L Trigonum Spinae L Angulus Inferior humerus_I L Bicep L Biceps Lateral ulna_l L Forearm femur_l L Thigh L Thigh Upper L Thigh Front L Thigh Rear LTHI tibia_ L Shank L Shank Upper L Shank Front L Shank Rear LTIB foot_l L MedFoot L LatFoot clavicle_r R Clavicle scapula_r R Scapula R Scapula Top R Scapula Bottom R Angulus Acromialis R Trigonum Spinae R Angulus Inferior humerus_r R Bicep R Biceps Lateral ulna_r L Forearm femur_r R Thigh R Thigh Upper R Thigh Front R Thigh Rear RTHI tibia_r R Shank R Shank Upper R Shank Front R Shank Rear RTIB foot_r R MedFoot R LatFoot F 31 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual F 32 Appendix G Synchronizing Digital Video with Cortex CortexDV Overview System Requirements Installation Using CortexDV Currently Open Known Issues CortexDV Overview Note CortexDV is a Digital Video DV capture application for use with Mo tion Analysis Corporation s Cortex software for the synchronized capture of reference video data on a separate Windows PC as avi files You can directly transfer digital information back and forth between a DV cam corder and your computer with t
40. Referenced Single Ended Differential Forceplates Autozero Forces The maximum analog rate is determined by one of the following consid erations 1 The maximum throughput of the National Instruments NI A D product 2 The video sample rate multiplied by 255 The NI USB 6218 A D unit which is often supplied with Motion Analy sis systems has a maximum throughput of 250 000 samples sec per unit So two units with 64 channels would have the ability to collect up to 500 000 samples sec Either way it is 250 000 32 channels or about 7500 samples sec per channel with all channels collecting data If you cut down to 16 channels you can have 15 000 samples sec per channel You can also connect up to 6 devices and use only 16 channels from each device For increased speed use the faster USB 6259 A D unit from NI This unit is 32 channels 16 bits same as USB 6218 but has a throughput of 1 25 Million samples sec or 5 times greater than the throughput of the USB 6218 The video sample rate multiplied by 255 limitation comes into play mainly if a slow mocap video rate e g 60 Hz is being used The max an alog rate in this case is 15 300 60 X 255 Under normal conditions cus tomers using higher analog rates would also be using higher mocap video rates With a mocap video rate of 200 Hz the max analog setting is 200 multiplied by 255 or 51 000 Hz Note that you can do this with the USB 6218 with fewer channels turned on
41. Right lateral ankle acceptable names R ANKLE R ANKLE LATERAL R ANKLE LAT RANK Left lateral ankle acceptable names L_ANKLE L ANKLE LAT ERAL L ANKLE LAT LANK Right heel acceptable names R HEEL RHEE Left heel acceptable names L HEEL LHEE Right toe acceptable names R TOE RTOE Left toe acceptable names L TOE LTOE Right medial knee acceptable names R KNEE MEDIAL R KNEE MED Left medial knee acceptable names L KNEE MEDIAL L KNEE MED Right medial ankle acceptable names R ANKLE MEDIAL R ANKLE MED Left medial ankle acceptable names L ANKLE MEDIAL L ANKLE MED F 25 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual Upper Body Critical Markers Semi critical Markers The upper body portion of the Mocap Model will be loaded if the critical markers listed below are present in the static trial The upper arm and lower arm segments will each be scaled separately based on measure ments made from the static trial Each of these segments will be scaled uniformly in the X Y and Z dimensions The torso segment will be scaled independently in two dimensions the X is scaled the same as the Z It is not possible to load the upper body with only one arm To load only one arm without the rest of the upper body use the SIMM file rightArm jnt or leftArm jnt as the Mocap Model 1 2 3 Right ASIS acceptable names R ASIS RASIS RASI Left ASIS acceptable names L ASIS LASIS LASI Posterior pel
42. Setup Files cal EUG aie eae cies ceeds 4 60 MarkerSet Files mars Extensions cccceeeescceeeeesseeeeeeeeeees 4 60 viewing Sample Dala nee ae Se ner ee eee Me Senn a eRe Teer mre 4 61 Digital Reference Video Option CortexDV Software 0068 4 70 Real Time Dashboard snammisainininiiaussiiiiendnaiasiiiannals 4 71 Pays Rae dL ieee renee nee eee ene ernie rte a ec meee eerste 4 72 Post Process Cr esac ee eens 4 81 Post Process Tool SIND siracicsinireinorareiiciacsisiarsiebamaboiiimmacwiigueindl 4 81 Zooming Rotating and Translating in the 3D View 00 4 82 Selecting Markers Virtual Markers Linkages and Segments 4 83 TORO ea EA 4 84 Chapter 5 System Tab Ea leeke i e P E E E E AE SE I E E 5 1 Cameras Panelci e na RR E a ERSA in 5 2 Loading New Camera Software c ccccessseceeeseseeeeeeenseeeeeeeseeeeees 5 5 Camera Display Sacchi nce eiee ARE 5 8 Creating and Clearing Masks ici cess ecient dan saccasecacaecaenieanc e 5 11 Gang LVE sisi ieee 5 11 Ad sting THRO Specs iciisiceinineaie ested veneiaienaieeueusien 5 12 Anapo ass 5 13 Ee Fane cesta eet N teas 5 17 Chapter 6 Calibration Tab Calibrating Your SSM esanen A Rn n 6 1 What is the Square and Wand Calibration c cccccccessessseeees 6 2 Calibrate Bacar esc ie Seetdacscceacscdatiec sanaetonmesbica ames 6 3 RY sata gaat stad cates yee ars plea as 6 18 Calibration from Previously Collected Files c
43. Skeleton Types Cortex 2 1 User s Manual Skeleton Builder SkB Skeletons Skeleton Builder SkB skeletons are relatively simple direct and fast cal culations of segments bones that are defined and calculated from one marker center to another The markers can be real or virtual calculated and are typically from one virtual joint center to a second virtual joint center A 3D local coordinate system is defined with 3 markers 1 One marker defines the origin 2 A second marker defines the bone axis 3 The third marker defines the plane The advantage of the SKB type skeleton is that they compute very quickly and they represent the method of how most biomechanical models have been computed for many years The disadvantage is seen when viewed on a skinned character in an animation package The bones segments change length as a result of the calculation method This is due primarily to the motion of the markers on the skin which change from frame to frame An animated character can be set up so that the character keeps a fixed length skeleton and the skeleton is driven only by the angles mea sured from the skeleton This has the visually undesirable artifact that the character s feet will appear to slide on the floor and possibly raise above or protrude below the floor Calcium Solver Skeletons Solver type skeletons are calculated quite differently than SkB skeletons Solver uses the Global Optimization method of calculating
44. The approximate volumes can be set up ahead of time using tape on the floor to mark the capture volume bound aries and the position for the tripod legs if used of each camera 2 1 Chapter 2 Planning a Motion Capture Session Cortex 2 1 Reference Manual If more than one subject will be performing in a capture session it is a good idea to mark out a capture volume practice area away from the ac tual capture area This will allow the next subject to practice before mo tion capture On the Cortex host workstation create the appropriate directories and capture files For batch edit work in Post Processing a separate file folder for each capture and its associated capture files is strongly suggested Make sure there is enough room on the Cortex workstation s hard disk If you know the number of trials you are going to capture and the approxi mate length of each trial you can estimate the amount of hard disk space you will need Use some form of backup medium e g CD ROM Zip disk to back up previous data and clear space on the hard disk for the new trials Prior to the Capture Session Several days prior to the capture session schedule a visit by the subject and any producers or directors involved in the motion capture session If the subject has not worked with reflective markers this will allow time to become familiar with marker placement and to practice in the marked out capture area You will want to specify the mo
45. The master camera is set as follows 1 In the Real Time Dashboard select the camera number button of the camera which you would like to set as a master camera 2 Click on the Set Master Camera button 3 Ifthe camera is not turned on or working select another camera in the Real Time Dashboard and then press Set Master Camera again 4 If you have an analog sub system the A D sync cable must be con nected from the master camera to the A D Interconnect box Any camera may be designated as a master camera but only one at a time Edit Button This button opens the Tools gt Settings gt Cameras interface which fea tures adjustment sliders for Threshold and Brightness settings Min Hori zontal Lines per Marker and Max Horizontal Lines per Marker Figure 5 2 Edit Button Tools gt Settings gt Cameras Interface Settings AllCamera Types Raptor Specific These settings apply to all Motion Analysis Digital Cameras Note The Min Max lines per marker values can be set per camera or per project This option is in the Tracking panel If per camera settings are not enabled the controls will not be enabled All controls are disabled if there are no cameras chosen for editing Threshold io is Brightness Min Horizontal Lines per Marker Max Horizontal Lines per Marker Edit These Cameras O All Selected Changing the You can change the IP address in this box for any ca
46. The primary model is a full body model with lower extremity muscles but others are available as well Critical Marker A marker that is required in the static trial and which must be placed in a specific location on the subject according to instructions in the OrthoTrak manual The coordinates of the marker in the static trial are used to deter mine joint centers and body segment lengths Semi critical Marker A marker that is optional in the static trial but if used must be placed in a specific location on the subject according to instructions in the OrthoTrak manual The coordinates of the marker in the static trial are used to im prove the joint center calculations Optional Marker A marker that is optional in the static trial and whose placement on the subject does not need to be in a specific location Fixed Marker An optional marker whose X Y Z offsets are not automatically calculated when the static trial is processed Rather the offsets in the marker defini tion in the Mocap Model file are used to position the marker on the model these offsets are scaled with the body segment however The Motion Module comes with four different Mocap Models for you to choose from Each of them contains parameters that turn on and off differ ent portions of the model depending on which of the critical markers are present in the static trial When you load a Model Model with a static trial the Motion Module reads the list of ma
47. U 620 8273 Principal Pt 497 3354 Focal Length 16 81047 1 Connect to cameras or select a Raw Video file Select and activate the Refine Camera Positions and Modify only the SELECTED cameras check boxes 3 Press the Run button on the Real Time Dashboard 4 Press All On on the Real Time Dashboard so that all camera views are displayed on the 2D Display 5 Right click on the 2D Display and select Smear Display This will show you how much of each camera s field of view is being filled by the wand over time 6 Start with the subject in one corner and as soon as the subject starts to move check the check box for Refine Camera Positions 6 15 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Note 7 Have the subject walk around the capture volume filling the entire volume The subject is acting like a wand calibration Have the sub ject walk with both arms slightly out so that all markers are easily identified Then have the subject walk the perimeter of the room spi raling into the middle 8 As soon as the subject has filled the room and reached the middle press Pause 9 A table of correction values will appear for all cameras included in the Refine panel The first three columns are the position changes of the cameras since the original calibration and the second three col umns are the rotational changes Changes of more than 1 mm are often significant and can result in a better calibration 10
48. chronize it with video motion data Analog cards known to work with Cortex software include the following A D configurations and the necessary NIDAQ software Cortex will sup port one or two of the devices listed in Table B 1 The devices must have the same resolution 12 Bit or 16 Bit Other NI Analog A D input con figurations should work but have not been tested Table B 1 A D Configurations Used with Cortex Software A D Configuration NIDAQ Software Win 7 Win 7 64 Vista Vista 64 NIDAQ 9 1 or later NI USB 6218 32 Channel 16 Bit up to 6 USB devices up to 192 channels NI PCI 6071E 64 Channel 12 Bit NIDAQ 8 3 or later EVaRT 5 0 4 or later NIDAQ 8 5 or later for Windows Vista Traditional NIDAQ 7 0 gt 7 4 EVaRT 4 4 NI PCI 6071E 64 Channel 12 Bit higher performance NIDAQ MX 8 0 or later EVaRT 5 0 NI DAQ Card 6024E 16 Channel 12 Bit Traditional NIDAQ 7 4 EVaRT 4 6 NI PCI 6254 32 Channel 16 Bit up to 2 cards NIDAQ MX 8 0 or later EVaRT 5 0 NI USB 6259 32 Channel 16 Bit up to 2 USB devices NIDAQ 8 1 or later EVaRT 5 0 2 Note If you do not find your NI device in listed in Table B 1 on page B 1 you may need to reference older versions of the EVaRT User s Manual B 1 Appendix B Analog Input Hardware and Software Cortex 2 1 Reference Manual Note Performance Specifications If you are using NIDAQ MX 8 0 or 8 1 versions and if you are
49. file browser and ask you to select the name of a static pose file This static pose is used to calculate joint center locations and segment lengths for the subject using the same algorithms implemented in OrthoTrak In other words the Motion Module recre ates the OrthoTrak skeletal model from the static pose and then maps this skeletal model onto the mocap model Thus to use the mocap model you need to use the same motion capture protocol as you would for OrthoTrak You can use either the Helen Hayes or Cleveland Clinic marker sets plus your own additional markers if desired as long as the marker names and locations match the protocol defined in the OrthoTrak manual The Motion Module uses the tracked marker data from the OrthoTrak static pose and also segment information from per sonal dat to scale the mocap model to the subject The algorithms for calculating joint center locations and segment lengths have been designed to be as similar as possible to the OrthoTrak algorithms This was done so that motion information in SIMM e g joint angles EMG levels would match the corresponding information in OrthoTrak and also so that you would not have to change your OrthoTrak protocol in order to use SIMM The mocap model and the algorithms used to scale it are described in the following sections The mocap model is a full body SIMM model that has been customized for gait analysis but can be used to import and display any type of full b
50. ghost markers are seen in the motion capture sequence Min Cameras setting of 3 cam 4 24 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface eras will generally give very good quality data but the setup needs more cameras in place Tools gt Settings gt The cameras tab in the settings popup allows cameras settings to be Cameras Tab changed There are two categories of settings Settings for all cameras types and Raptor Series specific settings All Camera Types Figure 4 19 Settings gt Cameras Tab I Settings Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins 100 All Camera Types Raptor Specific These settings apply to all Motion Analysis Digital Cameras Note The Min Max lines per marker values can be set per camera or per project This option is in the Tracking panel F por camem sees ara not eed th controls will not be enabled All controls are disabled if there are no cameras chosen for editing Max Horizontal Lines per Marker a 5 M The settings that are available for all cameras can be changed in the All Camera Types sub tab of the Cameras settings area pictured above These settings are Threshold Brightness Min Horizontal Lines per Marker Max Horizontal Lines per Marker Each of these settings can be changed for
51. goes on when you plug the cable into the hub This is also the best way to figure out whether or not your Ethernet cables are plugged in correctly It will not damage anything if you plug in the wrong type of cable patch or cross over into an Ethernet jack For the indicator light to go on there has to be a live Ethernet connection on both ends of the cables A 4 Cortex 2 1 Reference Manual Appendix A System Hardware Interconnections CP 8 Power Hub and Ethernet Switch Connections When first setting up your Motion Analysis system you will notice that both the power and Ethernet connections for the cameras are integrated through the CP 8 Power Hub and a 1 GB Ethernet switch Remember the system allows for 8 cameras per CP 8 Power Hub All camera power connectors are plugged into the power connectors of the CP 8 Power Hub Order is not imperative as long as each power con nector is close to an open Ethernet connector on the 1 GB Ethernet switch Figure A 3 Standard Digital Camera Configuration 1 to 8 Cameras Camera Host Computer CP 8 Camera Power Hub Camera Cable Ethernet Port wd Ethernet Cable 1GB Ethernet Switch A 5 Appendix A System Hardware Interconnections Cortex 2 1 Reference Manual Camera Connections Motion Analysis digital cameras are connected to the EagleHubs using camera cables with both power and Ethernet connectors When fitting connectors t
52. tents of the c3d file Figure 4 10 Import C3D File Interface Import Options Marker Data Up Axis posme OYU Ztp Channel Settings Ft Fy1 Fz1 Mx1 My1 Mz1 Fx2 Fy2 Fz2 Mx2 My2 Mz2 1 File gt Import ANC Imports ASCII viewable formatted Analog data anc File 4 13 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual File gt Profile Manager The Profile Manager opens a dialog which manages the customized set tings for individual users These customized settings include the follow ing e Hotkeys e Colors e Layouts and Data Views e Post Process Tool Strip The Profile Manager dialog has three main components e Current profile set for manipulation top e List of all available profiles left side e Profile manipulation buttons right side Figure 4 11 Profile Manager Profile Manager Current Profile Profile2 CortexUser Profilet teate New Profile2 Load Selected Create New A prompt to enter a profile name will be displayed A profile with that name and the default settings will be created This will be set as the cur rent profile Load Selected This will load whatever profile is selected from the profile list and make it the current profile Delete Selected This will delete the profile selected in the profile list Deleting the current profile is not allowed Save Current This will save the current profile Saving is also done a
53. typically created by exporting it from an animation package such as Maya This deletes and replaces any existing model information Ex ported HTR files are not automatically loaded as part of the capture unless you explicitly save the capture and list it in the Tools gt Settings gt File Structure tab Update Skeleton from HTR File Updates the pose of the current model skeleton with the information in the given HTR file The skeleton names in the HTR file must match the names in the current model skeleton This is typically used to change the pose of the skeleton joint orientations offsets and lengths without hav ing to re specify all the joint types and attachments Create SIMM Calcium Skeleton JNT File Calculates and stores a JNT file with the same name as the MarkerSet file which is scaled to the subject s bone sizes Export SIMM Motion File Exports a motion MOT file that can be loaded and used in SIMM Software for Musculoskeleton Modeling 4 12 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface File gt Import C3D C3D is a file format used by some applications for storing motion and an File alog data The C3D File Import Dialog allows data stored in this format to be imported into Cortex Some information about the capture configura tion is needed to convert C3D into the corresponding MAC file types Note that a separate folder and capture file cap is created with the con
54. 2 Select Join Virtual in the Post Process tab Verify that the Marker to Join is set for the marker you want to edit Figure 8 16 Join Virtual Virtual Marker Definitions Virtual Marker Definitions Three Marker Value Three Marker Ratio Two Marker Value Two Marker Ratio EMR Enter Name of Virtual Marker Origin Marker Long Axis Marker Plane Marker CenterHead 5 M_F_Head 3 M_B_Head 4 M_R_head Snap to this Marker optional Long Axis mm 0 00 Plane mm 0 00 Perpendicular mm ae DEn eee C eee Calculate Virtual Markers New Marker Definition Delete Y Marker Definition amp A 3 Click on Origin Marker It will be highlighted in blue and will allow you to choose which marker to use as the marker that is most rigidly attached to the marker to join See Origin Marker on page 8 25 Note Select markers using the 3D View or the marker grids 4 The function will then automatically jump to the Long Axis Marker input box Continue selecting the proper markers for each remaining input box Make sure they are all different You cannot have two of the same markers in the Virtual Marker Join definitions 5 Once you have defined the three definition markers for you Virtual Marker click on Join Virtual Note If data is missing for any definition marker Origin Marker Long Axis Marker Plane Marker in the frame field the gap in data will not be com pletely filled You will need to select a different definiti
55. 6 Run through some of the channels to verify that the board is seeing the data For example have someone step on the force plate 7 Close and launch Cortex and connect to cameras You should see that all cameras are found as well as the type of A D unit installed If you have NIDAQ 7 0 drivers already installed onto your system it is not necessary to un install the software when upgrading B 3 Appendix B Analog Input Hardware and Software Cortex 2 1 Reference Manual Analog Signal Naming Conventions Kistler Force Plates Note For AMTI or Bertec Force Plates EMG Signal Name Conventions When connecting force plates and EMG equipment to the Cortex system certain requirements must be met and conventions followed Typically force plates are connected to the first channels of the A D sys tem and then the EMG channels Specific Analog signal names for the force plates must be used if KinTools RT and OrthoTrak are used These names depend on the force plate manufacturer 8 channels per plate e Analog Channel 1 connects to the F1X1 signal e Analog Channel 2 connects to the F1X3 signal etc If there are two plates e Analog Channel 9 connects to the F2X1 signal e Analog Channel 16 connects to the F2Z4 signal The reserved names for OrthoTrak and KinTools RT are PLATE 1 F1X1 F1X3 F1Y1 F1Y2 F121 F122 F1Z3 F1Z4 PLATE 2 F2X1 F2X3 F2Y1 F2Y2 F2Z1 F222 F2Z3 F2Z4 These naming conventions are already set u
56. AVI WAV CGV TRC TRB and EVT and TC time code files are all associated in the Capture by their file names If you rename the output files they will not be recognized in the Capture and will cause the Load Capture function to issue an error message and the Capture will not be loaded This allows you to redo an existing file once it has been saved When using an external trigger mechanism you will need to check this box for the software to recognize it You can install an external trigger by plugging it directly into your COM1 port on your Host computer When the Post Trigger Mode check box is activated it enables the soft ware to record the data from the end of the session backwards based on the capture duration X that has been set i e from the end of the data capture to X seconds This is useful for captures where there is no de fined starting point or event but the ending is well organized and smooth and you would like to capture only the final moments Note this only works for tracked data TRB and TRC files and Raw Video Camera VC files This does not work for analog or Reference Video files This button will load the last TRB file captured with the current capture file By default it will load TRB files first If they don t exist only TRC files were captured then it will then load a TRC file 7 10 Cortex 2 0 Reference Manual Chapter 7 Motion Capture Tab Recording Data After setting up the templat
57. At this point all the props exist in memory They must be saved to disk in order for them to be able to be reused at a later time In Post Processing mode this can be done using the Save Capture function All the props are created with default names QuickPropXX where XX is a number that starts at 01 The first XX that results in a unique MarkerSet name between Live Mode and Post Processing is used All markers are named M1 to MN where N is the number of Markers Once created the names and other properties of the Props can be edited from the Model Edit gt TreeView panel 7 14 Chapters Post Processing Tab Editing Tracked Data Viewing Your Data Joining Gaps in Data Unnamed Markers Post Process Tool Strip Join Virtual Data Painting Time Lines Analysis Graphs Post Processing Strategies and Tips Editing Tracked Data The Cortex Post Process mode allows you to play back and edit tracked data stored in TRB binary and TRC ASCII files Markers can be iden tified if they have gone unnamed during the recording session Gaps and aberrations in data can be filled or fixed by hand frame by frame or by employing mathematical functions across entire sections of a data set Up to ten operations can be undone if you make a mistake but it is recom mended that you save your work frequently Typically an editing session requires having both the 3D View and the XYZ Graphs open at the sa
58. Capture Post Process Model Edit User Apps Calibrate Refine r Calibration with Square M Preview Calibration Deta Filename CalSeed Calibrate fa Gk to Gvernite r Wand Calibration Duration 60 Seconds Length 1000 Filename Calwand Collect E Gk te Gyenmnte 0 000 4 0 000 4 i 0 000 4 0 000 4 5 amp 7 B r Floor Calibration Marker Center to Floor h27 Calibrate Floor 0 000 4 i i 0 000 4 0 000 4 0 000 4 ms if 2fs fais f6 if7 fs 1 240 2 mm LAService CUSTDATA Bundeswehr5_O1 Bundesweli_20 4 4 Once the wand calibration duration has been completed the program starts to determine the volume calibration and a screen comes up with a series of numbers that decrease as the calibration nears the actual wand length and focal lengths of the camera lenses see Figure 6 10 5 At the bottom of the user interface a progress bar ticks toward 100 Once completed the camera lenses should be very close to what was installed on the camera body e g 6 023 mm for 6 mm lenses If this is the case and the wand length is very close e g within 0 10 mm difference for a 500 00 mm wand to the original wand length then the calibration is complete If not you can continue to click on the Run Again button until either the values stop changing significantly or the values start getting larger 6 Press Save Setup Cortex 2 1 Refer
59. Cattraton Notion Cepawa PostProcess Model Ecit UsarApos Colteate Refne Sees Cabraion F Prenen Cairan DSH k ai Mer M DR toO iinde Fici Coltraten Nate Cortet toMece 1 Colinate Fitoi Example The camera does not see the calibration L frame Click on the camera to identify it 6 9 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Once you have all of your cameras positioned and oriented correctly press the Collect and Calibrate button see Figure 6 8 This creates the CalSeed veX vcl vc2 vcN files and consists of one frame of data stored in your current data folder Your camera buttons at the bottom should now be yellow in color indicating that all cameras are seeded see Figure 6 9 Fully calibrated cameras show up as Green but this does not happen until after wand calibration is completed Figure 6 8 Properly Seeded Cameras CaSeed n UistaWyennnite All camera positions should be reasonable approximations of their actual positions in the room This completes the square part of the Square and Wand Calibration 6 10 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab Calibration with Wand Duration Length Calibration with Wand Procedure Note This function allows the user to set the desired time limit in seconds for the wand capture This function allows the user to set the length of the wand head in
60. Connections Camera Connections Network Interface Cards and IP Addresses Overview Note Note This chapter provides information and illustrations on how to set up the hardware to be used with Cortex When using Cortex in the Motion Analysis motion capture system hard ware connections are straight forward The connection of the cameras to the CP 8 Power Hub and Ethernet Switch all have unique labeled connec tors Frame rate shutter speeds and ring light brightness for the Eagle and Hawk digital cameras are set using the Cortex user interface When connecting the camera cables to the hubs switches you must use the end with the red indicator A 1 Appendix A System Hardware Interconnections Cortex 2 1 Reference Manual Standard Camera System Configuration Figure A 1 shows a standard Cortex system setup for use with Motion Analysis digital cameras Figure A 1 Standard Camera System Configuration Power Hub and Ethernet Switch Cortex Host Computer Cameras For more detailed diagrams please refer to Figures A 3 through A 10 The main components include e a set of digital cameras with network and power cables for each camera e a CP 8 Power Hub 1 for every 8 cameras and Ethernet Switch 1 for every 15 cameras see Figure A 2 e a Tracking Computer host with monitor keyboard and mouse Figure A 2 CP 8 Camera Power Hub and Ethernet Switch A 2 Cortex 2 1 Reference Ma
61. D GND D GND AOO AO1 AO GND Al GNO AlO Al 16 Al8 Al 24 The USB device pinouts are available online after you install the device To find them 1 Launch Measurement amp Automation which was installed when you installed the NIDAQ software 2 Select Devices and Interfaces then NI DAQmx Devices and the page should appear as shown above Note NI Numbering starts at Channel 0 where Cortex channel numbering starts at 1 For example AI 0 above corresponds to Cortex Channel 1 B 8 Cortex 2 1 Reference Manual Appendix B Analog Input Hardware and Software Note Which USB Device is Channels 1 32 which is 33 64 The first device you plug in should be channels 1 32 in your Cortex soft ware The second device should be channels 33 64 and so on for more de vices If you are not sure When you connect to the Cameras in Cortex the channel numbers 1 32 and the Serial Number of the USB device are reported in the dialog box The Serial Number for the USB 6218 device is located on the bottom of the USB device Clock Wiring for Single and Multiple USB Devices For Eagle Eagle4 and Hawk cameras the system will require a 4 7 kQ pull up resistor from 5 Volts to the PFI 0 pin as shown in Figure B 3 on page B 7 A Single Pull up resistor with a 4 7 KQ or close value will work for con necting up to 6 USB devices together as shown below You need only to connect PFIO and D GND signal
62. Display and choosing either Delete Mask or Delete All Masks Note that you can use masks after the VC data has been collected by discon necting from the cameras creating the mask and then loading or selecting the raw files This applies to the calibration files CalSeed and CalWand as well For Raptor 4 Raptor E Eagle 4 and Eagle cameras the first 12 masks are hardware masks Hardware masks are created in the camera and the marker edges do not get sent to the Cortex software Masks 13 become software masks the edge data is sent to he Cortex software and ignored no centroid is calculated Hardware masking is generally preferred as it reduces the Ethernet traffic and reduces the size of the VC files After having configured the software to the system and connected Cortex to the cameras 1 Place the calibration L frame on the floor in the capture volume The orientation of the calibration L frame determines the directions of your global X Y and Z axes 2 Press F2 on the keyboard to open the 2D Display The view seen by one or several cameras will be displayed To select multiple cameras press Shift click or Ctrl click on any of the camera buttons on the Real Time Dashboard or click All On 3 Click the Run button on the Real Time Dashboard Chapter 5 System Tab Cortex 2 1 Reference Manual Adjusting Thresholds 1 Choose Tools gt Settings gt Cameras from the Menu Bar 2 Slide the Threshold slider on the flo
63. EMG or other analog source signals for the analog signals to be collected properly This is done by following these steps 1 Choose the System gt Analog panel Figure 5 7 Analog Panel Cameras Analog Devices Configure channels for data capture If a channel s On box is not checked data for that channel won t be captured Name FIX F1Y Fiz MIX MIY M1z F2x F2Y F2Z 10 M2x 11 MZY 12 M2z oon On fF WN 29 OOOOOOOOO OOO 00000 55 5 5 5 5 8 5 S Terminal Configuration Range l l l l l i l i l l i i 10 10 10 10 10 10 10 10 10 10 10 10 RSE Referenced Single Ended default w Force Plates Analog Sample Rate Multiple of Frame Rate Current Sample Rate Hz C Autozero Forces 5 600 00 2 To open a list of force plate names right click anywhere on the Ana log panel grid and choose Channel Type Names from the pop up menu The built in names include Kistler AMTI Bertec and Muscles 5 13 Chapter 5 System Tab Cortex 2 1 Reference Manual Note 9 To edit a channel s name left click in its row in the Name column Left click on the arrow that appears in the cell and select a name Alternatively you can simply left click in the cell and type in a name directly Left click in the channel s row in the Active column if you wish to make it active You can also click in the Active
64. Erk e AEEA 10 7 Chapter 11 Skeleton Types O Fa S 11 1 Cortex 2 1 Reference Manual Skeleton Builder SKB Skeletons cesseeceeeeeeeeeeeeteeneeeeeeeeees 11 2 Calcium Solver Skeletons srein et ener eee ener 11 2 Which Skeleton Engine Should USe c cceeseceeeeeseeeeeeeeees 11 3 Cortex Skeleton Engine Selection ceeeecceeeeesceeeeeesseeeeeenees 11 3 Skeleton Option Details as selected from Tree View 0008 11 5 Exporting the Skeleton Data Into an HTR File ccceeeeeeees 11 11 Multiple Characters and Multiple Skeletons ceeeeeeeeeeeeees 11 12 Chapter 12 Sky Scripting Interface O E E A E salient E 12 1 Msiallation Fie SMOCIUTE senors 12 1 TERGO UY ose ner nen ae Eee ee ener eee reese eee er 12 2 The SCR CICA einun 12 2 Sopi Ea ee ea EREE 12 2 Updating Old Sky Files Seen eee ene app eee eri eer rte 12 3 Graphical User Merate mocracia ene ee 12 4 Sky Compiled Script Reference ssnsesosnensseseereereeresrrrrserrrnsrrree 12 8 Appendix A System Hardware Interconnections WETS ieina aea d aa ea A 1 Standard Camera System Configuration ccccceeeeeeeeeeeeeeeneeees A 2 Power Consumo areas er ene Me ger eee eee mene ener or A 3 CP 8 Power Hub and Ethernet Switch Connections 005 A 5 Camera COMES OINS scasecaziss rechsiaysdes aseseevacti vines eisai eeepc reiecaeaniaiais A 6 Network Interface Cards and IP Addresses
65. Figure 4 24 Motion Trails Example Hise Stab ett E A PE t gt Pat Tools gt Settings gt Post Process Tools Tab 3D Display gt Show Kinetics Options This hides or shows the kinetics options in the 3D Display Show Proper ties right click 3D view select Show 3D Display gt Dim unselected MarkerSets This applies when using multiple MarkerSets Only one MarkerSet can be selected at a time When this is checked then the unselected MarkerSets are drawn partially transparent These settings change how some of the Post Processing tools function and how the Post Processing Tool Strip looks 4 32 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools Tab Figure 4 25 Tools Tab SS SS Tools Search Undo Too Strip Smoothing Butterworth Freq tz 6 3 Point Average 5 Point Average Validate Joins with Template Smoothing This allows the user to select which automated smoothing filter to use with the Smooth tool in Post Processing The choices are Butterworth 3 point average and 5 point average Validate Joins with Template When this is enabled all joins that are done in Post Processing are first checked against the template of the MarkerSet If the data generated on any frame by a join would fall outside of the template the join is not per formed on that frame The default sett
66. Force units The information provided by the manufacturer may include only the basic sensitivities for each channel with no values for cross talk In this case the matrix should be filled with the basic sensitivities on the main diago nal and zeroes elsewhere Also notice that the upper right quadrant of the matrix contains the force sensitivities and the lower right contains the moment sensitivities In every case the force sensitivities are greater than the moment sensitivi ties Cortex uses this information to switch matrix quadrants permute the matrix if the manufacturer should supply the matrix with the moments on the left and force on the right Note The calibration matrix is intended to be used with your plate s coordinate system not the room s For this reason if your plate is not aligned with the room correct it with the 3x3 orientation matrix not by switching wires or A D signal names C 9 Appendix C Force Plate Configuration Forceplate cal File Setup Cortex 2 1 Reference Manual Using Kistler Force Plates Signal Names Gain Setting Calibration Matrix True XYZ Origin The Kistler force plate has 8 outputs Therefore two force plates will use 16 channels on the A D card The signal naming conventions are shown in Figure C 6 The names in the analog ANB or ANA file must appear exactly as shown in the Cortex ANB or ANA column With the Kistler force plate the Charge Amplifier model 9865 s
67. Forces 4 A Click AllNone Ctrl Click Toggle ear Acceleration Show KinTools RT Display Options Angor Veiocky 2 U2 Show SDK2 Latency i C Global Center of Mass 3 u3 Dim Unselected MarkerSets MOSER 3 Seve 4 U_4 lt Empty gt 5 U_S lt Empty gt 6 U_6 lt Empty gt 7 U7 lt Em Additional 3D Display Settings Ane ne lt Empty gt 0 704 41 0 B pty a a i1 a Emni i T meeer meeer re SERERERERRREREREERROA a 100 200 300 400 500 600 700 800 900 1000 ice Ke Kinetics il 4 amp WIE Emm 00500 00501 Selected Calculate 12 Loaded Capture C Program Files Mation Analysis Cortex2 Samples 16 Camera Calibration Face Body DaveROMIL cap 080 Frames 60 FPS Up Unitsimm You can adjust the depth of the camera view by moving the slider in the Camera Depth of Field function in Tools gt Settings gt 3D Display This does not change the depth of view the camera will have It only provides a visual aid to determine if an object at a particular distance will be in the camera s field of view 3 11 Chapter 3 Camera Setup Cortex 2 1 Reference Manual 8 To see the capture volume right click in the 3D view and then select the Volume check box from the 3D Display Show Properties window Figure 3 11 Show Volume Cumert Directory C Prog om Fios Hoton Anajyes Costes 2 Samples 16 Comme Caltnation Face Body gt Ewe ation Motion Capture Post Process Model Edt Plugins Presentati
68. Hand or Foot Both the streaming and the post process Join Virtual use a two pass pro cess to virtually join data across gaps The data passes through the Virtual Marker Join function twice with the second pass using filled or partially filled gaps that were not filled the first time These guidelines are intended for an audience with a good knowledge of motion capture theory and practice These are generalized guidelines only Individuals may find that different definitions may work better for their particular applications For best results it is recommended that you have at least three markers per effected segment Ideally for markers that have the possibility to be come obscured i e being covered up or lost between the ground and the subject s body you will need to place markers on the opposite side of the appendage or body For example if a subject is laying prone on the floor the back markers become obscured If you anticipate this you can apply more markers to the chest or front torso area For defining virtual markers when possible define and use markers that are always seen on that segment or neighboring segments If any data is missing from other markers in that segment the original data will improve but only if the dependent markers are present A subject s head usually will have four or five markers Missing marker data for the head is joined using Join Virtual definitions with any three of the other markers
69. Helen Hayes Lower Body Helen Hayes Full Body and Helen Hayes Full Body with Head It is also strongly recom mended that you include the medial knee and ankle markers in the static pose for more accurate calculation of knee and ankle joint centers You can also supplement the OrthoTrak marker set with your own custom markers as long as you do not move or remove any markers from the identified set Lastly the marker set used in the static trial must include all of the markers you plan to use for capturing motion This is because the Motion Module calculates the locations of all markers in the mocap model based on their locations in the static trial These are the steps you should follow when collecting the static trial 1 Choose which of the six OrthoTrak marker sets you would like to use for capturing motion 2 Add the medial knee and ankle markers for better calculation of knee and ankle centers not required but highly recommended 3 Add any additional markers that you would like to use e g extra markers on the feet more markers on the arms These markers must also be added to the mocap model The Marker Set F 10 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module Note average from frame load personal dat read marker names from subject mass 4 Capture the static trial using the protocol outlined in the OrthoTrak manual The subject should have their arms either down by their sides or straight o
70. If you have a live mode screen showing in Cortex it performs a Load Capture Live function to get ready for the next capture or re tracking session If you are in post processing mode when you load the capture it will load the capture into post processing mode Figure 4 36 Quick Files Interface H Size _ Animation cal 16081 Bytes 8 CalSeed1 cap 139 Bytes CalWand1 cap 139 Bytes HP Product Assistant 2 DaveBody mars 9561 Bytes IVI Foundation 2 DaveFace mars 6072 Bytes Microsoft 2 DaveROM1 cap 347 Bytes Microsoft Help Motion Analysis El Cortex2 E C1 Samples E Samples a B 16 Camera Calit CalSeed1 H CalWand1 E DaveROM1 E ProcFiles E 16 Camera Calit E BioFeedTrak 0A 0 0 A GH D E m al m C ProgramData Motion Analysis Cortex2 Samples 16 Camera Calibration Face Body Current folder 4 46 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Force Plate Configuration The Force Plate Configuration Popup is used to setup a force plate config uration The System gt Analog panel must still be used to configure of all analog channels including those used for force plates The configuration is edited in the popup and then applied by using the OK or Apply buttons Once the setup has been applied it will be used for future data capture sections and be maintained as part of the loaded Setup file N
71. Inspector Inspect Capture Capture Walk2 cap Walk2 cal Walk2 anb Wealk2 Unnamed trb ClevelandClinic mars Walk2 trb Wealk2 htr Walk2 evt Write Capture Manifest To Disk Find Missing File Remove File From Capture Add Reference Video File to Capture 10 8 Chapter 11 Skeleton Types Overview Skeleton Builder SkB Skeletons Calcium Solver Skeletons Which Skeleton Engine Should Use Cortex Skeleton Engine Selection Skeleton Option Details as selected from Tree View Exporting the Skeleton Data Into an HTR File Multiple Characters and Multiple Skeletons 11 12 Overview Cortex supports two kinds of skeleton calculations Skeleton Builder SkB skeletons and Calcium Solver type skeletons Either kind is calcu lated in the Cortex software and either can be calculated from live camera data simulated Real Time with VC files or from XYZ data in Post Pro cessing Both the marker data and the skeleton data are available to the Talon streaming plugins such as the Maya and MotionBuilder Talon streaming plugins The user can write their own plugin with the Talon SDK Software Development Kit also called SDK2 available from Mo tion Analysis Figure 11 1 Calcium Solver Integrated with Cortex HHE unaa sau 280 208 con a con Teo one su lone 1150 0un oun ene 1506 jain 1708 seen nen 2080 Zee Feu 7200 EEEE os u OO amea fe ji i Chapter 11
72. Min Max values for each link These values only get farther apart as you extend the template If this value becomes too great as might happen if you had bad data to create the template you must start the template creation process over from the beginning There is no function to revalue the numbers hence this is why there is a Sky script for this It makes it trivial to redo the tem plate creation process 9 21 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual Tree View gt SkB Segments Name Index Parent Origin Marker Long Axis Y Plane Axis XY RX Offset RY Offset RZ Offset Displays and edits the name of the selected SkB segment Displays the SkB segment number in the order the segment appears in the list for the capture This is not editable Displays the parent segment of the selected SkB segment To edit click on the property and select from the drop down menu Allows you to select and edit which marker is the Origin Marker of the SkB segment definition To edit click on the property and select from the drop down menu Allows you to select and edit which marker is the Long Axis Y of the SkB segment definition To edit click on the property and select from the drop down menu Allows you to select and edit which marker is the Plane Axis XY of the SkB segment definition To edit click on the property and select from the drop down menu RX is used to rotate the bone in the SkB
73. Ne 500 ee 510 am i zi x 520 ome m 4 ue 530 ie ee ae PeT Cece ier ESE domme pm ee 4 e pe 23 Stopper i 964 Frames 120 2 Up Unitsimm Analog 600 00 Hz Selected Frames Low Move 1 Frame Selected Frames High Visible Frames Low Time Code Visible Frames High Low and High The Low and High Visible Frames define the lower and upper limits of Visible Frames Low and High Selected Frames Play Forward Button Pause Play Backward Button Pause Play Speed the visible frame range The Current Frame is never outside of these lim its Absolutely no identifying or editing can occur on frames outside of the visible range with the exception of the join tools Their values are found in the white Visible Boxes and can be changed by typing numbers into these boxes and pressing Enter on the keyboard The Low and High Selected Frames are the lower and upper limits of the selected frame range These values can be changed with a middle click drag mouse action in the XYZ Analog or Skeleton Graphs panel or by typing numbers into these boxes and pressing Enter on the keyboard The Selected Frames region is shaded in light blue See Joining Gaps in Data on page 8 5 for details When editing data in the XYZ view only data in the Selected Frames region will be affected Areas outside of the Selected Frames are protected from the edit steps The Play Forward button default hot key is the gt key plays forward through the data until
74. RSSHOULDER RSHO Right lateral elbow acceptable names R ELBOW R ELBOW LATERAL R ELBOW LAT RELB 3 Right wrist a Lateral acceptable names R WRIST R WRIST LATERAL R WRIST LAT RWRI N or b Radius acceptable names R RADIUS RWRA Semi critical 1 Right medial elbow acceptable names R ELBOW MEDIAL Markers R ELBOW MED 2 Right wrist a Medial acceptable names R WRIST MEDIAL R WRIST MED or b Ulna acceptable names R ULNA RWRB Left Arm To load only the left arm set the MOCAP_MODEL parameter in your SIMM preferences file to leftArm jnt or choose that file using the Op tions Choose Model Model command in the SIMM menu bar Then use the markers listed below Critical Markers Left shoulder acceptable names L SHOULDER LSHO Left lateral elbow acceptable names L ELBOW L ELBOW LAT ERAL L ELBOW LAT LELB 3 Left wrist a Lateral acceptable names L WRIST L WRIST LATERAL L WRIST LAT LWRI NO or a Radius acceptable names L_RADIUS LWRA F 27 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual Semi critical Markers Right Hand Critical Markers Semi critical Markers Left Hand Critical Markers 1 Left medial elbow acceptable names L ELBOW MEDIAL L ELBOW MED 2 Left wrist a Medial acceptable names L WRIST MEDIAL L WRIST MED or b Ulna acceptable names L ULNA LWRB The right hand will always be included when the right arm is loaded even if there are no m
75. Select a plugin and then select the tab you wish it to appear in Plugins AssistantPanel Ox Available Tab System Calibration Motion Capture Post Process Model Edit Plugins Presentation 10 5 Chapter 10 Plugins Tab Cortex 2 1 Reference Manual In this example the X panel is moved to the Post Process tab see Figure 10 6 Figure 10 6 X Panel in Post Process Tab The X Panel is now located in the Post Process Tab iH File Layouts Data views Tools Help Current Directory C Program Files Mation Analysis Cortex2 Sgllgis BioF eedT rak GolfS wing System Calibration Motion Capture Post Process Model Edt Plugins Presentation So 2 9 0 GUEST Rectify QuickID Rectify eS deras Template RB MarkerID Exchange Linear Cubic RB Unnamed i Rectify Rectify Join Join Join MatkerSets isa Club Goler E Smooth a Ta ae a Click AllNone Ctrl Click Toggle Make Delete Copy Cut Unnamed Unnamed ry Cut Outside Click Alone Ctrl Click Toggle 4 U4 J u2 u3 U_4 lt Empty gt U_5 lt Empty gt U_8 lt Empty gt U_7 lt Empty gt U_8 gt _8 Empty a olo ulojn swn a 100 900 Tadon m _i lt fal ed sess DN a bie fee a Stopped 921 Frames 120 FPS 2 Up Units mm Analog 600 00 Hz 10 6 Cortex 2 1 Reference Man
76. TRB files TRB HTR files TAC EYT files EMR files HTR EVT EMR 3 VC files in All data files in ubfolders subfolders No subfolders Outline E lt working_folder gt TRC files Cortex allows a higher level of flexibility in organizing captured data than previous version so Cortex EVaRT Captured data can be sorted into sub folders by file type Additionally files can be named in a legacy naming convention which allows backwards compatibility with older versions of Cortex and other third party applications Folder Naming Settings This is the region of the settings area allows two types of customization specifying sub folders based on data type and enabling the legacy naming conventions Single MarkerSet legacy file naming enabled EVaRT and previous versions of Cortex only recorded one MarkerSet s tracks information As such all generated trb files had the name of the capture that was being recorded All other data types AVI ANB HTR etc used file of the same name naming conventions for saving and loading the data Cortex 2is capable of capturing tracks data for multiple MarkerSets and so has to use different naming conventions for the Mark erSet specific files TRB TRC HTR EVT EMR Cortex 2 names these files as lt trial_name gt lt trial_number gt lt MarkerSet_name gt X XX This re sults in each MarkerSet s set of files having unique names To handle this Cortex 2 introduces the ide
77. and has a Capture saved for it Creating a pair begins by se lecting a project file Once a project file is loaded a number of tracks files can be associated to this project A new project file can then be selected and tracks associated with it The files that will be generated are displayed in the Preview area along with the selected project file Once all pairs in the current folder are setup the Generate Captures button will go through the list and generate a series of Captures and Setup Files Cap ture Setup Files that already exist are not overwritten unless the Over write existing items box is checked The batch importer has a status log to indicate the progress being made When the batching is done the last Capture in the list will still be loaded Figure 4 7 Batch Importer Interface Legacy Data 2x C Documents and Settings ben ahiborn My Documents CortexD ata S amples Calcium Tutorial ExampleD ata Browse Refresh File Importing Quick Loader Batch Importer Select project file Add tracks files to batch list Remove selected item from batch list Clear batch list Generate captures Overwrite existing files items in red Preview Selected project file Matt2_ prj Project File Matt prj Tracks File MattRoll1 tre MattCartwheell tre Setup to Generate Import_MattRoll1 cal Import_MattCartwheell cal Capture To Generate Import_MattRolll cap Import_MattCartwheell cap
78. and run 3 Adjust the brightness and threshold For a typical full body volume in a room with little extraneous sun light or incandescent lamps brightness at 100 full and threshold at 400 500 are usually good starting points 4 Adjust the focus until as many as possible of the 12 discs are clearly seen in the 2D view Until the cameras have been calibrated at least once for a given lens set ting the show centroids should be ignored Later versions of the software allow zooming in and out of the 2D view Filling all the PC screen with the focus card view will make fine tuning the focus of the camera easier It is highly recommended that an assistant is used for this procedure One person adjusts the lens following the instructions of the person viewing 3 31 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Lens Aperture Ringlight Brightness in Cortex the computer s monitor Because the focus can be very sensitive the smallest movement of the focus ring can cause a large effect It can also be confusing as the focus is moved through the ideal setting Just out of focus one side looks much like just out in the other direction When you are close to the ideal focused place on the lens just touching the lens can seem to be enough to move the focus ring If the cameras have been mishandled it is possible the focus will be so far out that nothing will be seen A good starting point is zoom out minimum focal lengt
79. back of the Host computer Cortex tracking computer After you have plugged in a camera click on the Connect to Cam eras button on the Real Time Dashboard If this works unplug this camera and set it off to the side or label it as good Move on to the next camera doing the same and so on each time remembering that there should only be one camera plugged into the EagleHub at a time This will help you narrow down if there is a conflict After running through each individual camera it is very useful to power down the EagleHub to help clear out any stored data that may be in its memory You may also want to take the time to write down IP address for each camera If you run into a problem with multiple IP 3 26 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Socket Error Function Not Found In Library Error Addresses being the same this could be the problem Each camera needs to have it s own independent IP Address No two addresses can be the same This makes each camera unique and will help the system identify them When connecting to the cameras on the RealTime Dashboard if you en counter a SOCKET ERROR you will need to verify the following e that the Ethernet connector on the back of the Host Computer is working properly e that the Ethernet cable running from the EagleHub or switch con nected to multiple EagleHubs to the Cortex Host Computer is con nected If you get the message ERROR Function not fo
80. be used to help solve the frames of data in a motion trial Figure F 5 Optional Markers mun m EN A aa Rear W Fi A i f R Clavicle L Clavicle ai R Scapula m R Bicep j L Bicep R Forearm ie AN J L Radius R Uina R UIna ae N A 4 R Thigh Front R Thigh C L Thigh L Thigh Rear L Thigh Front 7 L Shank Rear L Shank Front y E R Shank Upper R Shank L Shank R Shank Front R Shank Upper y L Shank Front R Shank Front R Shank Rear L Shank Rear L Thigh Front ag R Thigh Upper A Thigh Upper kei bee LNIGN FTONE R Thigh Rear L Thigh Rear R Thigh Front R Shank L MedFoot R LatFoot F 22 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module The markers shown in Figure F 6 on page F 24 are used by the Motion Module to control the degrees of freedom in the hand If the three critical markers are present in the static trial the Motion Module will load a de tailed model of the hand with three joints in each finger By default all of the finger joints are fixed SIMM converts them into hinge joints as it de tects the presence of markers to control the joints For example if R Finger2 M1 R Finger2 M2 and R Finger2 M3 are all present SIMM will create three hinge joints in the index finger each with its own degree of freedom If only R Finger2 M1 is present SIMM will create the proxi mal finger joint with a degree o
81. becomes obscured the camera will stop providing focus feedback and go back to the mode where the spectacles are shown This will display a graphic to assist with focusing the camera Once focusing of this camera is done use the Right and Left but tons to select another camera to focus Initially an arrow pointing down will be shown in the LED display Begin turning the focus dial on the camera When the arrow points up stop and begin turning the dial in the oppo site direction Next a stop sign with an arrow in it will be displayed Stop turning and again slowly turn in the original direction As you turn a red box outline will appear Continue to turn slowly and the box will fill in as the focus gets better When the red box is filled in it will next turn into a green box outline Continue turning slowly until the green box is filled it When the green box is completely filled in an optimal focus has been reached 3 28 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Wireless Remote Top Button Toggle insight focusing Functionality While In Insight Mode Bottom Button Start focusing the camera Left Button Go to prev camera by camera number Right button Go to next camera by camera number 3 29 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Camera Status Indicators Figure 3 21 Insight Focusing Camera Status Indicators 1 Begin the focus procedure turning the lens focus ri
82. can be ordered by click and dragging on the buttons while holding the Alt key This can be opened by right clicking on the Post Processing Tool Strip Tool Strip Options These options change how the buttons are displayed in the Post Process ing Tool Strip The options are Text and Images Text Only Images Only Each button has a tool tip which is displayed when the mouse hovers over it These can also be enabled disabled The whole Tool Strip can also be shown hidden Tool Buttons This enables disables specific buttons in the Tool Strip 4 36 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Settings gt Misc Tab This settings area provides a collection of miscellaneous settings the con trol various portions of the Cortex software Figure 4 29 Settings gt Misc Tab Settings Calibration File Structure I Tracking Cameras Playback 3D Display Post Process Tools Misc Sound C Disable Sound Effects SDK Streaming C SDK2 Enabled NIC Address 0 0 0 0 Have Current Frame follow Mouse when selecting Yes O No XYZ Graph Zoom Options Time Code Post Trigger Recording Buffer Dieks id ae Max Frames 256 Marker Slots Max VC Filesize ao00000 Number ENE ax llesize 4000000 192 J Number of Cameras ANI Remote Signal Output Number of Cameras 16 NIC Address 0 0 0 0 3d Scene Zoom In Mouse s Zoom In Current Frame Located in UserFiles
83. cards in stalled in them Please make sure they are labeled so there is no confu sion If you or your IT department has changed the network address for your system or your cameras please make note of this for reference as it will save you time in the future If you see the error shown in Figure 3 17 there can be multiple reasons why Figure 3 17 Unable to Connect to Cameras Error Realtime x Unable to connect to Network Cameras The following are some steps to try and fix the problem starting with the simplest and progressing to the more complex 1 Under the System gt Cameras subpanel verify the Camera Network Address in the Camera Network Address box Figure 3 18 Network Address Box IP Addr 0 0 0 0 Set As Master Brightness 100 Threshold 326 New Camera Software Camera Network IP 0 0 0 0 v Reboot All Cameras If nothing has been changed this should have a network address of 10 1 1 199 Try and connect to cameras again If this does not fix the issue please move on to the next step 3 22 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Make sure that the Network cable going from the back of the com puter to the EagleHub is securely installed Motion Analysis uses the on board network port for the camera network If you purchased a computer from another source this may not be how your system is setup Please take note of this when checking the connections as it will be usefu
84. clicking on a specific camera will show only that camera s view Double clicking again will return to all camera views Selecting Shift double click selects the view for only the enabled cameras within the system For users collecting analog data from force plates an Analog Display pro vides graphs of output from up to 192 analog channels You can view any combination of channels at the same time As a convenience the Analog Display allows you to resize the label panel on the left side of the screen to accommodate long channel names To open the Analog Display and modify the number of visible channels 1 oa rwhd Channels Table Channels Name FAX Fig FAz M1x MIY MIZ F2x F2Y F2z M2x 11 j M2Y M2Z on Din s wo ny E All Channels Visible ODDO ess Shift the Analog Data f mlx Range Jee10V 10V 10V 104 104 104 10 lantov 10V 10V 10V H 10V Selected Channels Shift the data this number of samples Apply Press F5 on the keyboard or choose Data Views gt Analog Graphs from the Menu Bar With the right mouse click on the Analog Graphs From the pop up menu choose Visible Channels Left click on any one of the check marks in the Visible column Press Shift click in the Visible column to toggle multiple channels Click directly on the Visible header cell to toggle all of the channels at o
85. come to Cortex dialog enables check box in the Tools gt Settings gt Misc panel 4 5 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual File gt Trim Capture Provides an interface for altering the Post Process Capture This includes W Options changing which files are part of the capture TRB vs TRC discarding portions of the data virtual and unnamed marker data trimming frames from the capture and sub sampling the capture Figure 4 5 Trim Capture Options Interface Trim Capture Options al x M Default Directory File s Original Directory Export Directory c Documents and Settingsiben ahlbornimMy M Output files Tracked Markers IV Raw video vc I Discard Unnamed Markers OK Just save the settings I Discard Virtual Markers V Analog anb Cancel IV Colorvideo avi Frames IV Audio wav we Save All Frames Export Trimmed Capture JV Tracked ASCII tre C Save Selected Frames IM Tracked binary trb J Sub Sample fi V Auto Load Exported Capture File gt Close Unloads the Post Processing Capture This includes unloading all Marker Capture Sets and data files but the Setup information is left in place File gt Import Export This is a tool which provides compatibility between EVaRT Cortex 1 and Legacy Data Cortex 2 For importing this tool has two modes Quick Loader and Batch Loader Exporting provides three operatio
86. coordinate systems defined This is typically used by biomechanics and research customers Current Frame The absolute angles in the currently selected frame are written out in the file header of the HTR file The angles in the columns are zero referenced to the angles in the file header Use this method option if you are going to read the htr files into an animation package with the Motion Analysis File IO plugins 11 11 Chapter 11 Skeleton Types Cortex 2 1 User s Manual Licensing Notes SkB skeletons are defined and edited within the Cortex software and re quire a separate license item but they can be run and the skeletons data generated without additional licenses in Cortex There is separate docu mentation provided with the Skeleton Builder that shows how to set up and edit SkB skeletons Calcium Solver skeletons are imported or created in the Calcium soft ware Calcium software requires a separate license to edit or create the skeletons but they too can be run and the skeleton data created from Cor tex without a separate license Calcium also can create the HTR skeleton data using the same Solver engine as Cortex and the SIMM Motion Mod ule Multiple Characters and Multiple Skeletons When you specify additional marker sets the skeleton engine needs to be in each of the markerset files that you select The skeleton type is stored in the markerset file For previously stored MARS files open up each of the MARS file
87. data by drawing a vector in the model window at the appropriate point of application and with a size corresponding to the magnitude of the force force plate data in an analog file are voltages mea sured by force plate transducers These voltages are converted into forces using a calibration file forcepla cal This file is the same one used by EVa Cortex and OrthoTrak To use it with SIMM you should put a copy of it in the same folder as your motion data or in the folder SIMM Re sources mocap misc If you have only one force plate configuration for your motion capture system it is preferable to put forcepla cal in SIMM Resources mocap misc rather than copying it into every folder of motion data C3D files that contain force plate data also contain the calibration infor mation for the plates Thus there is no separate calibration file that SIMM reads when importing C3D files SIMM also uses another configuration file importVariables txt to map force plate channels to SIMM variables This file is located in SIMM Re sources mocap misc and contains mappings for typical channel names for up to six force plates You will only need to change this file if you use more than six force plates or use force plates that have exotic channel F 6 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module EMG Data Other Data Real time Import First time setup only configurations This file is used when loading ANB ANC files and
88. default method for determining shoulder elbow and wrist joint cen ters uses percentage offsets from the appropriate marker locations If me dial elbow and wrist markers are used in the static trial their locations are averaged to get the joint centers as is done with the knee and ankle It is recommended that you use medial elbow and wrist markers in the static trial if you want an accurate representation of arm motion Once the locations of the OrthoTrak joint centers have been calculated from the static pose the Motion Module determines the orientations of the OrthoTrak segment reference frames It then can measure the lengths of the OrthoTrak segments and use them to scale the mocap model to match the size of the subject The reference frames for the foot shank thigh pelvis and torso are all determined using the procedure described in Appendix H of the OrthoTrak manual OrthoTrak does not create reference frames for the upper and lower arms but the Motion Module does this using one of several methods If medial elbow and wrist markers are used in the static trial then the arm reference frames are found in the same way in which the thigh frames are found If no medial markers are present then the upper and lower arm reference frames are found using the line between the joint centers as the X axis and using the same Y axis as the torso The Z axis is then determined by crossing X and Y Once all of the segment reference frames ha
89. digital video layered with the 3D View Camera Coverage Displays the coverage of all cameras within the capture volume View Center Centers the display on the selected marker Keep Centered 3D View center follows the selected marker Mirrored Mitrors the marker in the field of view Auto Rotate Rotates around the capture area by selecting Play Relative Toggles display to view from selected markers Perspective View Selects the normal display options adjust with mouse Orthographic View Displays a flat view from either the X Y or Z axis perspective 4 66 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface 2D Camera View Pop Up Menu The 2D Display renders raw camera data as blobs and or marker cen troids You can choose to see the centroids either with or without lens cor rection To see the marker data as viewed from any one of the cameras or multiple cameras simultaneously 1 Press F2 on the keyboard or choose View gt 2D Display from the Menu Bar 2 Choose one or more cameras with Ctrl click or Shift click on the green camera buttons on the Real Time Dashboard or press All On To see the 2D Display options right click on the camera view 2D Dis play Figure 4 52 2D Camera View Pop Up View Options Delete Mask Delete All Masks Auto Mask Deletes selected mask Deletes all masks in the 2D display for the selected camera Draws a mask around all items in th
90. frame format If you have the optional Time Code Reader card installed in your computer this displays the current Time Code value when you are in the Motion Capture mode and connected to the cameras The Frame Counter displays a count of the total number of frames in the data set You can select each camera by clicking on it s respective numbered but ton that is listed across the Real Time Dashboard Clicking on a camera button will either activate or de activate that camera for setup features Right clicking on any of the camera buttons will open a function menu with various commands for that specific camera The menu and a descrip tion of each command is shown in Figure 4 63 Figure 4 63 Camera Buttons Right Click Menu Enable Selected Camerafs Disable Selected Camerats Enable Selected For Live Tracking Disable Selected for Live Tracking Sort All by L Frame Position Sort All by IPAddress Enables the selected camera to capture data if disabled Disables the selected camera from capturing data Enables the camera to capture and display data in Real Time Disables the camera from data collection in Real Time only Camera numbers are sorted in a counter clockwise order Camera numbers are sorted by IP address starting from lowest Delete Selected Camera s from Project Deletes the selected camera from the capture file 4 80 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Post Process Dashboard The P
91. gt Calibration Frame Required Settings Figure 4 13 Calibration Frame Interface a Settings Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc _ Id Params Plugins Calibration Frame Lenses Orientation Capture Volume Other Calibration Units Calibration Up Axis zs Measurements Note The settings here determine the coordinate system of your capture vol ume This is where you enter the measurements of the calibration L frame the Up Axis and your system units L Frame Measurements The distances from the volume s origin are measured and are entered into the Measurements spaces Observe the right hand rule and make sure that you enter the data correctly In the Z Up example points 1 2 and 3 are on the X axis and point 4 is on the Y axis but adjust this accordingly if your Up Axis is different The vertical distances are the distance from the center of the markers to the floor Click on the other tabs and fill in the values accordingly You can make your own calibration L frame by placing four markers on the floor and measuring their locations with a tape measure Measure ments should be within 1 mm Selecting a different calibration up axis will show the correct view on how to set up your calibration L frame Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Calibrati
92. have a Local Area Connec tion There may also be 1394 IEEE Connection this is for Fire Wire and can be ignored b Right click the appropriate network connection for the Motion Analysis Network and select Properties from the drop down menu c Under the General tab scroll down and select Internet Protocol TCP IP and click on the Properties button Figure 3 19 Internet Protocol TCP IP Properties Selection General Authentication Advanced Connect using Intel R 82559 Fast Ethemet LAN on This connection uses the following items M YF NWLink NetBIOS vi NWLink IPX SPX NetBIOS Compatible Transport Prot Internet Protocol TCP IP X gt Install Uninstall Properties Description Transmission Control Protocol Internet Protocol The default wide area network protocol that provides communication across diverse interconnected networks I Show icon in notification area when connected IV Notify me when this connection has limited or no connectivity Close Cancel 3 24 Cortex 2 1 Reference Manual Chapter 3 Camera Setup d You should have Use the following IP address selected If not please make sure you have selected the proper network connec tion You may close this window and return to Step 4b The IP Address should be 10 1 1 199 and the Subnet Mask should be 255 255 255 0 If either of these is incorrect please change them Figure
93. in the Model Edit tab Make triangles especially triangles that will be fairly rigid during the movements Lots of rigid triangles in your linkages make for solid Tem plates that have fast Template ID numbers Triangles with equal sides can cause mis IDs whereas triangles with unequal sides work much better This will help to determine where to place markers on a person You must have all of the markers present on the current frame or you will get the status bar message Template ID failed That means it did try out all possible linkages and could not get a match Possibly the markers have moved or you need a better template Rectify First collect the trial from which you will make your template It should be a simple trial with representative motions and not require any editing The goal is to represent the min and max of each linkage in your model Use Quick ID then Rectify If editing is required consider taking another trial Make sure there are no marker switches using the 3D and XYZ view and then create a template using all of the good frames Rectify may generate marker switches and you do not want those remembered in the template It will haunt you later Template Rectify For most motion trials the use of Template Rectify will do most of the work in correctly identifying the marker tracks Template Rectify is pre ferred method to use to rectify since it protects the named marker tracks they are locked It also keeps the
94. indicates the Low and High Visible Frames Double clicking on this control unzooms time or expands the Visible frames to encompass all of the frames in the data set If you only want to work with a specific range of frames right click on this slider to lock un lock visible frames To the right of the Post Process Dashboard controls are five Frame Selec tor buttons Refer to Figure 8 2 1 Select Backward selects from the Current Frame to the Low Visible Frame 2 Select Forward selects from the Current Frame to the High Visible Frame 3 Select Current Frame selects only the Current Frame 4 Select Visible Frames selects from the Low Visible Frame to the High Visible Frame 5 Select None Safe Mode nothing is selected Figure 8 2 Selecting Frames Buttons Clicking any one of these buttons sets the Frame Selector mode that you can return to at any time by pressing Esc on the keyboard The Frame Se lector mode is a User Preference The default mode is Select Visible Frames This will also highlight the selected area in blue Editing XYZ data is only done in the Selected Frames The frames out side of the Selected Frames are protected 8 3 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Zoom In Zoom Out Target Marker Scaling The XYZ Graphs right mouse pop up menu includes the time zooming features default hot keys are the and O keys These features zoom in time frames centering on t
95. is used to automatically identify a new person when they appear in the field of view It saves the steps of using the Quick ID feature to identify a new person in order to make a template for them The Template ID feature works in the Real Time mode when you are connected to cameras or it works when you are tracking the data from VC files after the collection The current template is size specific so a new person or a new ar rangement in the markers will not generally work for automatically identifying the markers When you click Update Template it also updates the Model Pose To use the New Subject button use the following procedure 1 Get a Range of Motion Trial a Get a good range of motion trial for your current tracks in Post Process Quick ID and edit so there are no mistakes or marker switches The data does not have to be highly complex but it should represent the minimum and maximum stretching for all limbs Jumping Jacks are a good example of the kind of dynamic motion that has worked well and does not obscure the markers or require editing For simple walking motion a single walking trial will suffice b Select one frame that represents a standard or neutral pose posi tion This can be with the arms down or the arms out feet apart or together but where no markers will be hidden You will want it to be a standard position that the next person will be able to repeat quickly and simply Have them face a certain direction
96. level Leave the Shutter Speed set to the default for normal data collection Click Connect to Cameras on the Real Time Dashboard if your cameras and connections are fully operational The system is now ready to go live with the Run button 5 1 Chapter 5 System Tab Cortex 2 1 Reference Manual Cameras Panel To connect to the cameras successfully you must have the Eagle Sup port item in your mac_lic dat file Figure 5 1 Cameras Panel Cameras Analog Devices Frame Rate 120 Shutter Speed 1000 1 sec Master Sync Internal v Slave Sync Ethernet v C Using Sunlight Fitter Current Camera Number 0 Model Unknown Serial Unknown Wersion Unknown Date Unknown IP Addr Set As Master Brightness 0 Threshold 0 FPGA Date Unknown New Camera Software Camera Network IP 0 0 0 0 v Tell Cameras the Network Reboot All Cameras Insight Focusing Frame Rate Sets the frame rate of the camera to any number ranging from 0 1 to the maximum frame rate The number does not have to be an integer it may be set to 59 97 for example Note The maximum supported frame rate for the Motion Analysis digital cam era system is 500 Hz Please contact Motion Analysis Customer Support for information and technical advice for using frame rates higher than 500 Hz Shutter Speed This sets the shutter speed of the camera ranging from 0 to 2000us This pulse is issued is in conj
97. options for im porting marker data reference the SIMM User s Guide The second component of the Motion Module creates a musculoskeletal model of a given individual by scaling a generic full body model the mocap model based on tracked marker data from a static pose The al gorithms that are used to scale the model are the same as those used in OrthoTrak a full body gait analysis package available from Motion Anal ysis For more information on the mocap model and how it is created and used see Section 5 3 Using the Mocap Model Opening Tracked Marker Files Selecting Tracked Marker Files SIMM can import tracked marker data that is stored in either a TRB or TRC data file These file formats described in the EVa and Cortex manu als contain X Y and Z coordinates for each identified marker for each time frame You can also import analog data files containing force plate and EMG data recorded during the motion These analog data files can be in either the ANB or ANC formats The Motion Module can also read XLS files containing other motion related data that you may want to view in SIMM such the kinetic data contained in an OrthoTrak single trial spreadsheet For more information on importing analog and XLS files see Section 5 2 3 Analog Data The Motion Module can also read C3D data files These files contain tracked marker and analog data in the same file so you only need to load one file to import all of your motion data from
98. or semi rigid lines to aid in the template identifying mechanism Marker Names Marker names are accepted in the markers grid when you press Enter on the keyboard Marker Color Allows the user to select a specific color for any marker Select the Selector marker from the list and simply click on the color of preference 9 3 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual Tree View Panel The Tree View panel provides an overview of the primary elements markers linkages virtual markers and segments of the model and al lows you to reorder the markers in the marker set by dragging and drop ping You can also insert and delete markers as well Figure 9 2 Tree View Panel Markers Treeview i Markers 41 VMarkers 0 E Links 111 SkB Segments inactive Calcium Segments 66 MarkerSet Name Jodi Skeleton Engine Calcium Solver 1 5 C Rotation Order ZYX Bone Axis Y Skin File FemaleFingers obj Skin Transparence O MarkerSet Properties MarkerSet Properties gt MarkerSet Name updating a template for this person MarkerSet Properties gt Skeleton Engine MarkerSet Name MarkerSet Properties The top line in the TreeView shows the important MarkerSet name Jodi which also shows up when you create a template for this person using this MarkerSet It is a good idea to save the MarkerSet locally after creating or This provides a way to select which skeleton engine will be use
99. plate objects from the model when loading a new file so that the display is not cluttered with multiple or redundant sets of objects Thus this option is turned on by default If you load a series of marker and analog files that all have the same force plate definitions then you should leave this option turned on For C3D import only This option allows you to choose from which pa rameter field in the C3D file to read the names of the tracked markers Be cause the POINT LABELS field in a C3D file is limited to four characters some software packages g Cortex store the full marker name in the POINT DESCRIPTIONS field Since the marker names in the tracked file must exactly match the names used in the mocap model if your C3D file does not contain full marker names in the POINT DESCRIPTIONS field you may have to edit the mocap model so that the marker names match the four character names stored in the POINT LABELS field F 5 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual Save HTR File Save Motion File Analog Data Force Plate Data Note This option allows you to save an HTR file containing the motion that SIMM calculates from the marker data This HTR file cannot be read back into SIMM but is useful if you want to import the motion into an other software package If this box is checked a browse button is enabled that allows you to specify the name and location of the HTR file This option allo
100. saved in a compact binary form In addition to the data in tre files trb files contain the following data for each frame e alist of the cameras used to calculate the 3D marker position e the residual of the 3D position calculation These are a special binary files that contains both scaled 3D track data and unscaled analog data For more information you can visit the C3D web site at www c3d org Appendix F SIMM Motion Module Introduction Opening Tracked Marker Files Analog Data Using the Mocap Model Analog Configuration Files SIMM Motion Module Guide to Mocap Model Markers Introduction The Motion Module is an optional component to SIMM Software for In teractive Musculoskeletal Modeling that allows you to easily import data recorded by a motion capture system It reads files containing tracked marker data 3D positions of markers in global space using the TRC or TRB file format developed by Motion Analysis Corporation It can also read analog files in the ANB or ANC format with ground reaction force and EMG data that was recorded in sync with the motion The Motion Module can also read C3D files which contain both tracked marker and analog data in the same file Additionally the real time version of the Mo tion Module can connect to a Motion Analysis system and receive and display motion and analog data in real time as it is being recorded Files of tracked marker data contain a sequence
101. segment along the X axis RX is not used very often compared to RY If you select a segment to rotate it will bring up the rotation gizmo RY is used to rotate the bone along the Y axis If you select a segment to rotate it will bring up the rotation gizmo RZ is used to rotate the bone in the SkB segment along the Z axis RZ is not used very often compared to RY If you select a segment to rotate it will bring up the rotation gizmo 9 22 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab Figure 9 12 Skeleton Builder Segments Property Values Tree View gt Calcium Segments Property Value Name LFoot Index 5 Parent LLowerLeg Origin Marker V_LAnkle Long Axis Y V_LFoot Plane Axis PSY M_LMidfoot Rx Offset 0 RY Offset 0 RZ Offset 0 The various skeleton types are described in Chapter 13 Skeleton Types Calcium is the graphical user interface to the Solver engine Solver is the powerful numerical tool for calculating skeleton motion from marker data The Calcium interface in Cortex is what allows you to correlate the positions of a marker pose to the initial pose of a skeleton The skeleton is usually created in an outside animation package such as Maya 3D Studio Max or Kaydara and then exported to an HTR file by a Motion Analysis file IO plugin for that package In this example we re using a skeleton from a Maya character Figure 9 13 Calcium Segments Property Values Units Global S
102. segment mapping This setting causes the Collada segments to resize to the segment data being solved in Cortex effectively stretching or compressing the skin to fit the tracking subject In this case the Apply Inverse Global Scale to Global Segments option for the skin should be disabled When the Skin Represents an Animated Character Animation One case for using skins is to represent a character whose dimensions are not the same as the mocap actor In this case the skin should use rotation data from the segments solved for in Cortex but the segment lengths should remain the same as their definition in the Collada file To achieve this affect the segment mappings should all be configured either by man ually or using the Auto Detect Segment Mappings button Once the cor rect segment correspondences and offsets have been configured disable the Use Skeleton Translations for each non global segment s mapping This setting causes the Collada segments to retain their length even though the solved data can differ The global segments MUST have this box checked however or the character will not move about the volume The result of this will be a skin which matches the dimensions of the char acter as opposed to the actor The skin will be rooted at the root of the ac 9 11 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual Making a Collada Skin for a Cortex Calcium Model in Maya tor however and the length of the extre
103. swContext _GetMarkerPosition 0 x y Z if iResult 0 then Message AutoID found at frame CStr i exit sub end if if swCancelled then Exit Sub end if next swPopups SetQuietMode 0 end sub 12 3 Chapter 12 Sky Scripting Interface Cortex 2 1 Reference Manual Graphical User Interface The user interface for Sky is found under the Cortex Tools menu Figure 12 1 Sky Graphical User Interface in Cortex Local Sky Scripts Tool Bar Cloud Button Current Script Sky Functions Help Filter Box EE Sky scripting interface DER CopyPerProject New Script Open Script Save Script Save Script s Run Cancel Refresh Options Help Clear Output Local Sky Scripts Sky Functions colt t sub kyMain yeral Functions Calibration Functions Camera Functions End Sub Context Functions Graphing Functions Load and Save Functions Loaded Tracks Functions Main Display Functions Marker Functions Model Functions Output Functions Global Sky Scripts Post Process Functions E Ga Batch Segro Functions O Examples Solver Functions 5 KinTools RT Motion Composer Functions O Markerset Relative Folder Functions 59 Skeleton Event Functions 29 UserGraphs H Other Functions CaptureLoop sk CubicJoinAll sk DeSpikeAll sky f Filter All sky Message Place script code here Set Location lt script output goes here gt N C Program Files Mo
104. template rigid and seems less likely to 8 21 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual make mistakes Correcting mistakes can take a lot of time If there are some incorrectly D ed markers it may be best to make all the markers Unnamed for all except the starting frame which can be frame 1 or any other frame To make all unnamed except frame 1 go to frame 2 select All Markers then select the time range Select Forward and press Make Unnamed under the Identifying tab Go back to frame 1 and press Tem plate Rectify On some complex trials where there is a crash or bang be tween people and or props have the actors start in the T pose do the ac tions and return to the T pose You can then work the data from the start to the middle and also from the end to the middle This working the data back and forth can save a lot of your time and not require that you hand ID many frames More on Templates and Template ID After a big crash of people with markers or extreme movement the mark ers may have moved and the template may not be as good You can Ex tend the template by D ing after the crash extend it based on one or more frames that have no mistakes then try Template ID to see if the template holds on the new frames Template ID tells you how good the template is working and it is the same template the Template Rectify uses Also think that Template Rectify gets used as much to un identify tracks as well as i
105. that are used in the post pro cess mode Figure 10 2 X Panel AssistantPanel X Delete Outside Volume Snippets l Delete Short Snippets w 2 ke s 3 Refine Tracks Global Marker Data Adjustment Translate X 0 0 Translate Y 0 0 Translate Z 0 0 Rotate X 0 0 Rotate Y 0 0 Rotate Z 0 0 Scale 1 0 Apply to Tracks Model Adjustment Refit Identifying Template Update Model Pose Markers Update Model Pose Update Model Delete Artificial Data Load Another Tracks File Frame offset 1 Delete Outside Eliminates all marker data outside of the volume defined in Calibration Volume Details Snippets Delete Deletes data strings in frames that are shorter than a specified length Short Snippets 10 2 Cortex 2 1 Reference Manual Chapter 10 Plugins Tab Refine Tracks This feature will smooth data that has become jumpy due to camera on off noise When a camera is turned on and off there is at times a small data spike in the frames before the camera is turned off and after it is on This is useful on facial data where small increments lt 1 mm will have a sig nificant effect on the final results animated character Figure 10 3 Refine Tracks 222m0 Y ENN AZ x 792 43 453 54 561 67 1896 47 881 26 ARIES Residuals 0 000 1 SS a Cameras a NS 2 _ a ell amp NNDS Missing data to be smoothed To Refine Tracks you will need to
106. that will also be easily repeatable for the next person along the X axis for example 2 Create a Template a Select Post Process gt Create Template b Select Body Template and check the box Include current frame as the Model Pose and select the correct range of frames where you have good data 4 74 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface c Save your capture file which now has a new feature called the Model Pose stored in it You may want to use the word Pose in the capture file name to distinguish it from earlier versions with out the pose but that is not necessary The normal template will also work for this person Note You can choose to see the Model Pose in your current capture by right clicking in the 3D View and then selecting Show gt Show Model Pose Figure 4 59 Create Template Window Showing Template Linkages Cortex Matt prj AkattCartwheelt tre E e Layouts Date views Tods Hep W MotionA System Calbration Moton Capture Post Process Model Edt Pugne EE n Segrmerts aan ar 7 Cock namne aaa Tope A rE II O Vey i OLH B gt 1 QURD Reckty Tepate Tomoiste Template Marker ID Exchange Obe Wus Cak Smooth Mae Rectfy Delete CR QR Search PP 2 iM Ju juos Creve D Ratt Jon Jon Me Unnamed Umaned Unnamed E Create Template Xx MarkerSet Name Template Prop Definition Golf Person Frames Range Frames Used Current Frames wit
107. that you do not need to use or learn the Calcium software Cortex creates an even more thorough JNT joint file when you export the SIMM Calcium Model You do need to have the per son standing in a neutral pose typically with the arms out in a T pose feet slightly apart and thumbs forward Chapter 11 Skeleton Types Cortex 2 1 User s Manual Model Edit gt The Skeleton Engine type is displayed and can be edited in the Model TreeView Edit gt TreeView panel when you select the prj name at the root of the Tree View The Skeleton Engine type appears as the Value of the Skeleton Engine Property at the bottom of the Tree View panel Figure 11 8 Model Edit TreeView Feel Model Edt Pi Te TEE Sw SOT LS S OPRANSS ee QuickID Rectfy Crete Template Template T MarkerID Exchange Cubic Virtual Gale Smooth Make Recily Delete Cut Cut Search PP Undo Hide Eaim emplate Rectify Join Join Unnamed eee Unnamed Outside Settings Marker fesse L SKB Segments inactive Markersets New Add Matt Root E Spinet E Spine2 W Spine E Spine4 Neck G Head amp LClavicle fa LUpperArm LLowerArm E LHand 6 RClavicle G RUpperArm E RLowerArm RHand 3 RUpperLeg E RLowerLeg a RFoot E RToes th LUpperteg 6 LLowerLeg H LFoot 6 LToes 16 Loaded Cap
108. the data None the less the user is allowed to change them indepen dently if necessary Refit Identifying Template This option takes the current frame in Post Process and compares the tem plate linkage lengths of that frame with the stored model pose The tem plate Min Max values are re calculated based on the amount of change in the linkage lengths Update Model Pose Markers This check box indicates that the stored marker model pose is to be re placed with the marker data on the current frame Update Model Pose This check box indicates that the stored skeleton model pose is to be re placed with the current skeleton data that has been calculated for the cur rent frame These last two options are used to update the model pose of a performer between motion capture sessions such as from one day to the next This avoids having to spend time refitting the position of the skeleton to the new day s model pose data The user should still verify that the fit is a good one but if the markers on the performer have not moved by very much then the fit is likely to be good Update Model The updates the model using the check boxes as set above in the panel Deletes the Virtual Join Cubic Join Linear Joint etc data that was cre ated for the current tracks file This merges another track trial into memory so you can view two differ ent data trials in the 3D window A Frame Offset lets you offset in time the merged data Only pos
109. the end and then repeat from the beginning This also acts as a Stop button The Play Backward Button default hot key is the lt key plays backward through the data until the beginning and then repeat from the end This also acts as a Stop button Sets the playback speed of the tracked data in ratio to the number in this box a value of 10 will play the tracked data 10 times faster than normal 8 2 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Time Code Frame Number Move 1 Frame Button Move to Lowest Highest Frame Time Zoom Slider Selecting Frames speed A value of 10 will set it at 10 times slower than normal speed The limits are 100 and 100 This shows the time code HH MM SS for the tracked data If a time code reader and a time code generator are used when data is collected the time code at recording time is shown If no time code reader or generator is used the time code starts at zero for each trial The Frame Number is the frame that is currently seen in the 3D View and is marked with a full height red line on the XYZ Graphs The Current Frame number is found in the very center of the Post Process Dashboard The Move 1 Frame Button default hot key for forward is the F key re verse is the S key moves the Current Frame forward or back by one frame This also acts as a Stop button This sets the current frame to the lowest or highest visible frame The Time Zoom Slider sets
110. the key modifier combinations that are being edited Ctrl Alt Shift Fl F2 Color 2 D Video Sg lt I gt ae Frames Frames Frame cae ies ae eal Peas ao oo Selection Centered Marker Unnamed Frames In Frames Out K L al Pa Prev Fe oye oe ae Zoom Linear Frame Marker Frame Help Selected Join x Vv B N lt gt Cut Virtual Toggle Search for lt Play Play gt Join Record Next Space F3 FS EZ 3 D Persp Marker Analog aa Analysis Doc View View Graphs Graphs Graphs ee ee Camera Only Toggle One Pane Restore Defaults Tools gt Sky Tools gt Time Lines For Sky information and functions please refer to Chapter 12 Sky Script ing Interface Shows the time line of the data for each marker indicating any breaks in the stream of data More information can be found in Time Lines on page 10 26 4 42 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Virtual Marker Definitions Tools gt New Subject Tools gt Colors Figure 4 33 Colors Form This sets the definition markers that are used to support a particular vir tual marker For complete information regarding Virtual Markers refer to Tree View gt VMarkers Virtual Markers on page 9 15 Please refer to New Subject Button on page 4 74 The Colors window allows you to choose RGB colors for the
111. three markers in decreasing importance that determine the replacement data These three markers are 1 the Origin Marker 2 the Long Axis Marker 3 the Plane Marker The Origin Marker should be the marker that is most rigidly attached to the marker to join If there are two choices pick the one that is more sta ble on the bone segment For example the elbow marker is a good Origin Marker It is usually attached close to a bone The shoulder is also good for the upper arm segment but not as good for the upper torso if the sub ject raises their arms For segments where you have multiple markers on a rigid segment such as the head it does not matter which marker is which For example if you have four markers on the head each of the four can be defined by any order of the other three markers But if you have only three markers on the head the Top_Neck marker may well be used as the Plane marker for the Join Virtual definitions The Long Axis Marker defines a straight line from the Origin Marker and the Join Virtual is not sensitive to changes in the length of this line For the left Biceps choose the L_Elbow as the Origin the L_Shoulder as the Long Axis Marker and the L_ Wrist as the Plane Marker 8 25 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Plane Marker The Plane Marker is the least strongly coupled marker to the problem marker to Join It defines only the rotation of the coordinate system lo ca
112. to give a real time view for positioning the cameras This is done in conjunction with using the Cam Field Of View function 3D Display Show Properties The cameras are positioned based on the 3D volume specified and you can zoom in and out to see the change in the field of view 6 4 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab Note Details Button Calibration Settings Window Tabs 2 Itis also used to make sure each camera can see all the markers of the calibration L frame If Camera Aiming is checked and Run is selected the calibration will be recalculated and previous calibration results will be lost Click the Details button located in the upper right corner in the Calibra tion panel The tabs for the calibration settings window shown in Figure 6 3 on page 6 5 are defined as follows Calibration Frame Tab Where you enter the measurements of the calibration L frame You can make your own calibration L frame by placing four markers on the floor and measuring their locations with a tape measure Measurements should be within 1 mm See Figure 6 3 for reference alignment using the Z up calibration method Selecting a different calibration up axis will show the correct view on how to set up your calibration L frame Figure 6 3 Calibration Frame Tab Settings f fel libration Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins Calibration Frame Origin Offs
113. when loading C3D files SIMM displays EMG data by varying the sizes and colors of the corre sponding muscles in the SIMM model EMG data in an analog file are voltages measured by the EMG system SIMM rectifies and smooths these data and then scales them based on an MVC value maximum vol untary contraction resulting in a smooth muscle excitation level that var ies between 0 0 and 1 0 If MVC values are located in the configuration file importVariables txt SIMM will use them to scale the EMG data If MVC values are not present SIMM will use each muscle s maximum voltage in the analog file to scale that muscle s EMG data thus each mus cle s excitation will peak at 1 0 sometime during the motion The file im portVariables txt located in SIMM Resources mocap misc contains mappings between typical EMG channel names and the muscle names in the mocap model It does not contain any MVC values In most cases however it is sufficient to not specify them and use SIMM s default scal ing method Other data is contained in XLS files and can represent any motion vari able that you choose to calculate and store in the file It is usually reserved for kinetic data e g joint moments and powers that OrthoTrak calcu lates and stores in its spreadsheet XLS format It may also include mo tion events such as toe off and heelstrike that are stored at the top of the XLS file SIMM does not perform any calculations on these data b
114. will want to select MOVIE mode 1 Record a capture with an avi located in an alternate location e g e data captures Move or copy the avi to the directory containing the capture or wher ever you want it 3 Click on the Capture Inspector tab in the Plugins gt Assistant panel 4 Select the avi in the capture location at the original location and select Remove File From Capture 5 Select Add Reference Video File to Capture and browse to find the moved avi N Currently Open Known Issues Known Graphic Card Issues e Interface is evolving e Resizing video window by dragging corner can cause a hang up Stop resize play is a resolution for this e File recompression functionality unstable with certain compressors e Multiple camera support is working however certain cameras Sony dislike it and will give a fail on run message e Snapshot tga image is incorrect There is a known problem displaying the AVI files when a 3D window is displayed on a Windows XP system The AVI file plays in a jerky motion and the screen is sometimes sliced into horizontal blocks This is a problem with Open GL and Direct X displaying at the same time Right click on your desktop then select Properties gt Settings gt Advanced gt Troubleshoot Slide the Hardware Acceleration down a few points Quit Cortex then re launch See if that fixes the problem The set tings depend on what your graphics card does and has for featur
115. with the scale that it is being rendered at If this is not the case as skin that is shorter than the actor would have feet that do not touch the floor Segment Mapping The Segment Mapping table displays and allows editing of all the Collada segment mappings segment mapping for short A segment mapping con sists of eight parts Cortex Segment This setting defines which segment in the MarkerSet skeleton drives the Collada segment This can also be set to lt unmapped gt in which case the segment maintains its relative position to its parent as defined in the Col lada bind pose Offset X Offset Y Offset Z Offset RX Offset RY Offset RZ These settings describe a transformation from the Collada segment s local coordinate system to the local coordinate system of the MarkerSet seg ment The angles are degrees applied in ZYX order This is used for ex ample if the bone axis of the Collada skeleton doesn t match the bone axis of the MarkerSet skeleton Use Skeleton Translations If this setting is enabled the Collada segment has the translation data from the MarkerSet segment applied to it If this is not checked only rota tion data is applied This box should always be set for any segments that have no parent otherwise the portions of the skin rooted at this segment won t move around the volume For parented segments checking the box means that the skin will be displayed in the scale of the MarkerSet skele ton probabl
116. with the mouse Color and Extra Stretch properties can be edited for set ting groups of links together 9 20 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab Create Template Show Template Linkages General Notes on Extra Stretch This is why there is a CreateTemplate sky script It shows how to use multiple TRB files as input to the template creation and extension pro cess Assuming a standard Range of Motion ROM file the Extra Stretch val ues are normally set as follows e 10 for the head e 15 for the links on the hips pelvis e 15 for the feet e 20 everywhere else 15 is the default value for new links This is a starting point As data is tracked you can fine tune the Extra Stretch values Smaller values that work consistently will result in fast identifying and fewer errors An effective tool in changing the settings and organizing the linkages can be found in the Create Template gt Show Template Linkages check box under the Post Process Tool Strip For more information refer to Tem plate Create on page 8 12 e Extending the template works exactly as if you took all the TRB data used to create the template and put it end to end and did a Create Template with the whole works at once e If the ES factors are too large you get misidentified markers e If the ES factors are too small and your template isn t complete enough you will get unidentified markers e The template is a pair of
117. written to the ASCII trialN forces file Analog Sample This is the current sample rate Hz of the analog signal in reference to the Rate capture frame rate of the cameras This can be adjusted by changing the Multiple of Frame Rate value This setting is typically set to a value of 10 Analog Sample Rate Multiple of Frame Rate x Camera Frame Rate Devices Panel The Devices panel provides a listing of the hardware devices that are cur rently used in the operation of the Cortex software e g color digital video cameras external trigger switch etc This panel also provides ac cess to enabling disabling the general features of these devices By click ing on the device you can control the it through the interface design of the original manufacturer Figure 5 10 Devices Panel with Example Reference Video Source Interface Cameras Analog Devices COM port trigger COM based angle encoder 5 Reference Video Sources Logitech QuickCam Web device B Reference Audio Sources Logitech Microphone Web devic SigmaTel Audio device cm 33D Enable Device Camera Video Only Sound No Sound Other Sound source File 3 File save location Capture default Other location 5 17 Chapter 5 System Tab Cortex 2 1 Reference Manual 5 18 Chapter 6 Calibration Tab Calibrating Your System What is the Square and Wand Calibration Calibrate Panel Calibration Files
118. 0 0 0 0 0 0 0 0 0 PRPPNPRPNNORPENNBRPEPRHPBREP EE WNNWWNWNNNWRWNWWWWNHNDN Appendix E Import and Export File Formats Cortex 2 1 Reference Manual TS Time Series Files from the Cortex Analysis Functions Velocity and Acceleration Calculations Cortex Analysis Functions F7 is a selectable view from the Data Views menu and allows the user to calculate velocity and accelerations of marker data distances between markers and Included Angles The Dis tances and Included angles are assumed to be self documenting and a de scription of the Position Velocity and Acceleration tabs is below These data can be Exported to the ts Time Series files Figure E 5 Analysis Functions Analysis PosiVel Acc Distances Angles Position Velocity Acceleration Position Velocity JA 3 Accel Export ts Time Series File There is a Frames Factor which can be set to 3 5 7 or 9 frames This se lects the number of frames to use for the velocity and acceleration calcu lations If the Frames Factor is set to 3 frames velocity data for the 5 th frame is calculated exclusively from frame 4 and frame 6 Velocity Data for frame 1 does not exist velocity and frame data starts at frame 2 If the Frame Factor is set to 5 the velocity data comes exclusively from 2 frames to 2 frames from the i th frame Larger Frame Factors have the effect of smoothing the data X1 Y1 Z1 Positional data is deter
119. 000 000000 0 000000 2 331526 2 552349 0 414928 1 000000 4 0 0000000 000000 0 000000 2 328715 2 410058 0 305621 1 000000 93 0 0000000 000000 0 000000 2 688713 0 354111 4 239368 1 000000 94 0 0000000 000000 0 000000 0 312819 2 503460 6 899297 1 000000 95 0 0000000 000000 0 000000 1 617305 3 427358 9 416446 1 000000 96 0 0000000 000000 0 000000 2 357207 3 05734110 941742 1 000000 LCollarBone Fr Tx Ty Tz RX Ry RX SF 0 0000000 000000 0 000000 2 648904 1 239630 0 547259 1 000000 2 0 0000000 000000 0 000000 2 753487 1 291442 0 549240 1 000000 3 0 0000000 000000 0 000000 2 832925 1 339503 0 493109 1 000000 4 0 0000000 000000 0 000000 2 839463 1 330919 0 571445 1 000000 193 0 0000000 000000 0 000000 2 837519 0 820427 3 997483 1 000000 E 9 Appendix E Import and Export File Formats Cortex 2 1 Reference Manual 194 0 0000000 000000 0 000000 195 0 0000000 000000 0 000000 196 0 0000000 000000 0 000000 EndoOfFile 1 948793 1 872437 2 747322 0 402037 3 829116 0 383394 3 696403 0 820163 3 692526 1 000000 1 000000 1 000000 E 10 Cortex 2 1 Reference Manual Appendix E Import and Export File Formats ANC Analog ASCII Row Column ANC anc files contain ASCII analog data in row column format The data is derived from anb analog binary files These binary anb files are generated simultaneously with video ve files if an optional analog input board is used in conjunction wi
120. 01416 0 329 0 329 0 149 R Shank 0 0433 0 251 0 246 0 102 L Shank 0 0433 0 251 0 246 0 102 R Foot 0 0137 0 257 0 245 0 124 L Foot 0 0137 0 257 0 245 0 124 Torso 0 3229 0 294 0 342 0 233 Head 0 0694 0 362 0 376 0 312 R Upper rm 0 0271 0 285 0 269 0 158 L Upper rm 0 0271 0 285 0 269 0 158 a Segment Sum 1 Normalize Load Save Calculate Kinetics T T VMs 7 Skeleton 4 1 i Kinetics SE 10 20 T T T rrr T T T mr T 60 70 80 90 100 110 120 130 140 151 os OOo mma E gt ie 4 e Calculate 6 Calculate 151 Frames 60 FPS 2 Up Unitsimm Analog 960 00 H2 Chapter 1 Introduction Cortex 2 1 Reference Manual For More Information Please contact Motion Analysis Customer Support with any questions problems or feedback about the Motion Analysis Cortex software We can be reached at Motion Analysis Corporation 3617 Westwind Blvd Santa Rosa CA USA 95403 Phone 707 579 6500 Fax 707 526 0629 http www motionanalysis com For technical support and licensing information please contact support motionanalysis com For information about sales please contact info motionanalysis com Acknowledgments Thank you to the users and Beta testers listed in Help gt About Cortex chapter2 Planning a Motion Capture Session Overview 2 1 Studio or Lab Preparation 2 1 Prior to the Capture
121. 04 41 0 Template Rectify RB Rectify Marker ID Exchange Linear Cubic Join Join Join E v Of ye WVWHREDSES amp Qal RB Virtual Calc Smooth Join gt Make Unnamed Unnamed Delete Copy Cut Cut Outside 3D Display Show Properties Subject World lv Markers Cameras V Links Camera Rays MarkerSet Names Cam Field Of View Marker Numbers Floor Marker Names Youna Frapdtories Reference Video Motion Trails Coreen eee Virtual Markers Center Unnamed Markers Skeleton Keep Centered Skin Mirrored Skeleton Axes Auto Rotate Forces Relative Viewing O Perspective View Forceplate Numbers BackCalc Orthographic View C Model Pose KinTools RT Display Options Segment Center of Mass Linear Velocity Joint CO Forces C Moments Linear Acceleration Angular Velocity Angular Acceleration Global Center of Mass Gravity Vector Additional 3D Display Settings oF GE ye 100 200 12 Loaded Capture C Program Files Motion Analysis Cortex2 Samples 16 Camera Calibration Face Bady DaveROMI cap T 300 PT T 400 500 T 600 T T 800 900 1000 1 TopHead 2 L_Head 3 B Head 4 R_head 5
122. 1 Strategies and Tips 8 33 Wand Data 6 21 Post Trigger Mode 7 10 7 11 Post Trigger Recording Buffer 4 39 Index 6 Power Consumption A 3 Eagle A 3 Hawk A 3 PP Settings 8 17 8 19 Preserve Layouts 4 15 PRJ Files E 3 Profile Manager 4 14 Prop Definition 7 3 Prop Files 7 13 Props 2 4 Q Questions and Answers H 1 Quick Files 4 46 Quick ID 8 17 Quick Loader 4 7 Quick Props 7 14 quick solve defined F 4 Range of Motion 7 2 Raptor Camera Physical Dimensions 3 16 Raw Playback 4 29 Raw Settings Button 4 79 Real Time Dashboard 4 59 4 71 camera buttons 4 71 real time import see Motion Module Record 4 45 Recording Data 7 11 Rectify 8 18 8 19 Rectify Functions 8 19 Rectify Unnamed 8 16 8 20 Reference Video 4 15 Reference Video Calibration Wizard 4 55 Reference Video option 4 61 Refine Tracks 10 3 Refining a Calibration 6 14 Refit Identifying Template 10 4 Refresh 4 48 Remove MarkerSet 4 10 Replace Loaded Analog Setup 4 45 Replace MarkerSet 4 10 Replace Tracks Data 4 57 Report a Bug 4 57 Requirements System 1 3 Reset IDs Button 4 74 Right 4 80 Rigid Body Join 8 19 Rigid Body Rectify 8 18 8 19 rigid objects 7 7 Ringlight Brightness 3 32 ROM 7 2 Rotating 4 82 Rotation Offset 9 22 Rotation Order 9 5 RSE 5 16 Run Button 4 79 functions 4 79 Run mode 4 71 Sample Data Viewing 4 61 Sample Form 2 5 Samples directory 4 61 Save A
123. 1 62 64 65 7026 363 133 974 288 875 28517 930 160 277 4739 449 70 087 3795 858 7148 751 152 024 18 000 32 967 18 000 18 000 36 000 18 000 3D Residuals Wand Length Avg 165 262 Avg 521 33 Dev 53 1926 Dev 74 47 Extend Seed Button Note 1 After you have clicked on Extend Seed check that the residual value for each camera is at a reasonable level If all cameras do not eventu ally seed you will need to check your Wand coverage Extending the seed can be done to half or more of your cameras with excellent results as long as you have overlapping wand data for all cameras 6 20 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab Post Processing Square and Wand Data Note Note Note Troubleshooting the Wand Calibration It is possible to process the square and wand data after the data has been collected This is helpful if you did not have the time to process it during the capture or if you lost the capture file that contains the calibration in formation The steps are as follows You must have the CalSeed vcX or CalSeed cap and the CalWand vcX or CalWand capfiles from the data capture session 1 Select Raw Files in the Real Time Dashboard and then select Cal Seed vc1 Select your CalSeed data set in the data capture folder You can create a mask to eliminate unwanted markers or reflections Re select the CalSeed vc1 file again and press the Calibrate button in the Calibrati
124. 11 Skeleton Types Cortex 2 1 User s Manual Calcium Solver The Calculate button refer to Figure 11 2 activates the Solver engine to Skeletons do the Global Optimization method and solve for the skeleton within the marker cloud If you have defined a Calcium Solver Skeleton in Post Pro cessing the process is as follows 1 Select the Skeleton check box Define a period of frames select a starting and end frame to calcu late from the current time slider 3 Click on the Calculate button Note The Treeview has an option to view the Skeleton as it renders Figure 11 2 Skeleton Check Box and Calculate Button TO Cortex BETA Setup cal Matt ROMILcap GS Pe Layouts DataViews Took Hep Camee Draco C Progeam Fiss Motion Anaiyes Cotan Samelee Sky Gxamolee stcrang weh Mae System Calbraton Movon Capture Post Process Modal Edt Pugns Presentaton rE OO AVLI SFOCHABSS Quick ID Rectify Creste Temelate Template Marker Exchange Cubk Vetual Cak Smooth Make Rect y Delete Cut Cut Seh PP Hide Terns D Ractty kin Join Vis Unnamed Unnamed Unnamed Outaide Settings Marker Matcervets New Ada Mat fab Seved Appture C Program Files Motion Anahysia Cortes Samples Sky Examples Batching with Mett Matt ROMI cap 2848 Fremes 120 FPS V Up Unitsmen Calculate Button Skeleton Check Box 11 4 Cortex 2 1 User s Manual Chapter 11 Skeleton Types This ca
125. 250 000 51 000 4 9 or 4 chan nels This sets the type of analog input configuration used in the capture ses sion for more information go to the National Instruments website http zone ni com devzone cda tut p id 3394 The analog inputs can be configured in one of three modes RSE NRSE and Differential per the capabilities of the A D device from National In struments This provides a single common ground for all analog channels This is used for smaller analog systems small number of devices This provides a single common ground that uses the AI Sense wire This is used for analog systems with a larger number of devices This provides a two wire and for each analog channel which halves the number of channels This is good for low level signals and noise re duction Consult NI com for more details on this feature or contact Mo tion Analysis Customer Support support motionanalysis com The Autozero forces do not change the raw data values If there is a drift or an offset in the analog voltage it is recorded in the analog binary anb file The Cortex software uses Autozero forces in the following places 5 16 Cortex 2 1 Reference Manual Chapter 5 System Tab 1 In the 3D view window that shows the force plate forces and stick figure 2 Inthe Tools gt Force Plate Forces box that shows the numbers 3 In the File gt Export gt Export Forces File item whereby the cali brated forces are
126. 3 Camera Setup Cortex 2 1 Reference Manual Figure 3 3 Typical 6 Camera Setup Note Capture volumes may vary depending on room size and the distance from the camera to the capture area Figure 3 4 Typical 8 Camera Setup 3 6 Cortex 2 1 Reference Manual Chapter 3 Camera Setup ope c enc ecceccanpopecccccepestessspeaseserpossesss Camera 4 Figure 3 6 Typical 12 Camera Setup Camera 7 Camera 6 a smacecccemesces eT ee ent bt See Pees Camera 4 3 7 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Figure 3 7 Typical 14 Camera Setup Gamera 9 poemas menean 1 anata a ne Circle of 2nd 8 camera 3 8 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Figure 3 9 Typical 32 Camera Setup dst Circleof Camera 7 Campra 6 Camera Ma i Camera 14 2nd Circle of 8 cameras i an a age ia oo _ per a Bd cameras aid irci of 8 panies we Cimeta 18 GG Camna Vt banira KE lt _ lt 27 Note The capture volume is divided into 4 overlapping regions each containing 8 cameras The regions are as follows Upper left quadrant Cameras 1 8 Upper right quadrant Cameras 9 16 Lower left quadrant Cameras 17 24 Lower right quadrant Cameras 25 32 3 9 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Setting Up the
127. 3 Left wrist a Lateral acceptable names L WRIST L WRIST LATERAL L WRIST LAT LWRI or F 28 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module b Radius acceptable names L RADIUS LWRA Semi critical 1 Left wrist Markers a Medial acceptable names L WRIST MEDIAL L WRIST MED or b Ulna acceptable names L ULNA LWRBb Head The head will always be included when the upper body is loaded and the neck will contain three degrees of freedom If the critical markers listed below are present in the static trial the head will be scaled separately from the torso Otherwise the head will be scaled uniformly by the scale factor used for the Y height of the torso If no markers critical or op tional are included on the head in the static trial then the degrees of free dom in the neck will remain fixed during imported motions Critical Markers 1 Rear of head acceptable names HEAD REAR REAR HEAD HEADREAR REARHEAD 2 Top of head acceptable names HEAD TOP TOPHEAD HEAD TOP TOPHEAD 3 Front of head acceptable names HEAD FRONT FRONT HEAD HEADFRONT FRONTHEAD F 29 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual The following optional markers are already defined in mocap jnt To use them just put their exact names in your Cortex capture pelvis R Trochanter L Trochanter thorax Offset Sternum T10 CLAV STRN RBAK cerv7 C7 C7 Spinous Process head R Ear L Ear RBHD RFHD
128. 3 20 IP Address and Subnet Mask Address Internet Protocol TCP IP Properties General You can get IP settings assigned automatically if your network supports this capability Otherwise you need to ask your network administrator for the appropriate IP settings Obtain an IP address automatically IP ai E 10 1 1 199 Subnet mask 255 25 255 0 Default gateway z C Obtam DNS server address automatically Use the following DNS server addresses Preferred DNS server Altemate DNS server 5 Ifthe software has still not connected to the Camera Network use the CMD Line interface in Windows to Ping the cameras to verify if there isn t a hardware failure a To Ping a camera select Start gt Run from the Windows desktop In the pop up window type in cmd This will launch the com mand prompt Type in Ping 10 1 1 201 and press Enter If the request times out it will try 4 times try doing the next number 10 1 1 202 and so on Your cameras should be set to 10 1 1 201 for camera number 1 and 10 1 1 202 for camera number 2 and so on unless changed by you or your IT personnel If the cameras do not respond then you may need to use your Eagle Test Cable to determine the Camera Network address The Eagle Test cable is the black cable about 1 meter in length one end plugs into the Aux port on the back of the camera the other end has a VGA port a COM port and a BNC connector
129. 3 Load Last Capture F2z H Generated Files l 9 379 35 0 231 36 d_a ml H E m itradeng events ConnectTo Cameras Disconnec Settings m m 7 rdentifying El Join Virtual 422 Rese s 9 Im C Skeleton A GolfSwing_1 cap X 00 00 03 062 New Subject I Wi 921 Frames 120 FPS Z Up Units imm Analog 600 00 Hz e Objacts Output Status Bar Messages Real Time Dashboard Information Center Cells 1 through 5 4 2 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Figure 4 2 Cortex Interface in Post Process Mode W G File Layouts DataViews Tools Help Current Directory C ProgramData Motion Analysis Cortex2 S amples Bio Feed Trak Golf Swing System Calibration Motion Capture Post Process Model Edt Plugins Presentation QuickID Rectify Create Template Template ID 0 885 4441 Goffer Template MarkerID Exchange Cubic Virtual Calc Smooth Make Rectify Rectify Join Join VMs Unnamed Unnamed ad S M_F_Head 6 M_RShoulder 7 M_LShoulder amp M_TopSpine 10 M_FLShoulder 11_ M_FChest 12 M_RBicep 13 M_RElbow 14 M_RForearm 15 M_RWrist 20 M_LForearm 21 M_LWrist _LPinky 23 M_LThumb 24 M_Midback 25 M_ShoulderOffset 2AM I nwRark Click AlvNone Ctri Click Toggle s
130. 4 in 10 7 m 15 0 m 25 mm 1 in 12 1m 16 0 m Note These are empirical tests taken from an Eagle camera with the 18 55 mm zoom lens at a capture rate of 60 Hz 100 brightness and a threshold 500 Hawk cameras will require markers that are approximately 50 to 100 larger than those listed in Table 3 2 When using 1 2 inch markers the useful distance for VERY CLEAN data Min 3 lines per centroid is about 8 meters Going to a minimum of 2 lines per centroid takes the usable distance to 12 meters Going to the 3 4 inch marker gains another 3 meters to 15 meters A note of interest is that going to a one inch marker does not give a big boost in distance Other factors come into play such as the inverse square law about light falling off as we get further from the source Above 16 meters the mark ers are self extinguishing Our experience indicates that if you go beyond about 10 meters in any di rection of the capture volume length or width it is best to have a second tier of cameras in the middle of the longer dimension This is a big benefit for multiple person captures as it minimizes editing time needed since you get lots of good solid 3D marker points 3 21 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Troubleshooting Camera Problems If Any Cameras Fail Motion Analysis sets the default network address in the software to to Respond 10 1 1 199 Please note some computers have multiple network
131. 41 285 322188 LLowArm0 000000273 4837570 000000 15 450962 0 327390 5 501311 318 246332 RLowArm0 000000285 3221880 000000 12 465152 0 572074 5 115813 305 910223 LHand 0 000000318 2463320 000000 10 682556 5 620492 27 438027 85 440039 RHand 0 000000305 9102230 000000 5 730878 2 097665 20 038204 98 351413 LPelvis0 0000000 0000000 000000 24 672467 6 972213 127 877478122 309825 RPelvis0 0000000 0000000 000000 39 808415 6 985094 127 739824133 924520 LThigh 0 000000122 3098250 000000 12 585726 15 440180 52 153190388 012318 E 8 Cortex 2 1 Reference Manual Appendix E Import and Export File Formats Beginning of Data Separated by tabs LowerTorso Fr Tx Ty Tz Rx Ry Rx SF 1 1262 497925 15 182068 2245 4418950 5336240 713565 1 0697651 000000 2 1262 534546 15 109411 2245 4282230 5902200 697084 1 1088881 000000 3 1262 367920 15 051557 2245 3151860 5882480 707301 1 1631961 000000 4 1261 811279 15 027791 2245 1335450 6069780 696131 1 3261221 000000 93 25 763012 11 505680 116 749229 85 78657582 456894 104 4607321 000000 94 31 705627 12 149048 131 977005 81 80329980 946663 100 7663191 000000 95 40 086079 12 445135 144 204391 77 85765879 605011 97 4399491 000000 96 49 986629 12 544500 152 518951 74 27449278 596512 94 2411671 000000 UpperTorso Fr Tx Ty Tz RX Ry RX SF 0 0000000 000000 0 000000 2 259649 2 946399 0 475843 1 000000 2 0 0000000 000000 0 000000 2 341502 2 767608 0 420984 1 000000 3 0 0000
132. 420 3916 4994 4994 3569 4994 4743 4994 4994 Appendix E Import and Export File Formats Cortex 2 1 Reference Manual HTR Heirarchical Translations amp Rotations HTR files provide the same information as HTR2 files but in a segment oriented method which is less suitable for information streaming The HTR format cannot created in Cortex This feature will be added to future revisions nformation about the structure and motion of hierarchical skeletons is Examples of Inf ion about th d motion of hierarchical skel i HTR Files stored in htr files There are two variations of htr files version 1 HTR and version 2 HTR2 The skeleton data is identical in both file versions however the motion data is presented on a segment basis in version 1 files while it is on a frame basis in version 2 files Thus version 1 files give the position data for all frames for the first segment followed by the position data for all frames for the second segment etc HTR Version 1 files are used 1 to save as HTR in Cortex under the Post Skeleton function in the Tools menu 2 for input and output from Si 2 0 3 for input and output for many of the animation package software Example of an HTR The example of a version 1 file shown in Figure E 3 on page E 8 was gen Version 1 File erated by Motion Analysis MoCap Solver and contains data for the movement of a hierarchical skeleton with one root and 19 child segments
133. 6 The cameras buttons on the Real Time Dashboard should turn Yellow which indicates calibration is square but not wand calibrated White means not square Green means fully calibrated N Select Raw Files on the Real Time Dashboard 8 Load the CalWand vc1 or CalWand cap file At this point you can mask out any extra data points that might be causing problems This feature allows you to utilize wand data sets if there are extra markers in the field of view of one or more cameras 9 In the Calibrate panel press Calibrate in the Calibration with Wand box You will see the wand results see the cameras move to their final place and see the measured focal distances Note You can use these steps to mask out unwanted data after you do a wand calibration Most of the time there is no need to collect a new wand data set If you have one or more wand files that contain many gt 100 frames with more than three images you can select File gt Load Capture Live or the CalWand cal file mask out the offending region s and calibrate from the previously captured and newly markered files Figure 6 13 Wand Results Frames with More than Three Images Cortex These cameras see more than three images Camera Number Example Number of Frames Frame Number 2648 350 All frames with more than three images will be tossed Some frames with only three images might include non wand data This stray data might interfere with the
134. 6 x can I use it in Cortex Yes if you go to the Model Edit gt Tree View panel and in the Skeleton Engine field you check Calcium Solver in Cortex You must also copy the MOD file into your current capture folder with the same name as your current PRJ file H 2 Cortex 2 1 Reference Manual Appendix H Questions and Answers for Specific Applications Question Answer Question Answer Question Answer Question Answer Question Answer If I have the EVa 6 X Solver setup can I get an HTR file from Cortex Yes Select the Calcium Solver Skeleton Engine button Bone button in lower left of the Post Process dashboard then select File gt Export HTR File What are the tradeoffs in capturing at 120 fps or faster or slower with Motion Analysis cameras With the older analog cameras there were tradeoffs in image quality as the frame rate went up With the newer digital cameras we see no degra dation AT ALL with the higher frame rates which is great for high speed captures The images are all taken off of the sensors in 2 msec which cor responds to the 500 fps Waiting longer between frames does not degrade or enhance the image quality The only considerations are Ethernet band width not generally a problem disk space used and time to process or post process the raw VC files Are there any rules that should be followed when deciding which camera should be set as Master Any camera can be mas
135. 69 7265 4414 usr people evademo Oct14 MichelleInitl tre NumFrames 232 232 232 232 232 232 232 232 232 233 233 233 90 Z1 2308 1284 1852 2152 2152 2152 3085 4143 7111 0335 4352 5973 316 316 316 316 316 316 316 316 316 315 316 315 LHead x2 7533 6074 1265 5659 7533 2800 4539 4539 1265 9777 4172 9770 NumMarkers 1608 1608 1608 1607 1608 1608 1608 1608 1608 1608 1608 1608 33 Y2 3785 2884 1984 9659 3785 3460 1409 1409 1984 3370 1043 0798 218 219 219 219 218 219 219 219 219 220 219 220 Z2 5500 0597 7480 6344 5500 1676 6402 6402 7480 0773 9638 2932 144 144 144 144 144 144 144 145 144 144 144 144 UnitsOrigDataRate mm RHead X3 7963 7684 7296 7652 7296 7963 7963 1222 7963 6867 7963 7963 1597 1597 1597 1597 1597 1597 1597 1597 1597 1597 1597 1597 60 0 Y3 3691 8106 8043 5711 8043 3691 3691 3621 3691 5786 3691 3691 274 274 274 274 274 274 274 274 274 274 274 274 Z3 4994 2137 3916 4
136. 9 Model Edit Tab Collada Skin Configuration Pop Up Cortex now supports the ability for skins to be imported from Collada dae files The Collada file format contains a lot of information For the purposes of skinning the main components are a mesh a skeleton and a relationship between the two This document refers to these three things as the Collada mesh the Collada skeleton and the Collada bind pose In order to use a skin in Cortex a way of driving the Collada skeleton must be defined This is done by using the Skin Configuration Popup to define a mapping between the MarkerSet s skeleton and the Collada Skeleton Figure 9 5 Skin Configuration Popup Skin Configuration B ea Skin Settings Segment Mapping Tools Skin Fle Kade dae gt Auto Detect Segment Mappings for Mapping for All Segments Skin Offset Representing the Subject Biomechanics Offset X 0 Offset RX 90 Offset X 0 Offset RX 90 Auto Detect Segment Mappings for Offset Y 0 Offset RY 0 Offset Y 0 Offset RY 0 Representing a Character Animation Offset Z 0 OfsetRZ o0 Offset Z 0 Offset RZ 0 n Cea MS mee 7 Use Skeleton Translations Appiyto All Segment Mappings Segment Mapping Kadee_Spine Kadee_Spine1 Kadee_Spine2 Kadee_Spine3 Kadee_Neck Kadee_Neck1 Kadee_Head Kadee_End_Head Kadee_Hair Kadee_Hair1 Kadee_Hair2 Kadee_Hair3 Kadee_End_Hair3 Kadee_LClavicle Ka
137. Area The left portion of this area contains tabs for each type of Event Cycle There are two general categories of Event User Defined Events and Built In Events There may be multiple sub types of Built In Events i e Gait Events Built In Events are discovered using algorithms that are em bedded in the Cortex software User Defined Events are Events which are discovered using algorithms provided by a user via Sky scripting There is a button next to the tabs for adding removing User Defined Events and Cycles The right portion of the Events Area is for editing the Events and Cycles Each type of Event Cycle has different properties that can be edited User Defined Event Properties Name The name of the Event All Events must have unique names Description A description of what the Event represents Color The color in which the Event is illustrated which shows up on the presentation graphs Event Script The Sky script that contains the functionality for this Event An Event script is optional if all the necessary functions are con tained in a graph script Enabled For Live Enables Disables the Event in Live Mode Enabled For Post Enables Disables the Event in Post Processing Built In Event Properties Gait Name The name of the Event This is not editable Description A description of what the event is detecting This is not ed itable Color The color in which the Event is illustrated which shows up on the
138. Bug Report Interface Cortex Bug Report DoR Customer Name E Mail To Send Updated after pressing Send Bug As E Mail Tuas A E mail this to support motionanalysis com if your Motion Capia Company e mail client doesn t work with the button below Bug Title 2 E Mail Subject Cortex Test Bug Motion Capture Company Cortex Test Bug Steps to Reproduce A from start of Cortex J i E M ail Body Opened file Motion Capture Company Cortex Test Bug BUG DESCRIPTION Opened file CORTEX INFORMATION Version 2 1 0 1074 Build Date Sep 30 2010 Number of Camera Slots 20 Number of Marker Slots 192 weesSYSTEM INFORMATION Operating System Name Microsoft Windows XP Professional Operating System Version 5 1 2600 196608 Operating System Platform Win32NT Culture Info en US Physical Memory Total 1071738880 bytes Physical Memory Available 151715840 bytes Virtual Memory Total 2147352576 bytes Virtual Memory Available 1253515264 bytes Clear Bug Cancel Help Menu The Help menu provides information about the software along with shortcuts interface panel information a searchable on line manual and access to the video tutorials 4 57 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Mode Tab These buttons are arranged to guide you through a motion capture session Buttons in a phase oriented order Refer to Figure 4 45 The first three mode but tons S
139. C 6 Cortex 2 1 Reference Manual Appendix C Force Plate Configuration Forceplate cal File Setup Using AMTI and Bertec Force Plates AMTI Gain Setting Bertec Gain Setting The Calibration Matrix For the AMTI force plates a gain of 4000 mV and a cutoff frequency of 1050 kHz is recommended Using the method outlined in the AMT liter ature this gain yields a scaling factor for the forcepla cal file of 25 The example in Figure C 4 uses an AMTI force plate A gain setting of 10 for Bertec force plates is recommended In the force pla cal file you should set scaling factor 1 gain 2 yielding a scal ing factor of 0 25 for a gain setting of 2 If using the AM6501 analog out device the gain is preset and the analog voltage range should be 5V The 6x6 calibration matrix Inverted Sensitivity is provided by the manufacturer AMTI It is used to transform the output of the force plate into three force vectors and three moment vectors The form of the matrix is shown in Figure E 5 The main diagonal of the matrix upper left to lower right represents the basic channel sensi tivities The off diagonal terms represent the channel cross talk If using Bertec plates with the AM6501 the amplifier is built into the plate and outputs data using a 15 pin D Sub connector cable to a small interface unit with signals in the range 5V In this case the amplifier is pre calibrated internally with no off axis elements in the 6x6 matri
140. Calibration from Previously Collected Files Extending the Seed Calibration Post Processing Square and Wand Data Calibrating Your System Calwand vc1 N Files A new calibration must be performed whenever e camera positions have changed e the coordinate system orientation has changed e the units of measure have changed It is imperative to complete an accurate calibration in order to collect high quality motion data Calibrating your system is a two step process First the seed calibration is done by employing the calibration L frame The exact positions of these markers must be known Next a wand with precisely located markers is waved around throughout the capture volume by somebody wearing no reflective material Wand calibration ensures that a direct measurement of an object of known size has been made by all cameras throughout the en tire capture volume This process locates the exact positions of your cameras and accounts for any geometric distortion the camera lenses may have as well as accu rately measuring the camera lens focal lengths The importance of this in formation is so great that a new calibration must be completed if a camera is moved or even accidentally bumped Calwand vcl N files one file for each camera get written when you press the Collect and Calibrate button in the Calibrate with Wand box and you are also connected to the cameras If you are not connected to the cameras the butt
141. Cameras The key to placing cameras around the capture area is to position them where they will yield the highest resolution without excluding any part of the adjacent capture volume In other words if you plan to track 2 gait cy cles do not set up an area suitable for 4 gait cycles When the tracking volume is increased the quality and accuracy of the tracking data will de crease First you will want to measure the room to establish the center of the tracking area An Example 8 For example if you have a 10 x 15 meter room and you are using 8 cam Camera Setup eras 1 Measure in from the walls 5 and 7 5 meters This should be the center of a 10 x 15 meter room 2 Mark the center of the room or tracking area with a piece of masking tape 3 Find the corners of the actual capture volume For optimum tracking the length and width of the capture volume should be no more than about half the room dimensions 4 Position the cameras evenly around the capture area Place the cam eras above the top of the capture space looking down to prevent cameras from seeing an opposing camera s ring light e For most gait analysis installations a height of 2 meters should be sufficient For a larger capture area e g full body or sports analy sis the cameras may need to be raised higher e Ifacamera must view an opposing camera use the mask function in Cortex to block the offending image e Position the cameras so that they are equally s
142. Click OK and save as a new setup 11 Press Run to start Cortex again You should now see lower residuals and fewer ghost markers There are a few things to be concerned about Since this behaves just like a wand calibration and if the subject does not fill the volume during the Refine trial the calibration can be poor and even worse than before the Refine If the subject spends a lot of time in one area and not much in an other it can also be poor If the markers are not identified then there is no information for the Refine so ensure that the subject is identified Save the Refine as a new setup e g Refined cal so that if the new calibration is not as good as before you can go back to the previous setup file The other thing to remember is that the Refine does not guarantee that the scale is exactly maintained It just optimizes the camera locations to track the markers better In effect the scale of the room may change slightly The reality is that Refining once does not change the scale It is not rec ommend to do many Refine Cameras in a row to improve the results since this may change the scale You do not need an identified stick figure to refine you only need to see 3D unnamed or named markers to refine the calibration You can use any 3D data points to Refine the calibration There does not need to be a template or a stick figure Any data that fills the volume will be sufficient You can have a markered subject walk in an
143. Cohu or Pulnix cameras using the Midas computer However you can use Cortex for post processing and analysis of motion capture data captured with these analog systems For Cortex operations the middle button is key for zooming and translat ing through the 3D and XYZ Graphs display You will need to verify that the middle mouse button is set to the middle button function 1 3 Chapter 1 Introduction Cortex 2 1 Reference Manual Software The Cortex program requires the host Windows operating system Installing the Software and Licenses To install Cortex for the first time simply insert the installation CD ROM into your computer and select the Setup Cortex 2 1 0 No Samples exe or Setup Cortex 2 1 0 exe file You can also download either of these files from the ftp motionanalysis com website Note To run Cortex you will need both a license file and a dongle from Motion Analysis Corporation The license file you receive is keyed to your Mo tion Analysis dongle number printed on the dongle Figure 1 2 USB Port Dongles and Flash Drive USB Port Dongles Motion Analysis Flash Drive Installation Using For new users Cortex licensing is now provided and setup using Flash the Flash Drive Drives For installation please follow these steps Note Please make sure to remove all Dongles from your computer prior to running the Cortex setup file on the CD Failure to do so may result in damage to your dongle Install the new ve
144. Cortex 2 1 Reference Manual Chapter 2 Planning a Motion Capture Session Job Assignments and Tasks During the Session Director Camcorder Operator Scribe Cortex Operator The director ensures that everyone involved is prepared for the capture session and controls the session including instructing and critiquing the subject s performance The video recording from the camcorder can be very important documen tation to aid in choosing the best takes A video recording may also be useful for post production promotions An optional reference video cap ture is available Refer to Digital Reference Video Option CortexDV Software on page 4 70 The camcorder should not be allowed to run during the entire capture ses sion This means that someone should be assigned to start and pause the camcorder for each take The camcorder operator should slate each of the takes This involves re cording the take number the Cortex trial name and number and any other relevant information on a slate board After starting the camcorder and before each take the slate board is held up in front of the camcorder for a few seconds The audio on the camcorder can also be used When the slate is held up in front of the camcorder the operator can say the take number the Cortex filename and any other information necessary When the take is complete the director can make audio comments on the quality of the take Someone should be assigned to ta
145. Cortex is capable of collecting up to 192 channels of analog data at any frequency between 60 and 5000 Hz In newer systems using the NIDAQ MX 8 0 or later software analog rates can be much higher The maximum rate can be up to 255 times the video capture rate but performance may vary with different computers The master digital camera provides the clocking signals to the A D card in the A D computer which provides the phase locking mechanism You must connect the A D cable from the master camera to the A D interconnect box Data can be collected in the pause mode or the run live mode without any delay or drift between an alog and video signals B 2 Cortex 2 1 Reference Manual Appendix B Analog Input Hardware and Software Installing NIDAQ Software on an Cortex Computer Note If NIDAQ Software is Already Installed New Installation of NIDAQ Software Note For Cortex 2 1 and later software we recommend installing NIDAQ ver sion 9 1 or later as it gives better analog performance and allows higher analog sample rates With NIDAQ 7 1 through 7 4 the maximum analog sample rate is 5000 samples sec for all channels With NIDAQ 8 and above you can go to higher rates typically 20 000 samples per second for all channels Free upgrades of the NIDAQ software are available from the National Instruments website NI com Cortex 2 x has not been tested with older versions of the NIDAQ soft ware It is known that NIDAQ versio
146. Definition A Virtual Marker is created Origin Marker has a fixed Long Axis Marker and Plane Long Axis and Origin relative to other markers distance to the Virtual Marker Origin Marker define a line Markers define a plane This form helps you define a Virtual Marker based on other markers The definition becomes a permanent part of the project once you Save Project A Virtual Marker s definition is used to calculate the Virtual Marker s position in each frame of a data set The Ratio relationships treat the offsets as a percentage of the distance between the defining markers The Value relationships treat the offsets as a distance from the defining markers When running live the Join Virtual tool only uses the first VM Join defi nition of the two that you are allowed However 4 passes are made over the list on each frame so that if a definition depends on another then after the first pass the second marker is reconstructed so that the first marker can be reconstructed on the second pass It also works this way in Post Process mode when you have multiple markers selected and do a Join Vir tual function The Real Time Join Virtual check box in the Real Time dashboard elim inates what might be seen as a possible pop on the frame when the real marker re appears At that time the Virtual Marker filling the gap is no longer used In the post processing Join Virtual mechanism the offsets between the marker to join and th
147. Factor X Width and Y Length Using AMTI and Bertec Force Plates Using Kistler Force Plates Notes General Information Note Forceplate setup information is saved in your Setup cal file and can be configured from the Tools gt Forceplate Configuration menu Up to eight force plates may be placed within the video capture space to measure gait forces While Cortex gathers video data it simultaneously acquires force plate data and calculates forces calibrated in Newtons or other force units In earlier EVaRT systems and in OrthoTrak the software used the force pla cal file for calibration and configuration In Cortex the force plate calibration and configuration is saved in the Setup cal file The legacy forcepla cal file can be imported or exported from the Tools gt Forceplate Configuration menu The forcepla cal file contains information describing the location orien tation and calibration of each force plate used The exact form of the file will depend on the force plate manufacturer Figure C 1 shows the file form for Bertec and AMTI force plates Figure C 2 shows the file form for Kistler force plates The forcepla cal file contains no text only numbers For multiple force plates the data for each force plate in the system is included in one force pla cal file see Figure C 4 The forcepla cal file must be in the same directory as either the Cor tex exe file or the prj file Otherwise t
148. Files then navigate to the folder containing the tracked marker file s you want to import Figure F 1 Windows File Browser Tracked Marker Options Dialog Import Frames To Increment SIMM 3 2 3 File Model Plot Help Look in E Simm323 gt amp el BI Documentation J Resources EVaRT Extras Models Motions J PipelineDemo File name Files of type Next select the appropriate marker file s in the file browser Click the Open button to import the file s At this point SIMM will display a dia log box allowing you to specify several options for importing each data file into SIMM Note If your analog data files have the same base name as your TRB TRC file e g subject14 trc subject14 anb and subject14 xls then it is not necessary to select analog files in the file browser SIMM will au tomatically open any analog or XLS files with the same base name and in the same folder as the tracked marker file there is an option in the dialog box to turn off this feature If you are loading C3D files this is not an issue since all of the data for the motion are stored in the C3D file Once you have selected one or more tracked marker files using the pro cess described in the previous section SIMM displays a dialog box for each one in sequence allowing you to set some options for importing the marker data In many cases you will want to use the default settings for these options so you can simply click t
149. Frame 1 selected as the current frame and you would check Include Current Frame as Model Pose for frame number 1 You should only need to do this once per marker set 3 When the New Subject comes into the volume they should be stand ing in the Pose position facing the same X and you select New Subject The PoseID will show and you should then select Pause The stick figure should snap to looking like the Model Pose 4 Update the template then select Pause Check that the ID is correct and that the position is similar to the Pose You can use the FIFO slider to make adjustments Save the capture file and then select Run 1 You will first want to obtain a good range of motion trial and set it as your current tracks in Post Process 2 You will then need to Quick ID and edit the trial if needed so there are no mistakes or marker switches It does not have to be overly complex but it should represent the minimum and maximum stretch ing for all limbs Jumping jacks is a good example of the kind of dynamic motion that has worked well and does not obscure the mark ers or require editing For simple walking motion a single walking trial will be sufficient 1 Facing Z or any other direction also works as long as Pose ID is used in the same orientation 4 77 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual 3 Select one frame that represents a somewhat standard or neutral pose position This can be with the
150. Frames Factor of 5 aX1 1 FR FR X 2 2 X i1 X 1 2 4 aY1 1 FR FR Y 2 2 Y i1 Y i 2 4 aZ1 1 FR FR Z 2 2 Z 1 Z 1 2 4 For Frames Factor of 7 aX1 1 FR FR X i 3 2 X 1 X 1 3 9 aY1 1 FR FR Y 3 2 Y i1 Y 1 3 9 aZ1 1 FR FR Z i 3 2 Z 1 Z 13 9 For Frames Factor of 9 aX1 1 FR FR X 4 2 X 1 X 1 4 16 aY1 1 FR FR Y 4 2 Y i1 Y 1 4 16 aZ1 1 FR FR Z 4 2 Z 1 Z 1 4 16 Resultant acceleration scalar aR1 frame i SQRT aX1 2 aY1 2 aZ1 2 E 13 Appendix E Import and Export File Formats Cortex 2 1 Reference Manual Binary Files ANB TRB and C3D ANB Analog Binary Note TRB Track Binary C3D The following are binary files and cannot be directly read or manipulated by the end user Their function and context are briefly described These files contain up to 64 channels of analog data collected simulta neously with video data by the optional analog board The data in these files can be converted to readable ASCII form as either an ANA or ANC file To do so from the main menu select File gt Export gt Export ANC The data contained in the anb file has a dynamic range of 2048 to 2047 which represents 12 bit signed numbers Cortex scales the speci fied input voltage range to this range of values These files contain the same 3D track data as ASCII tre files
151. Functions Velocity and Acceleration Calculations cc0 c cccsessseesseseeerseereeees E 12 Binary Files ANB TRB and C3D sccscrccretcresntieenseraieeicueestdaves E 14 Appendix F SIMM Motion Module Ae ellie fel pE a E eyanSr ere viee Mr artnr tesco ne en rere meer yr F 1 Opening Tracked Marker Files cccessseeeeeeeseeeeeeeeaeeeeeeeaeeeeeees F 2 Analog Daaraan F 6 Using thie Mocap Modal ssorirsaarn a F 9 Analog Configuration Files gic sctcs conctlaacecese sree hceceeccieshereseciecncetes F 16 SIMM Motion Module Guide to Mocap Model Markers 0 F 17 Appendix G Synchronizing Digital Video with Cortex COneX DY ie PTY sacar vscrasicacaacsies veckoadi te dncncenanessiseenntnideaaeanianes G 1 System Regurerne Sn nee ee ne ne eee ee ene er G 1 VESTN NI a sate chasse ete let ees axiada AE G 2 Usmo Corlox DU ersen anorni ee E G G 2 Cortex 2 1 Reference Manual Currently Open KNOWN ISS 06 ccc sccceccescs ccsntcacecsaksnetecsassscceciendeons G 4 Appendix H Questions and Answers for Specific Applications Appendix Useful Blank Forms Motoi Canine LO riin l 2 Human Body Outline Front esenneneooenenoeeseneeeennrererrsorrrnnnrrennreeenee l 3 Auman Body Outings Side serisine karrien l 4 Human Body Outlin Back 6 ccs csscscsascassatensscensnscarereassseaniencciunsanis l 5 chapter Introduction Overview System Requirements for Cortex Installing the Software and Licenses S
152. It is also the case if you have unchecked the Single MarkerSet legacy file naming enabled check box in Tools gt Settings gt File Structure 7 13 Chapter 7 Motion Capture Tab Cortex 2 0 Reference Manual Quick Props Figure 7 7 Quick Props Button Finalizing Details G File Layouts DataViews Tools Help Current Directory C Program Files Motion Analysis Cortex2 5 amples BioF eedT rak GolfS wing S ystem Calibration Motion Capture Post Process Model Edit Plugins Presentation MarkerSets Club Golfer ee a The Quick Prop tool is a fast and easy way of generating rigid tracking objects This tool can be used in post processing using pre recorded data or from live data without the need to record The functionality is the same in Live Mode and Post Processing The following example will be done running from VC files but it would be the same if connected to cameras 1 Find a good data frame In Live Mode press pause and scrub to a frame of data where all markers are visible 2 Select the unnamed markers Holding Ctrl select the unnamed markers that represent the prop 3 Press Quick Prop Press the Quick Prop button the MarkerSets tab The markers will become unselected you will receive a status mes sage and the prop will show in the MarkerSets list 4 Repeat this for all the desired props 5 Press Run Once all props are created press run to see them in action
153. Mocap Model and navigate to the motion folder Choose the tracked marker file containing the static pose Set the options as desired in the dialog box and click OK In the Model Viewer window choose Start gt Realtime Connection to lt hostname gt SIMM will display a dialog box allowing you to set some options for the connection The motion buffer size options con trol how many seconds of motion data are saved in SIMM s buffer The time scale options let you specify the minimum and maximum values in seconds for the time scale of the motion If you want the scale to remain fixed between minimum and maximum check the sliding checkbox otherwise the scale will continue to increase as new data is received SIMM will now wait to receive data from the Cortex computer Once the connection is established SIMM will display connected in its message window and the SIMM model will begin tracking the motion of the subject in real time You can pan zoom rotate and change the draw mode of the SIMM model as it is tracking the motion You can also create plots of kinematic variables and muscle properties and see the plots change in real time To disconnect SIMM from the real time stream click the Stop button in the Model Viewer You can play back the last N seconds of the motion When analog data is imported into SIMM in real time it is processed slightly differently than when the data is post processed in SIMM This is because the real t
154. PM Sales Order 09 xxx Entered By Support Cortex 2 aed50167 873b2d56 Analog Input b9806c31 d1567841 OrthoTrak b2df 5e69 8964274a Animation Plugins b1a50160 805b5c49 Director Sequencer ela04e65 85745819 RT2 Animation Plugins e3 05340 a069081b Analog Input b9806c31 d1567841 Calcium 4 e7ed5923 c363151f Skeleton Builder 4 a3 44279 99780c5b Reference Video 3 0 eb92592f cf636al3 Talon Streaming 4 ecb36136 d65b4b14 Talon Viewer 4 86 b0714 43d037e Motion Composer c7 00e25 c534083f This license has no expiration Computers with a new dongle installed need to load the dongle drivers so that the application will detect the dongle You can choose to install the dongle drivers when initially installing the Cortex software or you can run the drivers independently by running the program in the Sentinel Drivers directory under the Cortex folder If the operating system you are using on your tracking or post processing computer is a non English version some characters may not be recog nized and you may experience installation problems If you are experiencing this you will need to go into the computer and set it to allow for English Unicode characters In Windows XP you can do this by going to Start gt Control Panel gt Regional and Language Set tings This brings up a window that has 3 tabs and the second one is the Language Tab Under the Text Services and Input Languages tab you need to click on
155. Pose Show Template Linkages Create Template Extend Template Prop Definition Selecting Prop Definition creates a lt projectname gt prop file that is a rigid body measurement of the object This prop file can then be selected as one of the Additional Tracking Objects in the Motion Capture gt Ob jects panel 7 3 Chapter 7 Motion Capture Tab Cortex 2 0 Reference Manual Objects Panel The Objects panel provides the interface to work with multiple marker templates objects at one time This will include multiple persons and props Open Fusion The Fusion Objects Loader provides a method of managing tracking ob Object Loader jects in Cortex It can load and unload objects in Cortex from Capture files prop files and Fusion Group files The Fusion Control Panel fea tures a button which launches the Fusion Objects Loader window as shown in Figure 7 2 Figure 7 2 Fusion Control Panel and Fusion Object Loader Interface Objects Output Open Fusion Object Loader wW Local Objects L Club mars C Golfer mars DERK W Fusion 70 Objects File Types V MarkerSet Files mars Refresh Rawle Used ous v Prop Files proy p GP p Pause Load Objects Clear History Quick Load Project Files prj Pase Load objects clear History Quick Load Object Group Files zin 4 Unload Objects Club mars Club mars Golfer mars Golfer mars
156. Reference Manual 16 Camera Two Tier Setup Figure 3 1 16 Camera Two Tier Setup Tier 2 4 Cameras OoOo o ot bite kS A i A ee Tier 1 12 Cameras Mk E 28 Camera 3 Tier Setup Figure 3 2 28 Camera 3 Tier Setup Tier 3 8 Cameras ea at se w i a a Tier 2 8 Cameras me Fe 4 b 4A Tier 1 12 Cameras akez x gt k fr 3 4 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Ideal Capture Volume Sizes Calculating the ideal volume size for a specific camera setup can have many factors involved and it can become a very hard question to answer However a good starting point would be to assume a two person full body capture area in an ideal space no restrictions on camera placement etc For this we suggest the figures listed in Table 3 1 Table 3 1 Ideal Volume Sizes for Specific Camera Setups with standard lenses Number of Cameras Dimensions m Area m 6 5x2 10 10 7x5 35 14 9x6 54 16 13x6 78 32 13x11 143 a Standard lenses are 18 55 mm Zoom for Raptor 4 Raptor E Eagle 4 and Eagle cameras and 6 15 mm Zoom for Raptor H and Hawk camer as Why do 16 cameras give you 4 times the capture area of 8 cameras you might ask Mostly because when using a small number of cameras you end up wasting a lot of the usable viewing cone of each camera Using more cameras allows for more efficient usage of each individual camera 3 5 Chapter
157. S and sacral markers are critical for both portions of the body If one of these markers is missing from the static trial you will get an error when trying to load the mocap model Non critical markers are all other markers in the set Once the Motion Module has determined the locations of the joint centers and the orientations of the segment reference frames from the static pose it calculates the proper offsets for all of the critical markers plus the static only medial markers For example once the right thigh reference frame has been oriented within the static pose marker cloud the exact po sitions of the critical markers attached to the right thigh can be measured directly from the static pose and entered into the mocap model thus over writing whatever offsets were in the model input file After the offsets of all the critical markers have been determined in this fashion the mocap model is fit to the static pose marker cloud using only the critical markers to find the best fit This process orients the mocap model within the marker cloud so that the offsets of the non criti cal markers can be measured directly from the static pose These offsets are then entered into the model overwriting whatever values were in the model input file To summarize the Motion Module uses a two step process to calculate proper offsets for all of the markers in the mocap model The first step de termines the offsets of the critical markers whic
158. Same as Open Script operation in the Toolbar e Script Save As Same as Save Script As operation in the Tool bar Displays output from the scripting engine Error messages from the scripting engine will be displayed as well as any text messages from the script The output text area is refreshed when a new file is loaded All help information for Sky functions are displayed here as well Drag and drop features are implemented in a number of areas in the Sky interface e Dragging and dropping a Sky file onto the Input Text area automati cally generates the Sky command that will run the dragged script when the current script is run e Dragging and dropping a Sky file onto the toolbar creates a Sky but ton that when pressed will execute the script that was dragged onto the toolbar These buttons will be saved in the Startup script see the Options menu description above when you select Save Startup Script e Dragging and dropping a Sky function name from the list on the right onto the Input Text area will drop the function name onto the script e Dragging and dropping a Sky file from one list to another will copy that file from the original location to the dragged one If a script of that name already exists then nothing happens e Text from the output area especially sample Sky commands from the Example section can be dragged onto the Input Text area The scripting functions for the most part in Sky are simple wrappers fo
159. Scales Software VI Logger Tasks i 11 Drivers gt amp Remote Systems Attributes E Cal gt lt Basics What do you want to do B 6 Cortex 2 1 Reference Manual Appendix B Analog Input Hardware and Software Installing the Clock Wiring from the Master Camera Figure B 3 Clock Wiring Note Note Note e Master Camera Red or white Connects to Pin 1 PFIO e Master Camera Black Connects to Pin 11 D GND e 4 7kQ Resistor connects from Pin 1 PFIO to Pin 10 5 V A jumper cable is required if multiple NI 6218 units are being used to gether gt 32 channels NI USB 6259 uses PFI7 for clocking NI USB 6259 Analog Input Connections are listed in Table B 3 on page B 12 A 4 7 KQ pull up resistor is not needed on camera systems where a Raptor camera or a Hawk m camera is set as the Master camera B 7 Appendix B Analog Input Hardware and Software Cortex 2 1 Reference Manual Figure B 4 NI USB 6218 Pinouts N I DAQmx Device Terminals Help co gt P Hide Locate Back Forward Options a SA NI USB 6218 PFI O PO 0 In PFI 8 P0 4 In PFI 1 PO 1 In g h PFI Q PO 5 In PFI 2 P0 2 In PFI 10 P0 6 in PFI3 PO 3 in PFI 11 P0 7 in D GND D GND PFI 4 P1 0 Out PFI 12 P1 4 Out PFI 5 P1 1 Out PFI 13 P1 5 Out PFI6 P1 2 Out PFI 14 P1 6 Out PFI 7 P1 3 Out PFI 15 P1 7 Out 5V 5V
160. Scenes Forces w o Forceplates Standard Forceplate Usage lt NONE gt C welcome to Cortex dialog enabled Note Disable Sound Effects This turns the sound features of Cortex on and off Sounds are generated on data collection events and can be customized by naming files in the Cortex2 ReleaseXXX folder For more information reference the re adme txt file located in that folder Script generated sounds are not affected by this SDK2 Streaming When enabled this option streams all motion capture and post process playing data to the NIC address specified This must be a NIC Ethernet address of the Cortex host computer If there are multiple NIC cards in the host computer you must indicate which card will be used to stream the SDK2 Time Code This function sets the type of Time Code used with the system if any The options are SMPTE 29 97 FPS Film 24 FPS EBU 25 FPS same as PAL System Clock and None default To use the SMPTE Film and EBU options you need to have a Time Code Reader card installed in the 4 37 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Note Note capture computer With Time Code enabled each capture will have a CaptureName tc time code file created Contact support motionanal ysis com for details Marker Slots This function sets the number of marker slots the software will use Cor tex allocates memory based on this number and will v
161. Script Run the startup script Help Brings up this help information in Internet Explorer This contains a list of all the Sky files in the same directory as the current capture Load a file into the script interface by single clicking on the file name When you click a new file name any changes you made to the cur rently loaded file are saved automatically if the Autosave flag is set under the Options menu The currently loaded file name will continue to be highlighted for as long as that file is current The Cloud button to the right of the Local Sky Files label brings up the Windows Explorer for the local folder This makes for easy access to all the standard Windows file system browsing and editing tools This contains a list of all the Sky files in a standard global directory for all the users on this computer This directory is a sub folder of the Userfiles folder under the Cortex installation folder Load a file into the script interface by single clicking on the filename When you click a new file name any changes you made to the currently loaded file are saved au tomatically if the Autosave flag is set under the Options menu The cur rently loaded file name will continue to be highlighted for as long as that file is current The Cloud button to the right of the Global Sky Files label brings up the Windows Explorer for the global folder This makes for easy access to all the standard Windows file system browsing and edit
162. Select File and Begin Download All Other Motion Analysis Digital Cameras 5 Manually type in the Unit s IP address prior to clicking on the Down load button 6 Navigate to the Camera Software directory with the and select rom_ date bin 7 Click Download and wait about two minutes for the Writing to Flash operation to finish Note Ifthe message Send Failed appears ignore and press Download again 8 Once the software has been loaded the cameras may blink oddly After this you will need to reboot all the cameras by cycling the power on the EagleHub 9 Run the Cortex software and click on Connect to Cameras 10 Finally check all cameras for the new software version number Loading New The following example is for Raptor E cameras You can adjust this as Raptor Camera needed for different Raptor or Hawk M cameras Software 1 Copy the file Raptor E_Jun30 2010 cam into the C Program Files Motion Analysis Cortex2 Release2 X X XXX CameraSoft ware Raptor E directory 2 Launch Cortex and select Connect to Cameras 3 In the System gt Cameras panel click on the New Camera Soft ware button 4 Select the Raptor Series Digital Cameras and the All Cameras radio buttons Then click on the Select File and Begin Download button refer to Figure 5 4 5 Press the OK button in the Raptor Download Instructions box 6 Open the Raptor E_Jun30 2010 cam file located in the Camera Software Rapto
163. Series Cameras Setting Up a Motion Capture Laboratory Camera placement is the most important aspect of setting up your motion capture laboratory If properly done good camera placement will reward you with highly accurate and consistent results and greatly reduced edit ing time Optimum e Fluorescent lights are the best ambient light when red or notch filters Laboratory are used on the motion capture cameras tas e Windows should be covered with curtains to eliminate direct outside Conditions light e Carpeting or other non shiny floor surfaces are preferable to tile flooring which can reflect opposing ring lights Recommended e A stepladder for adjusting the cameras tripods Supplies e Masking tape to mark the floor when measuring the capture space and setting up the cameras e Reflective markers to attach to the subject and also enough to place on the floor when adjusting the cameras e Other supplies include surgical tape electrode collars for applying markers to people and gaffer s tape black masking tape 3 1 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Deciding On the Optimum Number of Cameras There are several objectives to consider when deciding how many cam eras should be used and where they should be placed 1 There should be a sufficient number of cameras to insure that at all times all markers will be visible by at least two and preferably three cameras In general the number of ca
164. Session 2 2 Job Assignments and Tasks During the Session 2 3 Additional Equipment 2 4 Motion Capture Terminology 2 5 Motion Capture Session Sequence of Events 2 6 Capturing the Data 2 7 Overview The motion capture process starts by collecting raw video data of the sub ject The success of the final motion data will depend not only on the quality of the subject s performance but also on the organization skills and experience of the Cortex operator The quality of the Cortex data can be greatly affected by the events leading up to and during the motion cap ture session An efficient motion capture session can ultimately save time and money Although this chapter is geared towards animation some information may be helpful for both animation and biomechanics What follows are suggestions that can help make the motion capture session run smoothly Studio or Lab Preparation At least a day before the capture session the Cortex user should know the capture volume required and the nature of the motion capture project This information is essential for an efficient motion capture session Knowing the capture volume allows for the advanced selection of the ap propriate marker size for the session It may be appropriate to use different capture volumes for the different moves of a capture session Changing the capture volume size and opti mizing this volume could take up to one hour so this switchover should be scheduled during a break
165. Since the file was generated by MoCap Solver the skeleton has fixed length bones The complete file contains data for each of the 20 segments The position of each segment is recorded for 196 video frames Such a file is quite large so we have included an abbreviated version here The file begins with a Header section containing general information such as the number of segments the number of frames the frame rate and other parameters which apply to all data in the file This is followed by the SegmentNames amp Hierarchy section which de scribes the child parent relationships of the skeleton Notice that only the LowerTorso segment relates to the GLOBAL coordinate system All other segments motions are described in relation to a parent segment In the BasePosition section the location of each segment s origin and rotation are described in the skeleton s base position using the six avail able degrees of freedom Translation in X Rotation about X axis Translation in Y Rotation about Y axis Translation in Z Rotation about Z axis For the child segments location and rotation are given in terms of the par ent In this skeleton the origin of all the children lie on the bone Y axis of the parent and therefore have only Y values The seventh column gives the length of the bone segment E 6 Cortex 2 1 Reference Manual Appendix E Import and Export File Formats The remaining sections contain motion data for each
166. Sky interface The Line and Column fields dis play the current location of the cursor They are convenient for locating the line in a script causing a syntax or other error in the VB Script engine Sky Compiled Script Reference NET These namespaces are supported within the Sky environment are those p Pp y Namespace supported in the following NET 2 0 assemblies Support e Microsoft VisualBasic e System e System Configuration e System Data e System Data OracleClient e System Data SqlXml e System DirectoryServices e System DirectoryServices Protocols e System Drawing e System Messaging e System Runtime Serialization Formatters Soap e System Security e System ServiceProcess e System Transactions e System Web e System Windows Forms e System XML Including a By using the appropriate Imports statement classes from these Namespace namespaces may be used in Sky scripts Example Sky Scripting example Imports System Data SqlClient Imports System Collections SqlDataAdapter is a class supported in namespace Sys tem Data SqlClient Dim MySqlAdapter as SqlDataAdapter ArrayList is a class supported in namespace System Collec tions Dim MyList as ArrayList 12 8 Cortex 2 1 Reference Manual Chapter 12 Sky Scripting Interface Including Sky Source files Further Resources By making source files with common function subroutine and related variable definitions the user can created a libr
167. Then press the Collect and Calibrate button in Floor Calibration You would not normally need this but it is there to level the floor if needed It is typical to take a single walk cycle and copy and paste it into 100 cycles If the Calseed device is slightly tilted up or down this can cause the stick figure to be walking above or below the floor at the ends of the cycles To correct for this you can spread 4 or more markers on the floor and press the Calibrate button in the Floor Calibration box Make sure no other markers ghost or otherwise are visible in the 3D View as it will tilt your new virtual floor to average them in as well This setting is used to adjust the floor level of the capture volume based on the size of markers in mm used to determine the plane of the volume floor For example if 12 mm markers are spread across the volume floor a Marker Center to Floor value of 6mm radius of marker plus any base pad thickness would be entered into this box After you calibrate the system you can use the Refine panel to either im prove your calibration or to fix the calibration if a camera gets bumped or the cameras have moved slowly over time You can choose to refine all cameras or refine only the selected cameras If you refine the selected cameras the calibrations will remain unchanged for the non selected cameras When performed well the Refine Cameras function can greatly improve the accuracy of the system and wil
168. Trim Capture W Options menu item and use ei ther Save all Frames or Save Selected Frames to make the capture smaller This forces Cortex to re write all of the files with the new names Be sure to check all of the output files you want saved and these check boxes will get remembered next time you launch Cortex Then you can delete the old capture files Only after you are sure the new files can be loaded into Live Motion Capture and Post Processing modes then use Windows Explorer to high light and delete all of the files and folders with the wrong capture name Note that the default is to have the Raw VC files stored in separate fold ers under the VCFiles folder so you should see the wrong capture folder names in the VCFiles folder that can be removed 2 11 Chapter 2 Planning a Motion Capture Session Cortex 2 1 Reference Manual 2 12 Chaptr3 Camera Setup Setting Up a Motion Capture Laboratory Deciding On the Optimum Number of Cameras Setting Up the Cameras Raptor 4 Raptor E Eagle 4 and Eagle Series Camera Physical Dimensions Raptor H and Hawk Camera Physical Dimensions Overview of the System Calibrating Process Overview of the System Calibrating Process Placing the Calibration L Frame Marker Sizes and Maximum Distances for Motion Analysis Cameras Troubleshooting Camera Problems Relationship Between Capture Volume and Marker Size Insight Focusing for Raptor
169. Typically the upper arm segment is defined by three markers Elbow Bi ceps and Shoulder Ideally a fourth marker on the Triceps would be present If not a marker on the forearm can be used as the plane marker for Join Virtual data If the shoulder data is missing you may use the markers for the top of the neck sternum or mid back to calculate the Virtual Marker data for the shoulder If you know of movements that are going to obscure the markers on a hand or foot you may want to set redundant markers on that particular segment For example if all lateral side markers on a foot are obscured from a sub ject laying down in a prone position you may apply redundant markers to the medial side to provide the data for that segment The hand will use the same technique with maybe a few less redundant markers on the opposite side 8 27 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Data Painting Data Painting allows you to directly manipulate the data in the XYZ Graphs pane Simply press Ctrl Shift and left click to modify or add data directly on the screen Since the outcome of using this feature is un certain for each user it should be used with care Figure 8 19 Data Painting 8 28 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Time Lines In the Menu Bar select Tools gt Time Lines Time Lines provide a gen eral overview of the quality of the data in the marker slots show
170. X Y and Z and rotations in X and Z This assumes that the Y axis extends from the right shoulder to the right elbow If we add a third marker to the right wrist and track all three markers we now have 6 degrees of freedom for the right upper arm segment 9 15 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual VMarkers Right Click Menu Figure 9 8 Markers TreeView Kadee Markers 42 VMarkers 0 ml Right Click l Add 1 2 3 Marker variations Add EMR Marker Add Relative to Bone Add 1 2 3 Marker Variations This launches the Virtual Marker Definitions interface refer to Figure 9 7 on page 9 15 Add EMR Marker This adds a virtual marker for use with the EMR Eye Mark Recorder Add Relative to Bone This adds a new virtual marker with the following properties e Name Name of new virtual marker e Index Number in the list e Type Relative to the bone e Marker Original marker to be transformed e Segment Defines the new origin and coordinate system that the Cal culate Virtual Marker button transforms the original marker to the new coordinate system Note Selecting Global as the segment give a status of Empty There is no data for the transformed marker Note The Type Marker and Segment properties can be changed with the drop down menus 9 16 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab Figure 9 9 Marker Number vs Degrees of Freedom One Marker
171. a of a capture manifest cap file which con 4 21 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Note tains all the needed file names and doesn t make the same naming as sumptions Some third party applications still depend on the file of the same name naming conventions For this reason Cortex 2 has the Single MarkerSet legacy file naming enabled setting When this setting is en abled AND a capture only contains one MarkerSet the file names gener ated for the MarkerSets s data do not contain the MarkerSet name They are generated as lt trial_name gt lt trial_number gt XXX In this way they fol low the same file of the same name conventions that Cortex and EVaRT used Data Specific sub folders These settings are used to specify a different sub folder for each type of data file These are all relative paths with the location of the cap file being the starting point The lt capture gt placeholder can be used to repre sent the capture name For example of you record a capture with trial name Walk and trial number 1 the capture name is Walk1 If the sub folder specified for the VC files is VCFiles lt capture gt the VC files for this capture will go in VCFiles Walk1 ce 99 The paths may not go above the working folder For example is an invalid path Outline This section outlines what the folder structure for any captured save
172. a single kin file which is a tab deliminated ASCII file easily viewed in Microsoft Excel spreadsheets Export Forces File Exports ASCII files containing force plate data This uses your current forcepla cal file and converts the raw force plate data into calibrated forces The units used are Newtons and Newton Meters and each line in the file equates to one analog sample Export ANC Exports binary formatted Analog binary data ANB into an ASCII view able format ANC Analog Numbered Columns Import Skeleton mod File Imports a previously saved Calcium Solver model definition into the cur rent markerset skeleton joint types and marker attachments This re places the existing definition if there is one The markers referenced in the mod file must match the marker names in the current markerset Export Skeleton mod File Saves the current Calcium Solver model information skeleton joint types marker attachments and skeleton pose into a mod file This file is Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual used by SoNIC to describe how streaming markersets are to be solved This file can also be imported by Cortex onto a matching marker set same marker names the markerset name can be different Create Skeleton from HTR File Creates a skeleton definition from the HTR file The joints are all set to the type Fixed and there are no attachments specified The HTR file is
173. a trial When you open a tracked marker file along with any associated analog files SIMM attempts to map the data onto the current musculoskeletal model thus creating a SIMM motion that is linked to the model There fore to open a tracked marker file you must already have loaded into SIMM a model that contains the same marker set used in the marker file For best results you should make sure that every marker in the tracked marker file is also in the SIMM model and that their locations in the SIMM model match where they were placed on the subject The marker names should match exactly except that they are case insensitive If the file contains markers that are not in the model their data will be ignored by the Motion Module Similarly if the model contains markers that are not in the file they will not be used to help fit the model to the motion data If you need to add rename or move markers in your SIMM model before loading a tracked marker file you can use the Marker Editor to do so See Section 2 12 Marker Editor for more details To import a tracked marker file into SIMM first make sure that the model you want to apply it to is the current model the topmost window in SIMM Then select File gt Open from the menu bar When the Win dows file browser appears change the Files of Type popup menu at the F 2 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module bottom of the browser to MAC Files or to C3D
174. acking Panel 7 2 Tracking Tab 4 23 Trajectory Length 4 31 Translating 4 82 TRB E 14 TRB TRC files see tracked marker files TRC E 3 Data Header E 4 Empty Fields E 4 Example E 4 File Header E 3 Position Data E 4 Tree View Panel 9 4 Trial 2 5 TrialN cal 6 2 Trim Capture Options 4 6 tripod mounting points 3 16 3 17 Troubleshooting Ethernet A 4 Troubleshooting Cameras 3 22 TS E 12 ndo 8 17 ndo Tab 4 35 nhide Markers 8 17 niform Scale 8 4 nload Tracks Button 4 86 nnamed Markers 8 10 pdate Model 10 4 pdate Model Pose 10 4 pdate Model Pose Markers 10 4 pdatete Skeleton from HTR File 4 12 se Joint Limits 9 24 se Per Camera Settings 4 24 GOTO 4 4 4 4 4 4 GG ae COC GOOG Use Skeleton Translations 9 10 User Apps Overview 10 1 11 1 12 1 User Interface 4 1 4 2 4 3 V Viewing Your Data 8 2 Virtual Join 8 15 Virtual Marker Types 9 15 Virtual Marker Definitions 4 43 9 15 Virtual Marker Tracks Calculating 9 19 Virtual Markers 9 15 9 24 Selecting 4 83 Visible Channels 4 68 Visible header 4 68 V Marker Definitions Button 9 19 VMarkers 9 15 Volume 3 12 W Wand 6 1 Wand Calibration 6 2 6 11 Wand Processing Status 6 13 Wand Processing Status Window Accept Button 6 13 Extend Seed Button 6 13 Reject Button 6 13 Run Again Button 6 13 Stop Button 6 13 Web View F9 4 16 When the skin represents an animated character A
175. ake an existing character skeleton and export it to an HTR file usually for use in Calcium and it can take an HTR file created by Calcium and apply it to the character in the animation software The Motion Analysis TRC file format is used for tracked markers mo tion capture data This data is generally only imported into the animation software It is used for bringing in full body marker data face data and prop data Figure 1 7 Animation Plugins Interface anos RemwppReRM E LORY O RIMS BOlOOe G T Germe Curves Suslscas Polygone Subse Mpat HTA Egon HIA inpor Acciai Exon Acclam ingot TAC Monon Arahyon HIR Fie Bicteninaber Customer MAS CST noe archer sobot 3 AOEOT In Bowe Ki CT Selaet Tonk salact an cbjaet Chapter 1 Introduction Cortex 2 1 Reference Manual Talon Plugins The MAC Talon Plugins also known as the Streaming Plugins are used to stream data from a live realtime connection in Cortex into an anima tion software package Both skeleton and marker data can be streamed This function is available for Maya Motion Builder and 3DSMAX Ad ditional animation packages are currently under development This same interface is used by outside developers to stream motion cap ture data into their own custom environments This programming inter face is called the SDK and is available upon request Figure 1 8 Talon Plugins Maya Interface Talon Options s loixi
176. al a L Elbow Medial R Elbow Med L ELbow Med R Elbow R Elbow Lateral L Elbow R Elbow L Elbow Lateral VSacral R Elbow Lateral Sacral L ASIS Sacral V Sacrum R ASIS R ASIS nM L Wrist Sacrum L Wrist Lateral R Wrist R Wrist R Wrist Lateral L Hand R Wrist Lateral 9 R Hand L Wrist Medial R Hand R Knee R Wrist Medial L Wrist Med R Knee Lateral R Wrist Med nergy R Knee L Knee Medial R Knee Lateral L Knee Med R Knee Medial R Knee Med L Ankle Medial R Ankle Ansie R Ankle Lateral Laat L Ankle Medial loe R Ankle Lateral L An s Mad L Heel 2 R Ankle Medial LToe R Ankle Med R Heel R Toe Riloe LLHeel Critical lower extremity markers Critical upper extremity markers Semi critical lower extremity markers that improve joint center calculations Semi critical upper extremity markers that improve joint center calculations Semi critical upper extremity markers that allow for additional degrees of freedom F 21 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual The markers shown in Figure F 5 are optional If any of these markers is in the static trial its location on the corresponding body segment in the Mocap Model will automatically be determined after the model has been scaled using the critical markers i e these optional markers are not fixed so their X Y Z offsets in the model file will be overwritten when the model is loaded These markers will then
177. alculated in the standard way Calc Without Forceplates A standard walking gait is assumed and the mass model is used to calcu late the ground reaction forces for both feet 4 38 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Welcome to Cortex dialog enabled Setting this will display the Welcome to Cortex dialog whenever Cortex starts If this is not enabled the dialog will only be displayed when the on line content that it displays is updated Post Trigger Recording Buffer This sets the recording session to begin at the specified frames before the end frame of the capture Max Frames 256 frames is the default setting This value can be in creased if necessary uses more RAM Max VC File Size the default max file size is 4 MB per camera This value can be increased if necessary uses more RAM AVI Remote Signal Output Currently only for Windows 7 users This sets the primary address for the Network Interface Card used to capture the AVI files streaming from Cortex 3d Scene This allows you to select which background scene dae file to use if available You must have the Collada Models license item in your mac_lic dat file 4 39 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tools gt Settings gt ID Params Tab These setting change how the Rectify tool in Post Processing works Figure 4 30 Settings gt ID Params Tab Mr
178. alibration or the numbers are not improving during a lengthy calibration click the Stop button The Stop button is not a cancel button You can click Stop and then Ac cept if you wish to keep the calibration numbers 6 13 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Floor Calibration Floor Calibration Procedure Optional From VC Files CalFloor vcX optional Note Marker Center to Floor Refine Camera Positions Button It is necessary to perform a floor calibration if your floor is uneven or if the L Frame is placed in a location that does not adequately represent a flat floor in the capture volume 1 After the Seed and the Wand calibration is processed place several markers on to the floor 2 Press the Connect button and then the Run button You should see the unidentified markers on the floor 3 Enter the distance from the floor your y 0 plane for Y up to the cen ter of the markers maybe 20 mm and press the Collect and Cali brate button in Floor Calibration 4 It will tell you how much the calibration origin was moved and rotated with a six number display which stands for the XYZ and yaw pitch and roll adjustments If you are doing this from VC files you will need to do the following 1 Select the CalFloor ve1 file from File gt Load Capture with the cameras disconnected 2 Then press the Run button so that you see the unnamed markers on the floor in the 3D view 3
179. alog Display 4 68 Analog Graphs pop up menu 4 68 Analog Input Channel Connections B 10 B 12 Analog Input Hardware Connections B 1 Overview B 1 Analog Panel 5 13 5 17 Analog Setup 5 13 Analysis Exporting Information 8 32 graphs 8 30 Analysis Graphs F7 4 16 ANB E 14 ANC E 11 Example E 11 Animation Plugins 1 13 Apply Inverse Global Scale to Global Segments 9 10 Apply Mapping Offset to All Segments 9 11 Assistant Panel 10 7 Asymmetry Limit 4 28 Auto Scale 8 4 Auto Detect Segment Mappings for Representing a Character 9 11 Auto Detect Segment Mappings for Representing the Subject 9 10 Backup Media 2 4 Batch Loader 4 8 4 15 Bertec Force Plates Calibration Matrix C 7 forcepla cal C 2 Using C 7 Bertec Gain Setting C 7 Binary Files E 14 ANB E 14 C3D E 14 TRB E 14 BioFeedTrak Event Editor 4 51 BioFeedTrak Event Timeline 4 54 Blank Forms I 1 Index 1 Cortex 2 1 Reference Manual Human Body Outline Back I 5 Human Body Outline Front I 3 Human Body Outline Side I 4 Motion Capture Log I 2 Bone Axis 9 6 Building a Template 7 2 Butterworth Filter 8 7 C3D E 14 C3D files see tracked marker files Calcium 1 8 Calcium Segments 9 23 Calcium Solver 11 8 Calcium Solver Skeletons 11 4 Calculate Virtual Markers 8 16 CalFloor vcl 6 14 Calibrate Panel 6 3 calibrating system overview 3 18 Calibrating Your System 6 1 Calibration 4 58 Coordinate System 3 18 Floor 6 14 fr
180. alog data I show markers calibrate forces IV remove old forceplates read marker names from POINT DESCRIPTIONS z r Save Options I save HTR file ATRAE CATEMPS ial Htr I save motion file moton ne ERTER aki Tot Browse Cortex 2 1 Reference Manual Appendix F SIMM Motion Module Show Markers X Axis Units Start at Zero Auto Load Analog Data Calibrate Forces Remove Old Force Plates Read Marker Names From This checkbox turns on the display of the global marker positions in each frame when playing back a motion When it is on SIMM will add spheri cal motion objects to the motion representing the location of each marker as recorded in the marker file When you animate the model according to the motion the blue spheres represent these actual recorded marker loca tions These are the marker locations that the Motion Module is trying to fit the model to for each frame It can be helpful to display them in the model window in order to visualize how good the fit is and to help debug problems with the data These options give you control over the specification of the X axis of the motion that is created from the marker data The units along the X axis can be either time in seconds or frame number The starting X value of the motion will be 0 0 if the units are time and 1 if the units are frame number unless frames of data are cropped because of missing markers see Crop Ends o
181. amera Dimensions 3 17 Physical Dimensions 3 17 Power Consumption A 3 Help Menu 4 57 Hide Markers 8 17 High Frame Button 8 3 Hinge Joints Example 9 18 Hot Keys 4 42 Hot Keys and Tips 4 82 HTR E 6 HTR Version 1 Example E 6 ID Params Tab 4 40 Identifying 4 72 Identifying Markers 8 11 Import ANC File 4 13 Import File Formats E 1 F 1 G 1 Import Export Legacy Data 4 6 Index 4 Included Angles Tab 8 32 Information Center 4 59 Insight Focusing 3 28 5 8 Installing Software 1 4 International Society of Biomechanics 3 19 IP Addresses A 7 ISB 3 19 Join 8 24 Join Linear 8 15 Join Virtual 4 72 4 81 8 24 Guidelines 4 82 8 27 Joining Gaps in Data 8 5 K KinTools RT 1 17 Kistler Force Plates B 4 Calibration Matrix C 10 Example C 10 forcepla cal C 3 Gain Setting C 10 General Notes C 11 Signal Names C 10 True XYZ Origin C 10 Using C 10 Laboratory Conditions 3 1 Motion Capture 3 1 Supplies 3 1 layout control 4 3 Lens Aperture 3 32 Lenses Orientation 6 7 Required Settings 4 18 Levenberg Marquart 9 24 L Frame Measurements 4 17 Library Error 3 27 License File Sample 1 5 Linkages Selecting 4 83 Links 9 20 Load Analog Setup 4 11 Load Calibration 4 10 Load Camera Calibration 4 10 Load Capture 4 62 Load Capture Live 4 9 Load Capture 4 3 Load Last Capture 7 10 7 11 Load Setup 4 9 Load System Setup 4 9 Loading New Camera Softwa
182. ameras Playback 3D Display Post Process Tools Misc Id Params Plugins Positioning Normal Normal Normal Normal Normal Normal Normal Normal 3 15 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Raptor 4 Raptor E Eagle 4 and Eagle Series Camera Physical Dimensions The following diagram illustrates the physical size and weight of the Rap tor 4 Raptor E Eagle 4 and Eagle digital cameras The tripod mounting points are the holes used to hold the tripod bolt There are four tripod mounting points on each camera Figure 3 14 Eagle Camera Physical Dimensions 189 60 mm 441 10 mm Tripod Mounting Points 1 4 in diameter x 20 threads inch Camera Weight 2 22 kg with lens 4 90 Ibs Cortex 2 1 Reference Manual Chapter 3 Camera Setup Raptor H and Hawk Camera Physical Dimensions The following diagram illustrates the physical size and weight of the Rap tor H and Hawk digital camera The tripod mounting points are the holes used to hold the tripod bolt There are four tripod mounting points on each camera Figure 3 15 Hawk Camera Physical Dimensions 189 60 mm Tripod Mounting Points 1 4 in diameter x 20 threads inch Camera Weight 2 13 kg with lens 4 70 Ibs Chapter 3 Camera Setup Cortex 2 1 Reference Manual Overview of the System Calibrating Process System Calibration is performed in two stages a
183. and frames 6 21 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual The most thorough method and needing the most good wand data Do the full Calseed Calwand Calibration with Protect Lens Protection UN CHECKED This must be done if you change any lens focus or zoom settings Disabling cameras from the calibration process for further troubleshoot ing If you cannot figure out which camera s are causing the wand calibration to fail you can disable cameras and process the data until you find the problem cameras Disconnect from the cameras Select the CalSeed cap file press the Calibrate button in the Calibration with L Frame section INSPECT the locations of the cameras If any are flipped to the other side of the room toggle the Lenses Orientation from Normal to Alternate and repeat If this does not help try disabling half of the cameras at a time process the CalSeed and the CalWand files This procedure of disabling half of the remaining cameras should pinpoint which cameras are causing the problem s 6 22 Chapter 7 Motion Capture Tab Overview Building a Template from the Range of Motion Trial Objects Panel Output Panel Recording Data Tracking Strategies and Tips Prop Files Overview Motion Capture is the mode where you will spend most of your time dur ing a recording session In this mode you can e Create and improve a template e Set the tracking parameter
184. and slide thumb nails The Motion Composer authoring interface also makes it simple to create presentations As data is added the author uses Motion Composer s one touch slide generation to store the view as a slide Presentation viewing becomes as simple as a slideshow Figure 1 6 Motion Composer Interface ex SetupWithEvents cal SD Fe mos Ossis Took Camar Directory C Prager Fes Mtn Arab Sosunge BaF ret System Calbeaton Monon Capture Post Pro s Model Edt Plugins Presentation 0 MXP SO a B gt QO Poafy oen SAAD Daa OE bras a ON ened ened eed on eT eas Natans Hien Yast Edu Toe sxe t a x A i Is Sate ae he KN parii u Sides KS S a a OH ob yy 7 aak gag 0 883 4262 ove i 2i 700 306 Ot p Dwe rea e cae f mmea E e kea Cprog an Fes Mean Raha ont Tames Seng wah BeF ooN mare 3 a ote Frames 1200S up ures anog 400 00 HE Chapter 1 Introduction Cortex 2 1 Reference Manual Digital Video Option CortexDV Software Note The color Digital Video option allows you to record a time matched Ref erence Video along with your motion capture trial on a separate computer With this option you will record a time matched Reference Video AVI file with the same trial name in your motion capture folder A separate computer is used in order to not burden your Cortex Host computer which is an issue if y
185. ant to create these files so that you can make changes to them or to be able to re load the model without going through the scaling process again F 12 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module Calculation of Joint Centers Scaling the Mocap Model Once the static pose has been loaded the Motion Module recreates the OrthoTrak skeletal model from the marker cloud The first step is deter mining the locations of the joint centers for all of the joints in the OrthoTrak model The pelvis hip knee and ankle centers are all found using the same procedure used by OrthoTrak The hip center is determined using percentage offsets from the pelvis markers The Motion Module reads these offsets from personal dat as written by OrthoTrak The default values for these offsets are taken from Bell et al Journal of Biomechanics 23 6 1990 pp 617 21 posterior displacement 22 lateral displacement 32 inferior displacement 34 To change these values edit the file personal dat as described in Appen dix D of the OrthoTrak manual The knee and ankle centers are found using the medial and lateral mark ers It is strongly recommended that you use medial markers for a more accurate calculation of joint centers If you choose not to use them you should enter knee and ankle diameter measurements into personal dat The Motion Module will use them to locate the knee and ankle centers if no medial markers are used The
186. apture mode except for centroid function instead of tracking 2 Set the minimum number of cameras to 3 3 Increase the minimum number of lines per marker How do I control the length of a recorded file in Cortex All the recording options are set in the Output function in the Motion Capture mode When the record button is clicked using the trigger or the mouse a new file is recorded and saved with the name directory and output type s you have specified The recording will stop when either e the duration in seconds is reached e the Stop button is clicked using the trigger or mouse The default duration is 60 seconds If you always want to control the end of the take with the trigger or mouse we recommend setting the duration to a number that is higher than the trials you usually capture such as 10 minutes 600 seconds H 1 Appendix H Questions and Answers for Specific Applications Cortex 2 1 Reference Manual Question Answer Note Question Answer Question Answer Question Answer Can Cortex be used in a large capture volume for example 50 x50 50 cameras If care is taken during setup motion capture will work well in a large vol ume The four areas requiring attention are 1 Camera Setup Are your cameras covering your volume effi ciently Are you using an overlapping volume setup If not you may have too many cameras seeing the same area Over coverage can result in an over abu
187. apture file Optimize the threshold settings Collect calibration data sets both seed and wand Ensure subject s clothing is appropriate Allow the subject to warm up Attach the markers according to predetermined placements Asymmetrical marker placement on the subject is critical for obtaining the best marker data 4 With the markers in place take still photos of the subject from the front side and rear view If you are taking photographs do not use the flash attachment on the still camera while you are collecting data A flash during data collec tion can corrupt the data Allow the subject to practice in the capture volume with the markers on Prepare for the calibration collection Explain to everyone the impor tance of not bumping the camera tripods 2 6 Cortex 2 1 Reference Manual Chapter 2 Planning a Motion Capture Session Capturing the Data Calibration Note Collect the Square Seed Calibration Collect the Wand Calibration Collecting Captures Subject Initialization This section provides a general overview of the calibration process 1 Fill out the Motion Capture Log and slate board for the first square seed calibration This would be Take 1 and an Cortex filename for example CalSeed 2 Prepare the Cortex system for data collection Press the Collect and Calibrate button to trigger the event button 3 Verify that the camera buttons turn yellow after the Seed calibr
188. aptured must exist If such a marker set does not exist it must be built using the Model Edit tools described Chapter 9 Model Edit Tab Once an appropriate marker set exists follow these steps to create a tem plate 1 Choose Motion Capture from the Mode Buttons 2 Choose Output from the panel buttons 3 Check the Tracked ASCII TRC or Tracked Binary TRB check box on the Output panel 4 Type a file name in the name box and press Enter Set the Duration seconds between 10 and 20 6 Start collecting the range of motion data of the subject by having the person stand in the middle of the capture volume with arms extended palms parallel to the floor with thumbs facing forward and all mark ers in full view 7 Click Record on the Output panel 8 The subject must stay in an initial frozen position for two or three sec onds 9 After standing frozen in this initial position for up to five seconds the person must move through a complete range of motion by moving and twisting ensuring that each linkage exhibits the full extent of stretch that will be experienced during subsequent motion capture sessions Exaggerated motion must be avoided and all markers should remain in full view This step should not require more than fifteen seconds 10 After ten seconds passes from the moment Record was clicked the system will automatically stop collecting and tracking marker data o At this point a Tracked ASCII TRC or Tracked Bina
189. ariably assign mem ory according to the number of marker slots used The maximum number of marker slots that Cortex will allow is 2000 The default number of marker slots is set to 192 More slots require more RAM in your computer to work efficiently This setting does not take effect until Cortex is quit and re launched Number of Cameras This function sets the maximum number of cameras the software can use Cortex allocates memory based on this number It can be set anywhere be tween 2 and 250 The default number of cameras is set to 16 More cam eras require more RAM in your computer to work efficiently This setting does not take effect until Cortex is quit and re launched Have Current Frame follow Mouse when selecting When using the mouse to select a range of frames in the XYZ graphs the current frame will change as the mouse moves when this is enabled XYZ Graph Zoom Options When zooming in the XYZ graphs the central point of the zoom can be set to the current frame red frame line or the mouse s position in the XYZ graphs Forces w o Forceplates This specifies how Cortex should try to calculate ground reaction forces when no forceplate data is present Standard Forceplate Usage Only calculate ground reaction forces from the forceplate data One Foot Off Forceplate Use the mass model to calculate the ground forces for the foot that is off the force plate The foot that is on the plate will have its forces c
190. arkers on the hand The presence of critical markers con trols how the hand is scaled and what degrees of freedom it has The right hand will be scaled separately from the right lower arm if the three critical markers listed below are present in the static trial The individual finger gencoords will be added to the model if the three critical hand markers and the appropriate finger markers are present in the static trial 1 Right thumb acceptable names R THUMB R THUMB M3 Right middle finger acceptable names R MIDDLE FINGER R FINGER R FINGER3 M3 3 Right wrist a Lateral acceptable names R WRIST R WRIST LATERAL R WRIST LAT RWRI or b Radius acceptable names R RADIUS RWRA 1 Right wrist a medial acceptable names R WRIST MEDIAL R WRIST MED or b Ulna acceptable names R ULNA RWRB The left hand will always be included when the left arm is loaded even if there are no markers on the hand The presence of critical markers con trols how the hand is scaled and what degrees of freedom it has The left hand will be scaled separately from the left lower arm if the three critical markers listed below are present in the static trial The individual finger gencoords will be added to the model if the three critical hand markers and the appropriate finger markers are present in the static trial 1 Left thumb acceptable names L THUMB L THUMB M3 Left middle finger acceptable names L MIDDLE FINGER L FINGER L FINGER3 M3
191. arms down or the arms out feet apart or together but where no markers will be hidden You want it to be a standard position that the next person will be able to repeat quickly and simply Have the subject face a certain direction that will also be easily repeatable for the next person along the X axis for example Figure 4 62 Create Template Interface Create Template MarkerSet Name Template Prop Definition Golf Person Frames Range Frames Used Current Frames with complete Selected Total frames to use visible All Include current frame as the Model Pose Show Template Linkages Create Template Extend Template 4 78 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Create a Template Using the Pose ID Feature Connect Cameras Button Disconnect Use Raw Files Button Raw Settings Button Run Button 1 Select Post Process gt Create Template Select Body Template 3 Activate the Include current frame as the Model Pose check box and select the correct range of frames where you have good data 4 Save your capture file which now has a new feature called Pose stored in it You may want to use the word Pose in the capture file name to distinguish it from earlier versions without the pose but that is not necessary The normal template will work for this person N This feature allows the software to automatically identify markers based on a Model Pose that y
192. ary of source files which can be included and used from may Sky scripts SkyIncludeFileFunc tions sky is a very simple example of this methodology It defines several utility file functions SkyCopyFile SkyDeleteFile and SkyMoveFile By including SkyIncludeFileFunctions in a script with the Include keyword the functions within it may be used in the script Example Include SkyIncludeFileFunctions sky SkyMain Dim bForceOverwrite as Boolean True CopyFile SourceFile txt DestFile txt bForceOverwrite CopyFile Source2 txt Dest2 txt End Sub Any Sky source file intended to be used as an include file should NOT contain a SkyMain subroutine or a compile error will occur There is a wealth of information about Visual Basic and NET on the in ternet the interested user can find descriptions of the classes and syntax with little difficulty This is currently a good place to start with Microsoft http msdn microsoft com en us library default aspx Searching on this Microsoft site will give the user a good place to start Some suggested search terms Visual Basic Language Specification Visual Basic Language Reference NET Framework 12 9 Chapter 12 Sky Scripting Interface Cortex 2 1 Reference Manual 12 10 Appendix A System Hardware Interconnections Overview Standard Camera System Configuration Power Consumption CP 8 Power Hub and Ethernet Switch
193. ating Thresholds control until the markers on the floor appear on the screen Figure 5 6 Threshold Slider Settings Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins All Camera Types Raptor Specific These settings apply to all Motion Analysis Digital Cameras Note The Min Max lines per marker values can be set per camera or per project This option is in the Tracking panel If per camera settings are not enabled the controls will not be enabled All controls are disabled if there are no cameras chosen for editing Threshold Brightness Min Horizontal Lines per Marker Max Horizontal Lines per Marker Edit These Cameras O All Selected 9 Select a camera 4 Ifyou are not seeing any blobs on the screen choose Motion Capture from the Mode Buttons Then in the Tracking Panel set the Min Hor izontal Lines per Marker to 2 and Max Horizontal Lines per Marker to 100 5 Mask out any unwanted light sources by creating a mask with the middle mouse button held down Delete masks by clicking on a mask and pressing Delete on the keyboard or right clicking in the 2D Dis play and selecting Delete Mask 6 Repeat Steps 4 through 5 for all cameras 5 12 Cortex 2 1 Reference Manual Chapter 5 System Tab Analog Panel For users who have integrated force plates into their motion capture sys tem you will need to configure the
194. ation is complete 4 Remove the calibration seed device calibration L frame from the capture volume For best results it is recommended that you collect and use wand calibra tion data Prepare the Cortex system for wand calibration The duration of the wand calibration is directly correlated to the capture frame rate A typical dura tion for a small capture volume is 30 to 60 seconds Large volumes with ten or more cameras can take 120 to 180 seconds and very large volumes may take up to 240 seconds Collect and verify that the wand calibration data is good It may be neces sary to reposition or move cameras and to retake both the seed and the wand calibration data if one or more cameras has large areas without wand calibration data You can continue pressing Run after it finishes until the calibration numbers stop changing Your wand data should cover the entire capture volume A common method of ensuring better wand data is to use a 1 3 method That is hold the wand markers in alignment along each axis X Y and Z for 1 3 of the wand capture session The type of subject initialization depends on the application e In animation applications it is the I Pose or Init Pose trial e For OrthoTrak it is the Static Trial In general the procedure is as follows 1 Have the subject stand in the capture volume with the markers on On the Cortex system Look for any reflection and light source that might interfere with
195. ations The Mocap Model is then scaled to match the subject and then a least squares optimization fits the model within the cloud of static trial markers considering only the critical markers This positions the model within the marker cloud so that the Motion Module can then di rectly calculate the offsets from the optional markers to the model seg ments to which they are attached If you do not want the offsets for a marker to be calculated in this manner then you must turn on the fixed button for that marker in the Marker Editor and enter accurate X Y Z offsets into the number fields This tells the Motion Module to scale the marker s offsets when the model is scaled but not to recalculate their val ues as it does for the other optional markers Note on adding markers You can create new markers using the Marker Editor and then save the model by writing out a joint file but you should not replace the original model file e g SIMM Re sources mocap mocap jnt with this new file This is because the model file contains many comments and special parameters that enable SIMM to automatically modify it for a particular static trial as described above However when this file is loaded into SIMM and then written back out these comments and parameters are lost Thus after saving your new joint file you should use a text editor to copy the new marker definitions from the file and paste them into the existing model file Shown in Fig
196. board centroid calculation algo rithm When the camera s image processing algorithm finds a centroid it determines the number of horizontal and vertical pixels that the centroid spans If the difference in these two dimensions is more than this setting the centroid is discarded 4 28 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Settings gt Playback Tab Figure 4 22 Settings gt Playback Tab e settings s one Soo Calibration File Structure Tracking Cameras WAV Frame Offset Mocap frames Raw Playback These settings modify how raw data playback VC files AVI files etc is done in Cortex CPU Speed The data is played back as fast as the CPU will allow RealTime The data is played back at the speed it was recorded Loop Raw Files This option is only available when playing back at RealTime speed When the end of the data is reached it automatically resets to the beginning and continues playing 4 29 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tools gt Settings gt 3D Display Tab Frame Offsets When AVI and WAV files are recorded there is often a frame offset be tween the AVI WAV and the VC or tracks data file data These settings allow that offset to be specified They apply to both Live Mode and Post Processing AVI Frame Offset If a delay occurs between the reference vi
197. cal Capture Folder The Message Bar indicates the directory requested by Cortex 8 CortexDV On Record A red RECORD will display next to the player control panel indicating system is recording and a message will be displayed in the Message Bar indicating record start time 9 Cortex Stop recording by pressing either the Stop button or after reaching the duration specified If you have more than one computer running Cortex on the same net work the CortexDV software does not consume the plugin port as does the streaming Alias MotionBuilder online plugin for example The mes sage about starting and ending the data capture is broadcast to the x x x 255 address which means that all computers connected can hear the message and start and stop the recording So you should be able to con nect as many CortexDV recorder computers up as you need You probably will not want the AVI files streaming across the network When VC files are collected AVI files are collected If VC files are not collected AVI files are not collected G 3 Appendix G Synchronizing Digital Video with Cortex Cortex 2 1 Reference Manual Suggestion for DV Camera Setup Procedure for Moving Reference Video Files from Another Location Sony DV cameras have a setup mode called FRAME FIELD The FRAME setup mode works best as it eliminates the motion blur which results from the FIELD also known as Interleaved mode On Canon DV cameras you
198. calculations It is usual to start with this at 500 half Raise this value if there is a lot of stray light or reflec tions Lower the value to see smaller markers or markers at the far side of the volume The number of frames per second or Hz Set for all MAC cameras in the system Note there are different maximums for each camera type Also above certain speeds each camera type will start to operate in partial scan mode Note there are different shutter types for each camera type The default is 1000 th of a second In most circumstances it is unlikely that this will need to be changed If a very small from factor lens is used with a very large sensor film less light would get to the corners of the image than the middle This makes the corners and edges appear faded Motion Analysis cameras have been optimized so there is no significant vignetting However closing an aper ture means that only the middle part of the lens is being used so if an aper ture is closed too much then this effect will begin to be noticeable Depth of field is the distance between the nearest and furthest parts of a scene that can be imaged with acceptable sharpness In motion capture we need to have the near and far ends of the capture volume in good fo cus This is not the same as range Depth of field is affected by many as pect of lens design and these parameters have been optimized at the de sign and manufacturing stage for Motion Analysis cameras It
199. cale Matrix Method Property Units m Global Scale 1 Matrix Method Levenberg Marquart Accuracy 0 0001 Max Iterations 100 Use Joint Limits True Orient Body True Units of the Calcium segment lengths Select from the drop down menu in meters centimeters and millimeters Changes the scale of the entire hierarchy multiplied by the number set e g a value of 10 would scale the hierarchy by 10 times the original size This provides a quick method for scaling the HTR file to fit the marker cloud in the model pose There are two matrix methods to choose from 9 23 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual Accuracy Max Iterations Use Joint Limits Orient Body Note e Gauss Newton Which is faster at solving but not as robust This is generally used in Real Time applications e Levenberg Marquart While is more robust but not as fast This should only be used in PP mode This is the accuracy parameter for the solve It is generally set to 0 0001 and then left alone It can be useful to debug and troubleshoot the Cal cium segment This is the number of iterations the solver goes through to solve When the solver gets stuck it can potentially iterate forever Usually the solve happens in a very small number of iterations 1 5 Setting it to 100 is more than enough Enables or disables the use of joint limits in the Calcium model Gener ally it is recommended to be turn
200. calibration 6 19 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Extending the Seed Calibration If one or more cameras are not seeing the four point calibration L frame device for any reason they have not been properly calibrated and it shows up as a white camera button The camera is shown on the floor at the ori gin point down as shown in Figure 6 7 on page 6 9 This will result when you have a large capture volume and only some cameras see the calibra tion L frame or a camera threshold may be set incorrectly This is not a problem You can use the wand data to get the camera calibration seeded then process the wand data again so the camera or cameras get both square and wand processing The steps for this are as follows 1 Calibrate using the calibration L frame as described in Calibration Frame Tab on page 6 5 Cameras that are Yellow are seeded Those that remain White are unseeded and show up on the floor at the origin pointing down Process the wand data The cameras that saw the calibration L frame will show as Green camera buttons the unseeded cameras remain White Extend the calibration seed by clicking Extend Seed This will then seed those cameras previously unseeded Click on Run Again This runs the wand data again for all cameras After this all cameras should be Green calibrated Figure 6 14 Extend Seed Calibration Button Wand Processing Status Camera Extend Seed 60 6
201. cally send you to the Post Processing mode 7 11 Chapter 7 Motion Capture Tab Cortex 2 0 Reference Manual Tracking Strategies and Tips Speeding Up Tracking in Cortex Max Speed Max Predictor Error Changing the Max Speed to 30 mm frame and the Max Prediction Error to 10 mm greatly enhances tracking for most normal speed data sets While this needs to be adjusted up for high speed trials keeping a 3 1 ratio works well This can cut your CPU load by 50 or more Here is what is under the hood see the Tools gt Settings gt Tracking panel If a marker has NO track history i e a new marker just found on this frame how big of a sphere do we draw around its current location to look for its continuation in the next frame This should affect only startup tracks It can affect performance if it is TOO BIG by making the software check more points than are necessary If it is TOO SMALL it will not create contiguous tracks the tracks will have many holes and lots of un named markers Max Predictor Error determines a sphere around the projected extrapo lated path trajectory into the next frame If the marker is not found in that projected sphere it is assumed to have disappeared This should affect only continuing tracks with a history which is the bulk of what is being tracked This can have a big effect on performance if it is TOO BIG If it is TOO SMALL tracks will be broken up into smaller path fragments and th
202. can also be used for walking on treadmills up and down stairs or other activities Gait data are presented in graphs which describe the kinematic i e joint angles kinetics i e moments and muscle activ ity EMG Data can be exported as industry standard XLS data sets which can easily be imported into Microsoft Excel or other graphics and analysis packages Figure 1 9 OrthoTrak Interface File Edit Operate Tools Window Help gt 5399 MotionAnalysis ORTHOTRAK 6 6 0 Clinical Gait Analysis Software Multiple Trial Processing Module File Name Boyes te Cycles Sai gt a isl Patient Information WALKI 2 Mamually Enter Personal Info we Condition One w Daie D B eos a ees WALKI Condition Condition 3 Description Analysis ojee EE E oroe o O Status Processing Data O g g Tum ON f Data Ave 1 SD wf Stride Cycle for Truri Scale EMG Tum OFF Mf Non 2SD WI Print Color if Print Chapter 1 Introduction Cortex 2 1 Reference Manual SIMM Applications SIMM Software for Interactive Musculoskeletal Modeling is a software system that enables you to create and analyze graphics based models of the musculoskeletal system In SIMM a musculoskeletal model consists of a set of bones that are connected by joints Muscle tendon actuators and ligaments span the joints The muscles and ligamen
203. can range from 0 to 100 mm N A negative scale setting will show the forces below the force plate 3D Display gt Camera Coverage Sets the number of cameras used for displaying the Camera Coverage re gion right click 3D view select Show A small number in this setting re sults in a large camera coverage display shown as blocks A larger num ber limited to the number of cameras in the system will show a smaller coverage volume 3D Display gt Trajectory Length Number of Frames Behind The Current Frame When marker trajectories are being displayed right click 3D view select Show this adjusts the length of the trajectory shown behind the marker s position in the current frame 3D Display gt Trajectory Length Number of Frames Ahead of The Current Frame When marker trajectories are being displayed right click 3D view select Show this adjusts the length of the trajectory shown ahead of the marker s position in the current frame 3D Display gt Camera Depth of Field When the camera s field of view is being displayed right click 3D view select Show this option adjusts what depth of field is displayed 4 31 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual 3D Display gt Motion Trails This feature shows the data for markers links skeletons and forces as a trail over a set number of frames The data frequency can be adjusted to show the information every n frame
204. cccceeeeseeeeeeees 6 19 Extending the Seed Calibration siscsasiniiscanissinrsineracsviorenveresieianesies 6 20 Cortex 2 1 Reference Manual Post Processing Square and Wand Datta ccccccssssssteeeeeeees 6 21 Chapter 7 Motion Capture Tab CAE cincinnati aine 7 1 Building a Template from the Range of Motion Trial 06 7 2 6 oll eho ig 1 eee mene Re tne ee nO eee ue OREN en tC von P Een nnn rene teen irs 7 4 BTL cae ene mene escent eee nS einen E ue be dears emer sheer rererers 7 9 i 2 LY Dal ee a ee ee er Se 7 11 Tracking Strategies and Tips asics tssinsreniaciainesicvisimissiarieianeincraiets 7 12 Fiap Flee annaa 7 13 GUIER FPrODS cerae a Me er ne SSP 7 14 Chapter 8 Post Processing Tab elt i 2 Tace d Doi ee e 8 1 Viewing Your Dala Senne eee ee ence et ea ees ener eee eee aaia 8 2 Unnamed MarkG Sisiane aaa 8 10 Past Process Tool SNID aisniincaieinmnninamuenatmrmumietaienn 8 11 I a l ca er eee Ser eee pe eer reece 8 24 Baa RN tit aes tna ese ee te aces a a ana heer adias 8 28 UE LAGS E E A N E EN E E E E 8 29 Analyse CaISOINS seroit aani 8 30 Post Processing Strategies and TipS c cceeescceeeeeseeeeeeeeees 8 33 Chapter 9 Model Edit Tab VOI OW seccina nra dadaulndvdairedsuawaavareayaulbavglraguvaedantadae 9 1 Makers SNe renies E AAA EA Ri 9 2 TOS Vow Panola ia ii 9 4 Chapter 10 Plugins Tab OON N aa AE 10 1 eA EERE T EE RE A A EA E EERE E E E E ER 10 2 Asistani PANGS ucisi ee
205. ce Manual MarkerSet This specifies which local coordinate system axis will be used for the Properties gt Bone bone Axis MarkerSet Skin files are flexible mesh skins that can stretch across joints and differ Properties gt Skin ent sized subjects File The Skin File function allows you to select the two types of skins that work with Cortex e Collada dae skins e Legacy OBJ obj skins These skins that are defined for two different skeleton types and are lo cated in the User Files Skins directory If you are looking to develop an entirely new skin file you will need to contact Motion Analysis Customer Support support motionanaly sis com for information Skin Transparency This sets the transparency attribute of the skin 100 means the skin is invisible 0 is solid 9 6 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab OrthoTrak Example with OBJ Skin This shows one of the Samples files installed from the full Cortex setup file If you do not have this you can download the Samples from the Mo tion Analysis FTP site Contact support motionanalysis com for details 1 In Cortex use the Browse button in the upper right corner to C Program Files Motion Analysis Cortex2 Samples SIMM_ OrthoTrak Helen Hayes MarkerSet 2 Select File gt Load Capture Walk1 cap Layouts 2 Panes Left Right Left Pane 3D View F3 Right Pane Reference Video F1 3 Play You will see the stick
206. centers to bone seg ments The disadvantage is primarily for high resolution animation use since the joint centers are calculated directly from real and virtual marker locations Bone lengths will vary slightly from frame to frame due to marker skin motion which can cause the animated character s skin to dis tort and not look as good as expected Cortex 2 1 User s Manual Chapter 11 Skeleton Types Figure 11 5 Skeleton Builder Bone Attributes Markers TreeView E Dave_SkB a Markers 41 B VMarkers 25 Links 98 B SKB Segments 24 m LHip LUpperLeg LLowerLeg LFoot LToes RHip RUpperLeq Name DaveRoot Inde 1 Parent Segment GLOBAL Ongin Marker V_Root Long Axis Bone V_SpineA Plane Axis M_Root RX Offset 0 RY Offset 0 RZ Offset 0 11 7 Chapter 11 Skeleton Types Cortex 2 1 User s Manual Calcium Solver Figure 11 6 The Top Level of Calcium Markers Treeview e Root Spine1 Spine2 Spine3 Spine4 Neck Head LClavicle LUpperArm LLowerArm LHand X m H H H 0 Units mm Global Scale 1 Matrix Method Levenberg Marquan Accuracy 1E 05 Use Joint Limits False Use Foot Contact False Render w Cak False This is a very different method of calculating the skeleton motion from marker locations Typically the skeleton is defined within one of the sev eral animation packages and exported and saved in an HTR file This skeleton is not allow
207. cific Camera Settings a x i I Calibration File Structure Tracking Playback 3D Display Post Process Tools Misc Id Params Plugins All Camera Types Raptor Specific These settings apply to Raptor Series Digital Cameras Any non Raptor cameras that are selected will not be affected 2D Centroid Calculation Onboard Camera greyscale D In Cortex edge based Greyscale Visualization Above Calculation Floor Above Threshold 4 26 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Figure 4 21 Advanced Raptor Specific Camera Settings settings Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins Bion Binary 5 Saturated Pixels Unprocessed All Camera Types Raptor Specific These settings apply to Raptor Series Digital Cameras Any non Raptor cameras that are selected will not be affected 2D Centroid Calculation Onboard Camera greyscale Greyscale Calculation Floor raw sensor value In Cortex edge based 343 le 3 Greyscale Visualization Above Calculation Floor D Above Threshold Advanced lt lt Advanced Settings X Greyscale Calculation Margin pixels Asymmetry Limit pixels The settings that are available only for Raptor Series cameras ca
208. collecting data for only one channel in Cortex you will need to install a jumper wire from screw terminals PFI 7 to PFI 0 on the A D interconnect box This may be changed in future versions of the NI software drivers If you have two analog acquisition devices installed the same is applied for each de vice If only one channel is sending data on that device the PFI7 to PFIO jumper must be installed It is recommended that you upgrade to NIDAQ 9 1 or later software to avoid this problem The latest version of the NIDAQ software can be downloaded for free from National Instruments NI com This appendix documents both of the 32 channel 16 bit setups and the 64 channel setups of analog input available A list of the location of chan nel numbers in the Analog Terminal Box for digital camera systems is given for the type of A D setup You may find it useful to make a copy of this chart Table B 2 on page B 10 and use the column titled Setup Name to record the connections for your installation The connections for a typi cal application using two AMTI Force Plates and ten EMG channels for digital cameras is shown for each setup Although connecting analog inputs is not particularly difficult it is impor tant that certain naming conventions be followed for the external data to work smoothly with supplementary Motion Analysis software such as KinTools RT and OrthoTrak This is described in Analog Signal Nam ing Conventions on page B 4
209. column s title cell or right click on the Analog panel grid and select Activate All Named Channels Both actions activate all named channels Left click in the channel s row in the Range column and click on the arrow to select a voltage range The range must match the output of your analog device Select the correct sample rate for your system from the Sample per Second drop list at the bottom of the panel To select EMG muscle names right click in the Analog panel and select Muscles For any particular analog channel number left click in the Name column and scroll through the drop down menu for the EMG muscle name you want see Figure 5 8 The Force Plate and EMG muscle names are consistent with the names used in the Orthotrak Gait Analysis and KinTrak software from Motion Analysis Figure 5 8 EMG Muscle Name Selection Cameras Analog Devices Configure channels for data capture If a channel s On box is not checked data for that channel won t be captured Name On Range a 1 FAX Iv e 10V 2 Fy v 10 Y s FIZ v 10V 4 MIX vj 10 Y 5 MY vj 10 Y 6 MIZ v 10 V 7 F2X vj 10 Y 8 F2y Iv e 10V L Rectus vj 10 L Hamstring v e 10V L Lateral Ham L Medial Ham Kistler L Gastrocnemius i Bertec L Tibialis Ant L Tibialis Post Tec Gihan L Vastus Medialis Kargi L Vastus Intermedius a cee L Vast
210. ctoy C Program Fiee Motion Analjsic Corten2 Sarple BioFeedTrak GofSwing Browse System Calibration Motion Capture Post Process Model Edit Plugins Presentation Cre v OF VWHYMED SYS nL Rectify QuickID Rectify Create Template Template RB Marker ID Exchange Linear Cubic RB Virtual Calc Smooth Make Delete Copy Cut Unnamed Template 1D Rectify Rectify Join Jon Join Join VMs Un Unnamed 2 Click AllNone Ctrl Click Toggle Cut Outside MarkerSets New Club Golfer E tae ii niara A 1 W tr ai 1500 00 1500 00 ea 200 300 400 500 600 700 8 i I 900 ac 00100 wae Selected LJP 00003012 4 BK poe cacate ed Loaded Capture C Program Files Motion Analysis Cortex2 Samples BioFeedTrak GolFSwing GolFSwing_1 cap 921 Frames 120 FPS 2 Up Unitsimm Analog 600 00 He 4 63 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Pop Up Menus 3D View Pop Up Menu The Graphics Panes have viewing options and associated tools that can be accessed through pop up menus In all cases the pop up menus are acti vated with a click of the right mouse button while the pointer is in the dis play region 1 From the Menu Bar select Layouts gt 1 Pane 2 From the Mode Buttons left click on the Post Process button in order to be in the Post Process mode 3 Ifthe 3D View i
211. cusing Selecting a 1 Camera To Focus Focusing a Camera N N Place the Insight Focusing Marker into the volume This marker should be at least 8 pixels high and have a centroid calculated for it Select Run in the Real Time dashboard Enable greyscale centroid calculations for the cameras in Settings gt Tools gt Cameras Shift Left Mouse click on the marker in the 2D display of a camera e This will set the greyscale region about the clicked marker e Ensure that only this marker is visible within the greyscale region e If other markers are visible move them in the volume or change the greyscale region to not include them e The marker should be at least 8 pixels high and have a centroid calculated for it Do these steps for each camera you will be focusing Opening this dialog put the cameras into Insight mode e When in this mode the camera to be focused will have a pair of spectacles in its LED display The other cameras will have a tar get symbol While in the volume use the Right and Left buttons to switch between which camera will be focused e This is reflected by a pair of spectacles on the LED display board e You can use the Top button on the wireless control to toggle the cameras in and out of Insight mode e Closing this popup will take the cameras out of Insight mode Use the Bottom button on the wireless remote to start focusing the selected camera e Ifthe marker
212. d Subject Hybrid Skeleton Model C Update The Skeleton AutoFit Zero Pose Directly AutoFit New Segment AutoFit Using Global Scale rj Refit the Identifying Template When the subject is correctly identified and near the displayed pose then PAUSE the system The update will use the current Update the Model frame of data on the screen At this point the old Template ID feature is not working but instead the generalized automatic Pose ID feature is looking to identify the unnamed markers As soon as the ID is recognized and catches you will see two stick figures the static one from the Model Pose and one that is the newly ID ed person that is moving If the person is not ID ed right away have them face the same direction and assume the same general posture as seen in the Model Pose The Auto ID feature works as long as the person is facing within about 45 of where the Model Pose was recorded The status display in the lower left tells you how fast the ID process took A small number is a fast ID a bigger number would be slower but still working Using the Reset IDs button on the lower right will force the soft ware back to the Pose ID if something gets switched and you want to cor rect it 4 76 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Figure 4 61 Pose ID in Message Center and Reset IDs Button
213. d a CAL file it will overwrite the calibration information in memory with the contents of the PRJ or CAL file Both contain calibration information but the legacy PRJ file also has the marker set information and template information Every time you collect a trial in the Motion Capture gt Output panel the system writes out the current calibration to a file that has the same name as your trial name but with a cal extension This is normally not needed but will allow you to load up the calibration at the time of the capture with the File gt Load Calibration menu item If you changed the calibration for some reason and you know you were calibrated when the trial was col lected you can load up that as the current calibration in the software at a later time 6 18 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab Calibration from Previously Collected Files This section describes how to simulate a calibration using previously re corded data A simulated collection of Cortex square or wand data is done the same way that you can simulate tracking Raw VC data Just fol low these steps 1 Disconnect from your cameras Select Raw Files on the Real Time Dashboard 3 Load the CalSeed vc1 or CalSeed cap file At this point you can mask out any extraneous data points if necessary 4 Press the Run button on the Real Time Dashboard 5 Inthe Calibrate panel press Calibrate in the Calibration with Square box
214. d a Project file and then select Load a Tracks file Select Data Views gt Analog Display In the existing capture file go to System gt Analog and change the name of the analog channel to the correct name Go to the Tools menu and select Misc gt Replace Loaded Analog Channel Names To see the replaced name reload the capture file you are working with This will show the changed name in the Analog display sidebar To save this change to the analog file you must follow the next steps ex actly 6 Select File gt Trim Capture W Options Figure 4 34 Trim Capture W Options Interface lt lt lt Trim Capture Options zlo xi m Default Directory C Export Directory File s Original Directory Ic Program Files Motion Analysis EVaR T5055 amples Golf Swing with Temper m m Output files M Raw video vc IV Analog anb IV Colorvideo avi MV Tracked ASCII tre IV Tracked binary trb Tracked Markers Discard Unnamed Markers OK ust save the settings Discard Virtual Markers Cancel Frames Save All Frames r Save Selected Franses Export Trimmed Capture Under the Trim Capture W Options choose Save Selected Frames Make sure you have highlighted all the frames that you want by using the middle mouse button to highlight an area in the Post Processing window or by using the Select All Frames button in the lower right corner 4 44 Co
215. d an example C program that is available at no charge that demonstrates how to use the SDK This allows our cus tomers to use this as a starting point and creating their own program The sample program shows you how to connect to the Cortex software and request that the kind of data that you want be transferred Marker XYZ data and or Skeleton HTR data The sample C program then writes out the data to a disk file Please also note that the data can be streamed either from the live camera data that is happening in real time or from the Post Processing software when you press the Play button The data is the same either way and the SDK program does not even need to know since it comes across the same way So the customer can write the pro gram from previously edited X YZ data in the Post Processing part of Cor tex and get that to working Press the Play button you see the edited tracks and the data is streamed to the SDK Then they can connect to the cameras and get the same XYZ or HTR type data from the live cameras D 1 Appendix D SDK Software Developers Kit Cortex 2 1 Reference Manual D 2 Appendxe Import and Export File Formats Overview E 1 mac_lic dat E 2 PRJ Legacy Cortex Project File E 3 TRC Track Row Column E 3 HTR Heirarchical Translations amp Rotations E 6 ANC Analog ASCII Row Column E 11 TS Time Series Files from the Cortex Analysis Functions E 12 Velocity and Accelerat
216. d around the capture volume with emphasis on the edges The ray intersection of both the named and un named markers can be used to refine the calibration However if a camera was severely bumped calibration will be far enough away from ray intersections that the Refine Calibration will not help In that case you must redo the L frame and wand calibration steps 6 16 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab Show Camera Volume Show Camera Volume is useful for telling you about how well your cam eras are aimed and how much camera overlap you have To see the cam era volume 1 Right click in the 3D View and then select the Camera Coverage check box in the pop up You will need to select the camera num ber s button at the bottom of the Motion Capture panel Also you can change the minimum number of cameras that see that part of the volume in the Tools gt Settings gt 3D Display gt Camera Coverage gt Minimum Number of Cameras setting 2 Right click in the 3D view and select Show Volume Figure 6 12 Show Camera Coverage Volume W G File Layouts Data Views Tools Help Current Directory C Program Files Motion Analysis Cortex2 Samples 16 Camera Calibration Face Body x Browse System Calibration Motion Capture Post Process Model Edit Plugins Presentation ie Y te Rectify QuickID Rectify Create Template Unnamed Template ID 0 7
217. d files will be It is shown as a directory tree with lt working_folder gt represent ing the folder that data is captured into and lt capture gt representing the name of the capture 4 22 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Settings gt Tracking Tab Figure 4 18 Tracking Tab The Tracking settings allow modification of the key parameters used when acquiring and tracking data These settings are all saved in the Setup cal file settings Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins Centroid Parameters Min Horizontal Lines per Marker Max Horizontal Lines per Marker Shape Analysis None Normal Use Per Camera Settings Tracking Parameters s e Max Residual mm Max Speed mm frame Marker Size mm Max Prediction Error mm Weak Min Cameras to use Centroid Parameters Centroid Parameters control the minimum and maximum number of video lines that are permitted for marker images If an image size falls outside these limits no centroid will be calculated for it and it can never become a marker image Min Horizontal Lines per Marker Sets the minimum number of scan lines a marker must occupy on the camera s sensor for it to qualify as a marker The value of the parameter entered is dependent on the size of the markers and the distance the cam era is away from t
218. d to create the bone structure if used The choices are 9 4 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab MarkerSet Properties gt Rotation Order None Turns off any skeleton calculations for the Motion Capture and Post Pro cessing panels Skeleton Builder SkB Turns on the skeleton builder definitions if present in the capture file and allows the skeleton to be calculated To see the skeleton in the Motion Capture or Post Processing panels you must have the Show Skeleton fea ture turned on in the 3D view right click in the 3D view and select All Cortex users can calculate the SkB or Calcium skeletons after they have been defined but creating and editing skeletons requires a separate soft ware license Calcium Type Skeleton Checking this option tells the software to use the Calcium Solver type skeleton You must have the Show Skeleton feature turned on in the 3D window and you must have clicked the Calculate Skeleton button with check box in Post Processing to have the skeleton calculated Model files created and edited in the Si 2 0 Calcium software can be imported from the File gt Skeleton Definitions gt Import Skeleton mod file menu item Any user can run and calculate the Calcium Solver skeletons but it takes a separate license to edit and create the MarkerSet files The skele ton can be calculated in the Motion Capture panel from either live camera data or in the simulated realtime mo
219. de when you Disconnect Use Raw Files Note that this can have an optional MOD file associated to it SIMM OrthoTrak Skeleton This skeleton calculation uses the Calcium Solver type skeleton and re quires that you use the anatomically named marker set defined in the SIMM and OrthoTrak software The OrthoTrak SIMM basic marker set uses fixed names like L Shoulder L Wrist and L Knee for prominent marker locations There are several required markers and many more op tional markers If you use this marker set you do not need to use the Si Calcium software for creating a model mod file You must also use an additional Static trial with inside medial knee and ankle markers You load the Static capture file load the Static Trial click this SIMM OrthoTrak button and then the Calculate Skeleton button Then load the Walking motion trial and click the Big Bone button on the Post Process ing screen The Calcium Solver skeleton is calculated To see the skeleton in the 3D window select Show Skeleton The skeleton can be calculated in the Motion Capture panel from either live camera data or in the simu lated realtime mode when you Disconnect Use Raw Files Note that this requires an associated JNT file and an Init or Static trial This specifies the default Euler angle rotation order for the child parent angles defined for the Skeleton The default is ZYX for historic reasons 9 5 Chapter 9 Model Edit Tab Cortex 2 1 Referen
220. dee_LUpperAm Apply Inverse Global Scale to Global Segments Cortex Segment Offset X Kadee_Hips vid Kadee_Spine vo Kadee_Spinel v 0 Kadee_Spine2 w 0 Kadee_Spine3 wv 0 Kadee_Neck vid Kadee_Neck1 vid Kadee_Head vid lt unmapped gt vio Kadee_Hair vid Kadee_Hair1 vo Kadee_Hair2 vid Kadee_Hair3 vid lt unmapped gt vid Kadee_LClavicle 0 Kadee_LUppe v10 a Use Skeleton Translations W bjejejlejesejejejejejejejojejejejeoje pjeojejojejejejojejejejojejeojejoje p88 8 8 8888 8 8 88 8 8 88 blejlelolsjeojsislesjejejsisjeojojsje Pioleieseiolioleieseisilelesiesisielejoio Skin Settings The Skins Settings area is in the top left of the Skin Configuration Dialog These settings are where skin wide settings are located Skin File This drop down is used to select a skin from the files in the UserFiles Skins folder Skin Offset The global coordinate system that defines the Collada mesh and the cali bration coordinates of Cortex do not always match These offsets are used to align the two coordinate systems Different up axis is one example of why this would be used Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual Apply Inverse Global Scale to Global Segments If the skin is being displayed in the scale defined in the Collada file see Segment Mapping gt Use Skeleton Translations below then this box should be checked so that the skin s global position is consistent
221. dentify them If any link stretches beyond the allowable range plus a small amount of give then Template Rectify will cause the offending marker or markers to become unnamed while it seems perfectly obvious to you what is right If Template Rectify does this manually ID that marker on that frame and Extend the Template an option under the Cre ate Template button You can see this when the subject bends over and causes stretches that might not have been recorded when creating the tem plate Figure 8 15 Template ID and Rectify Used for Link Stretch Rigid Body Rectify This takes the most time to use in that you must select a few markers and process a few frames then repeat the process over the possibly many seg ments and frame sequences If it stops it means that the rigid body disap peared You can re start it again and it starts with new measurements on 8 22 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Correctly Identifying Markers Automatically Post Processing Mode Max Speed mm frame Max Prediction Error mm the starting frame Where it is very useful is where it can slug through some tough sequences Start with something simple like the 3 or 4 or 5 markers on the head As with Template Rectify it may be best to Make Unnamed all markers on all frames if there are any mistakes in the D ed data If one of the head markers is incorrectly ID ed as a neck marker then Rigid Body Rectify
222. dentifying Skeleton Events Check Template Join Virtual The Tracking check box triangulates tracks the markers from frame to frame You might want to uncheck this if your computer is not fast enough to calculate the marker coordinates or if your system is not cali brated for any reason You can still collect raw VC files and track them at a later time Collecting raw VC files is the highest priority thread in the motion capture Record mode to ensure that you do not lose your raw data The Identifying check box identifies and names the tracked markers ac cording to the current template If you do not have a template it is best to disable this function to keep the software from attempting to ID the data The Skeleton check box is set to calculate the skeleton using the currently active skeleton model Executes in real time the once per frame event scripts for BioFeedTrak users Allows Join Virtual in real time only if the data meet the stretch criteria of the template Join Virtual is an extremely powerful editing tool used to fill gaps in marker data with simulated data based on the relationship positional in terpolation with other markers on or near the particular problem seg ment This positional interpolation is defined by the settings in the Tools gt Virtual Marker Definitions function Figure 4 57 Join Virtual Check Box 0 878 51 23 Stopped Connect To Cameras Disconnect Use Raw
223. deo AVI files and the raw video or tracks files this adjustable slider is used for correction Offsets are limited to 100 frames in both the and temporal direction To de termine what the offset should be find a frame of 3D mocap data in the 3D or XYZ view where you see a distinct action like a golf ball impact or the club being horizontal in the backswing Adjust the AVI Frame Offset so that the AVI view corresponds to the 3D mocap data view WAV Frame Offset Mocap frames If a delay occurs between the reference audio WAV files and the raw video or tracks files this adjustable slider is used for correction Offsets are limited to 100 frames in both the and temporal direction These settings affect the rendering of the 3D display Figure 4 23 Settings gt 3D Display Tab Settings Calibration File Structure Tracking Cameras Playback 3D Display Past Process Tools Misc Id Params Plugins Force Vectors Scale 1 mind Camera Coverage Minimum Number of Cameras Camera Depth Of Field Display Only Trajectories Num Frames Behind Num Frames Ahead J Motion Trails Markers J Links Skeleton Forces Show KinTools AT Display Options Dim Unselected MarkerSets C Show SDK2 Latency 4 30 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface 3D Display gt Force Vectors This sets the scale of the force vectors shown in the 3D display Scale val ues
224. develop models of the human body for vir tual environments can use SIMM to create the models and compare them with biomechanical data for verification e Animators can use SIMM to develop realistic representations of human and animal movements World objects can be added to pro vide a context for the animation KinTools RT is a full body three dimensional engine capable of calculat ing kinematic and kinetic information from models that are created and saved in the capture file s The kinetic calculations can be done on either of the two skeleton types available in Cortex Skeleton Builder and Cal cium The Skeleton Builder models are generally simpler to use as they automatically scale the bone lengths to the subject s actual bones The Calcium based models use an the entirely different computation method of Global Optimization With either skeleton type used the end results are similar Figure 1 10 Cortex KinTools RT Interface Cortex Fie Layouts Data Views Tools Help 0 368 41 System Calibration Motion Capture Post Process Model Edit Plugins Markers Segments A Index Name _ Mass Model Editor Units Personal Information Weight None anoe Height Mae O Female Standard O Zatsiorsky Custom Mass Model Fractions of the whole Center of Mass Radius of Gyration Segment Mass z x Y Zz Pelvis 0 1117 0 551 0 615 0 587 R Thigh 01416 0 329 0 329 0 149 L Thigh
225. differ ently in two dimensions For SIMM segments that do not map directly to an OrthoTrak segment their scaling information is copied from the most relevant segment For example the right hand in the mocap model copies the scaling information from the right lower arm so that the hand is scaled the same amount as the lower arm The marker set in the mocap model that comes with SIMM includes every marker used in all six marker sets that OrthoTrak recognizes plus the me dial knee and ankle markers In addition many other markers have been added such as medial elbow and wrist markers For a complete list of the markers in the model as well as information on when they should be used and where they should be placed on the subject read the Guide to Mocap Model Markers document The mocap model contains over 80 markers which is more than the number used in most applications When the static trial is loaded any marker in the mocap model which is not in the static trial is removed from the model Thus it is not a problem to have extra markers in the mocap model In fact you should add to the model whatever extra markers you may need for any of your motion capture ap plications Then for a particular application the mocap model will have all the necessary markers and the unused ones will automatically be re moved when the model is loaded into SIMM To add or change markers in the mocap model use the Marker Editor You should be careful not to
226. e Shift F11 Defines a place in the menus for the Shift F11 hotkey It is not expected to be used from here to make a new slide Tools gt Misc gt Solver Logs On Off Ctrl Alt S This enables disables the generation of log files for the Calcium skeleton solver Tools gt Misc gt Dump Solver Log Ctrl Shift S This prints the solver logs to the status bar Double click on the status bar to read them 4 45 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tools gt Quick Files The Quick Files function allows you to easily navigate through frequently used directories making it easier to address and manage motion capture sessions Figure 4 35 Quick Files Icon Quick Files Icon 4 E Fie Layouts DataViews Tools Help Curent Directory C Program Files Motion Analysis Cortex2 S amples 16 Camera Calibration Face B ody 7 SST System Calibration Motion Capture Post Process Model Edit Plugins Presentation 8 o 0 VAN Rectify QuickID Rectify Create Template Template RB Marker ID Exchange Linear Cubic RB Unnamed Template ID Rectify Rectify Join Join Joir MarkerSets DaveBody DaveFace The Quick Files window will automatically open upon launch of the Cor tex software if the Auto Open check box is active You can also launch Quick Files from the icon to the left of the File menu Note that Quick Files is context sensitive for loading captures
227. e always be sure to save the capture file File gt Save Capture Use the following procedure to record a motion capture session Select the Output panel Select the output file types to be generated Enter a name for the file Enter a trial number This is optional and will self increment if multi ple trials of the same name are recorded Enter the estimated time length for the motion capture recording Select Enable COM1 Trigger if you are using an external trigger Ponsa on Note The wireless trigger also works to toggle the record function 7 Select Post Trigger Mode if you only want the last portion of your motion capture session This function allows you to select from the end of the session working backwards to a specified time point 8 Click Record You should see the word RECORDING in large red letters on the lower right corner of the interface See Figure 7 6 Figure 7 6 Recording Data erg vith Nef eaT ea System Calbeston Mk Model Edit Plugris Presentaton Cypers Ovi e C ter aora eo rA N masi Aitoncrenert f X Min Trad 6 Dts Daden secon 20 omom C JPO w wen a x ct Une Rane Piles Settings 1 1 Reset Ds Patt S ETTA RECORDING IC JE CEA nres zu uree anay eoo ve 9 When recording is complete click Load Last Capture to replay the tracked data that was last recorded This will automati
228. e Ctrl Click Toggle 1 TopHead Rectify Quick ID Rectify Create Template Template RB Marker ID Exchange Linear Cubic RB Virtual Calc Smooth Make Delete Copy Cut Cut 2 L_Head Unnamei Template ID Rectify Rectify Join Jon Jon Join VMs Unnamed Unnamed Outside J MarkerSets Quick Prop DaveBody DaveFace 4 Ensag a O 4 BOT 5 Topspine Camera Coverage 7 RSheiser Ji Subject 7 Markers Cameras Z Links Camera Rays C MarkerSet Names Cam Field Of View G Eea Marker Numbers Floor 17 LBicep C Marker Names Volume 18 LElbow ieee Reterence Video e Camera Coverage inky Motion Trails 21 LThumb Virtual Markers 22 Midback Unnamed Markers 23 LowBack 24 RootOffset Skeleton Keep Centered ft J i Mirrored 26 BRHip Skeleton Axes Auto Rotate 27 BLHip Forces Relative Viewing 28 FRHip 29 FLHip Forceplate Numbers Perspective View 30 RThigh woe BackCale O Orthographic View ar laces Model Pose he 32 RAnkle 33 RHeel KinTools RT Display Options al Segment Center of Mass Joint 35 RToe Linear Velocity O Forces 38 LThigh Click Alone Ctrl Click Toggle Linear Acceleration CI Moments m S 1lua Angular Velocity oS Angular Acceleration Globa
229. e Join Virtual Origin Marker are measured both at the start of the gap and the end of the gap and a linear interpolation is used for all in between data points The result is always a perfectly fluid transition on both ends of the gap The Join Virtual mechanism is a powerful tool in creating and editing data quickly with good results It is the result of working with our customers to define and develop techniques to get good motion capture data quickly and efficiently 4 73 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Reset IDs Button New Subject Button Note The Reset IDs button forces the current template to be used for that spe cific frame It is used when a marker is misidentified Press this if you see markers that are incorrectly identified If this fails to fix the problem you may need to create a new template or adjust the marker set to be less sym metric After pressing the New Subject button and with the Pose ID window open the Reset ID button will use the current marker pose to identify the markers This feature allows the software to automatically identify markers based on a Model Pose that you create when you make a template The result is that if you use the same marker set repeatedly you will not have to ID the new person each time the marker set is used The marker identification is automatic and instant saving you time The Model Pose has its own kind of generalized template that
230. e a marker or add additional markers you must re record the static trial and re load the Mocap Model All of the markers described in this document are already part of the pri mary Mocap Model located in SIMM Resources mocap mocap jnt To use any of them you do not need to make any changes to the file just place the markers on the appropriate locations on the subject and make sure the marker names in the static trial match the names shown in the fig ures below Many of the markers can have one of several names as listed F 19 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual in the box pointing to each marker in the figures These names are case insensitive and may contain spaces If you want to add markers to the Mocap Model you can do so with the Marker Editor in SIMM This tool allows you to create new markers at tach them to the appropriate body segments and specify their X Y Z off sets The exact values of the offsets are not important they are used only for display of the marker while creating it The offsets will be overwritten with values calculated by the Motion Module when the static trial is pro cessed and the model is scaled to fit the subject This process is described in more detail in Chapter 5 of the SIMM User Guide but here is a brief summary After loading the static trial the Motion Module places all of the critical markers that are in the trial on the Mocap Model in their corre sponding loc
231. e field of view Software Masks Only Show Raw Data Show Raw Centroids Show Corrected Centroids Show Back Calculated Centroids Show Names Show Numbers Show volume Floor Smear Display Show Greyscale Image Reset Zoom Reset Zoom For All Reset Greyscale Region Reset Greyscale Region For All Take Snapshots Show Snapshots Allows the capture of raw data with any masks in 2D display Toggles black raw data blobs Toggles red raw centroid crosses Toggles centroids corrected from lens distortion Toggles image of centroid with 2D residual from triangulation Toggles marker names Toggles marker numbers Toggles outline of volume floor Leaves smeared paths of the markers Displays the greyscale image for the selected Raptor camera Resets the selected camera to standard zoom settings Resets all cameras to standard zoom settings Resets the Raptor greyscale image to full camera view Resets all cameras to standard greyscale image zoom settings Takes greyscale snapshots for each Raptor camera Shows the snapshots previously taken overlaid on edge data Show Greyscale Image This shows an 8 bit greyscale image from a 10 bit greyscale sensor Markers blobs appear in blue for better separation This used only with Raptor class cameras 4 67 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Analog Display Pop Up Menu Figure 4 53 0 797 51 2D Display Shortcuts Double
232. e file using the property value selections at the bottom of the panel You can also insert delete and select a range of markers The marker values that can be changed include the following Displays and edits the name of the selected marker Displays the marker number in the order the marker appears in the marker list This is not editable This is not used at this time Displays and edits the color associated to the maker in the 3D View To change the color click on the color property and select from the drop down menu False means this marker is not Optional it is REQUIRED to be present when identifying markers with the Template mechanism in real time and with Template Identify mechanism in Post Processing In Cortex 1 and earlier software all markers were REQUIRED to be present for the tem plate to identify them in real time or in Template Identify in Post Process ing This means this marker is NOT needed for the real time Template mecha nism to work Optional markers can be used for adding additional mark ers to a MarkerSet without interfering with the template identifying mech anism It is expected that only a few of the Optional markers will be used 9 13 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual X Y and Z Values The 3D coordinates of the marker in calibration units at the frame number where the marker is selected It is not updated with every frame change but is updated when you select the marker
233. e not only with dance but athletic moves as well A stop watch is handy for calculating the duration of each new move You should decide at the outset whether you will build a hierarchical skel eton If you decided to there are two software methods available SkB Skeleton Builder and Calcium Blank forms to help you define skeleton parameters for each of these methods can be found in Appendix I Useful Blank Forms You may want to copy one of these forms for recording your project measurements Motion Capture Terminology Move Capture or Trial Take Some terms that are useful to a motion capture session are moves trials and takes A move is an event or routine performed by the motion capture subject A move can be as simple as a neutral stance position or as complex as a 2 person 30 second dance routine The director and subject will work from a move list Multiple captures or trials of a move should be taken The number of tri als depends on the complexity of the move the subject s performance and quality of the Cortex raw data Usually three trials per move is ade quate It is important that the director or subject s comments about the quality of the trial which trial was the best be recorded on the Motion Capture Log Knowing which trial of a move is the best will allow the Cortex user to track only the best trial A take is the master number used to relate what is on the camcorder s video tape to the Cor
234. e plate position and orientation in the lab For moving force plates this information is not used since the plate position is determined by marker tracking Moving Force Plate Options In this area a force plate can be specified as a moving force plate and the means for tracking it can be defined To track a force plate it needs to have a skeleton segment SkB or SIMM Calcium defined which repre sents the force plate s position and orientation This will generally involve placing a unique marker configuration on the force plate so that the seg 4 48 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface ment can be uniquely identified A configuration similar to the calibration L Frame should work well Additionally a positional and rotational offset can be applied to the segment position and orientation to get the force plate s final tracked position To specify that the force plate is to be tracked check the Track Position Orientation check box and select a tracking object and tracking segment from the pull down menus Enter a translation vector in the Position Offset fields and a rotation matrix in the Rotation Offset fields Note Itis not necessary to have a segment for every force plate as long as they remain in a fixed configuration In this case a single segment can be cre ated used to track all force plates and each force plate can use different orientation parameters to offset its
235. e top left of the screen The Panel Buttons along the top right of the screen The Panels on the right side of the screen The Real Time Dashboard along the bottom of the screen The Post Processing Dashboard replaces the Real Time Dashboard while the program is in Post Processing mode 9 The Status Bar Messages in the lower left corner 10 The Information Center in the lower right corner ONO PHN 4 1 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual An image of the interface is shown in Figure 4 1 Note that multiple 3D views can be rendered simultaneously Figure 4 1 Cortex Interface in Real Time Mode Quick Files Icon Cortex W File Layouts Menu Bar Mode Tab Buttons Data Views Tools Help Panel Tab Buttons Current Directory C AProgramData Motion Analysis Cortex2 Samples Bio Fed Trak Golf Swing System Calibration Motion Capture Post Process Model Edit Plugins Presentation Cb Goter tert ow J ae Pai X E Tracked ASCH trc E Tracked Binary trb Graphic Panes E Events evt Settings Panels Capture Name i olfSwing_ Tias 1 A Auto increment 0 860 51 Min Trial Digits 1 amp t Duration seconds 20 t il Fiz at ve 8 279 32 6 265 33 8 339 31 M mi e are i e g E Enable COM port trigger i 2 3 E Post Trigger Mode 8 277 35 0 219 27 8 265 29 7
236. e with Square box it completely removes all of your calibra tion information and replaces it with the seed or approximate calibration for each camera vcX means the set of files that end in vcl vc2 vcN if you have N cam eras Calwand vcX and Calwand cap files get written when you press the Cal ibrate button in the Calibration with Wand box and when you are con nected to the cameras If you are not connected to the cameras you can process the data in the simulated real time mode as above The software uses the current system calibration which is normally the results of the seed calibration but can be otherwise and refines the calibration The calibration includes the exact location and orientation of each camera with respect to the origin the lens distortion parameters for each camera and other details about the cameras At the successful completion of the wand calibration the software asks if you want to save the system calibra tion A Yes answer means that a file called SystemSetup cal gets written to the system directory Other uses for the SystemSetup cal file are when you launch Cortex the software automatically reads the SystemSetup cal file and when you exit the Cortex program it automatically writes the SystemSetup cal file into the UserFiles System folder The intent is so that you can launch the Cortex software and it will remember its last good calibration without having to load any files If you load a PRJ file or loa
237. ed for the Events engine from this dialog If the script fails to execute at run time a run time error will be set in the grid and the script will not be executed until the error is cleared This is done by re compiling the script presumably after the script has been fixed to avoid the run time error Gait Events Note To calculate the automatic gait events it is required that Cortex can find the pelvis and the feet This is done using the following assumptions 1 The markerset has only one global segment and it is at the pelvis If there is more than one global segment it will use the last one in the list which may cause problems if the foot segment is parented to glo bal and listed below the pelvis segment The name of the pelvis seg ment does not matter but what matters is that the origin be located near the L5 S1 joint for the automated gait event algorithm to work properly The pelvis and feet may be either Skeleton Builder or Cal cium segments 2 The foot segments follow this naming conventions Left foot We look for LFOOT L FOOT LFOOTPAD or L FOOTPAD The last one found is used Upper or lower case letters may be used Right foot Without regard to case we look for RFOOT R FOOT RFOOTPAD or R LFOOTPAD The last one found is used 4 52 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface If a FOOTPAD segment is present it takes precedence over the other foot bones The FOOTPAD segment wo
238. ed off for animation applications If the solution has joints flipping around turn it off Any model created from a joint file should have the limits enabled This is important on the first frame of any solve First orient the root bone to the root bone markers then do the solve This helps to eliminate some first frame errors when bones get oriented incorrectly There is still a bug where joints get turned around on the first frame The solve changes randomly whenever these last two flags are changed User beware It is recommended that Orient Body is set to False when Real Time opera tion performance is a factor For complete information on Calcium software and Calcium segment def initions please reference the Calcium for Cortex Quick Start Guide p n 651 1920 010 9 24 Chapter 10 Plugins Tab Overview X Panel Assistant Panel Overview The Plugins tab houses the X panel Other plugins can be added by copy ing the pluginname dll file into the C Program Files Motion Analy sis Cortex2 Release2 x x x folder and relaunching Cortex Figure 10 1 Plugins Tab Delete Attica Ota Lond Ancien Tracks Fie Femme crrect 1 0 846 5 1 SE Egle Sa Te e E TTT TT oo abe Owae a SETS m E fE e c T fei hanss fios zap anaa arabe ean nore 10 1 Chapter 10 Plugins Tab Cortex 2 1 Reference Manual X Panel The X panel provides a set of extra functions
239. ed raw video file Reference Video file and analog file generated by the force plates If this were an actual real time capture session the action on the screen would be similar but the data would be coming directly from the cameras and force plates Having loaded all of the related data files we can now exercise all of the six different Graphics Panes available to us We will now look at four si multaneously 1 From the Menu Bar select Layouts gt 4 Panes Left click on the empty lower left pane This action will select this pane 3 Press F1 on the keyboard or choose View gt Reference Video to show the color reference video If you are interested in the Reference Video option contact your Mo tion Analysis sales representative Left click on the empty upper right pane Press F2 on the keyboard or choose View gt 2D Display Select All On to view the 2D display of each camera Left click on the empty lower right pane Press F4 on the keyboard or choose View gt Marker XYZ Graphs Select any of the markers in the 3D Display to view their XYZ Graphs SONOS The displays can be controlled by hand if you click Pause click on the FIFO slider on the Real Time Dashboard and then drag from side to side The First In First Out FIFO slider can only manipulate the 256 frames of data that are currently stored in the FIFO memory space but not all of the data in the data set Figure 4 48 should be similar to what yo
240. ed to change size to fit the motion data but the Solver engine software uses a best fit Global Optimization of the marker data to conform to the rigid underlying skeleton This results in the very best way of animating characters from mocap data The Calcium software allows you to export a mod file The Solver Global Optimization method is resident in three of Motion Analysis Corporation s software products Cortex Calcium Sonic and the SIMM modeling package Cortex 2 1 User s Manual Chapter 11 Skeleton Types Figure 11 7 Calcium Bone Attributes SIMM Calcium Model Markers TreeView E Matt a Markers 40 VMarkers 0 Links 134 SkB Segments inactive Calcium Segments 23 ie H Spine H Spine2 H Spine3 x Name Root Parent GLOBAL Translation 0 31 0 98 0 29 Rotation Angle 3 99 Rotation Axis 0 96 0 02 0 25 Length 0 1 Joint Type Global Attachments 5 This uses the Solver engine with the same advantages as the Calcium Solver method above but with a known and fixed marker set that was de veloped for biomechanics use To use it you must use some variation of the OrthoTrak marker set which has several required markers such as the Knee Ankle Hip and Shoulder markers and many optional markers that will introduce more detail and more bone segments into the solution The big advantage over the Calcium Solver model is that you do not need to create a MOD file which means
241. eedTrak scripting Figure 4 42 Sound Manager Interface EE Cortex Sound Manager Available Sounds BioFeedT tak Name test Way file C Program Files Motion Analysis Cortex2 UserFiles Soun Volume ms s J Pitch J Loop Sound to test Right click sliders to reset to default Play Selected Sound Turn off Selected Sound Delete Sound Add a Sound Tools gt Merge This function is used to merge multiple capture files into one This is use Captures ful for combining both prop captures and multiple subject captures There is also a frame offset function to adjust the timing of the start end of the various captures Figure 4 43 Merge Captures D0R J Remove jii Merge Status Log Merging Captures Frame Offset 15 MarkerSet file Kadee mars Used by 1 captures Capture Soccer Kadee cap 1609 Frames 0 Frame Offset Captures To Merge f Add Soccer Kadee cap Setup cal Soccer Kadee Unnamed trb Merge complete E Kadee mars Soccer Kadee trb Soccer Kadee htr 4 56 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Replace This replaces the currently loaded tacks data with data from another cap Tracks Data file Tools gt Report a If you encounter a bug in the software Motion Analysis has provided a Bug quick and easy way to enter the information and email it to the software development group Figure 4 44
242. een edited in the Post Process mode Figure 4 67 Unload Tracks Button Unload Tracks Button SY otionAnalysi Markers Segments gt f Ka a Click AllNone Ctri Click Toggle A 4 aH gt RIJ 1 M_TopHead th Make Rectify Delete Cut Cut Search PP Undo Unnamed Unnamed Unnamed Outside Settings 4 5 6 M_RShoulder 7 M_LShoulder 8 M_TopSpine 10 M_FLShoulder 11 M_FChest 12 M_RBicep 13 M_RElbow 14 M_RForearm 15 M_Rwrist 16 M_RPinky 17 M_RThumb 18 M _LBicep 19 M_LElbow 20 M_LForearm 21 M_LWtist 22 M_LPinky 23 M_LThumb 24 M_Midback 96 lM Shou ilderAtteet 4 86 Chapter 5 System Tab Getting Started Cameras Panel Loading New Camera Software Camera Display Codes Creating and Clearing Masks Going Live Adjusting Thresholds Analog Panel Getting Started Before using Cortex you must configure your software to match the o ti b 1 2 3 4 5 6 verall system The System tab provides tools to do this The camera set ngs do not need to be reset before each and every motion capture session ut they do need to be reset after changes are made to the cameras Choose File gt Load Setup from the Menu Bar and load a recent or sample capture Choose System from the Mode Buttons Choose the Cameras panel from the panel buttons if it is not already open Change the frame rate to the desired
243. eleration Tab Note The Analysis graphs and their related control panel provide tools to ana lyze your realtime and post process data This window has three tabs which calculate data for the following e Position velocity and acceleration Distance between markers e Included angles The Analysis graphs are activated by pressing the F7 key This tab creates graphs of the position data calculated velocity data or calculated acceleration data for up to 10 selected markers Any number of marker data can be exported The number of frames used to calculate the velocity and acceleration data is set by the user The number of frames used can be either 3 5 7 or 9 Using the higher number of frames to calculate the data will result in smoother output through noise reduction Figure 8 21 Position Velocity and Acceleration Tab Fle Layouts DetaViews Took Hep System Calibration Motion Capture Post Process Model Edt Plugs Markers Segments 4 o A Ae te f 7 Click Abone CiieGick Toggle A 2 e O WVedyrsi amp E g an Quek ID Rectily Templte Temelate Temelate Marker ID Exchange Cube Vetudt Cok Smooth Make Retty Delete Ot Ot Seach lad 15 M Avrit Create 1 Rectiy Jn Ms Unnamed Ureamed Ctsde Settings K 1684 40 1326 92 1 M Rineb EJ 10M LEa 20 MLForearm Pos VetiAce Distances Anges Postion Velocity Acceleration D Posten Z Residus Resutart
244. eleton Builder and KinTools RT but they cannot use Cortex 64 for collecting analog data 1 6 Cortex 2 1 Reference Manual Chapter 1 Introduction Where Cortex Gets Installed in Different Versions of Windows Note Note Note Firewall Settings in Windows 7 Windows XP Vista and 7 32 bit Versions Everything is installed to the C Program Files Motion Analysis Cortex 2 folder by default You need administrative privileges to run software from this location since Cortex reads and writes files into sub folders from this location To run WITHOUT ADMINISTRATIVE privileges copy the Cortex folder to the user s desktop You can launch and run Cortex from there You will want to remove the Cortex link from the desktop and establish a new one for launching Cortex Windows XP Vista and 7 64 bit Versions Programs get installed to C Program Files Motion Analysis x86 Cor tex 2 Samples Tutorials and UserFiles get installed to C ProgramData Mo tion Analysis Cortex2 ProgramData may not be visible after installing Windows 7 for reasons known only to Microsoft To make the ProgramData folder VISIBLE you will need to search the Control Panel for hidden This will show the following options X Don t Show hidden files or Folders Change to X Show hidden files folders and drives Windows Vista users must turn OFF the feature called UAC User Access Control from the Windows Control Panel If not there wi
245. elf from the segment Buttons e The OK button will apply the force plate configuration to the cur rently loaded Setup and close the form e The Cancel button will close the form without applying the configu ration e The Apply button will apply the force plate configuration to the cur rently loaded Setup and leave the form open Tools gt Force Plate Selecting this feature will display the force plate measurements in numer Forces ical values This works when you are live and connected to the cameras or when you are simulating Real Time from VC files and you are Post Processing mode You can change the units to one of the following Force Newtons default Force Kilograms Force and Force Pound Force Figure 4 38 Force Plate Forces Newtons Xx D Z 0 00 0 00 j 231 78 254 00 0 00 1 87 19 42 836 71 196 09 0 00 0 00 0 00 1450 98 254 00 0 00 4 49 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tools gt Mass Model Editor Figure 4 39 Mass Model Editor Cortex 1 0 0 Kinetics_HH_male prj Walk_1 trb E Fie Layouts Data Views Tools Help System Calibration Motion Capture Post Process Model Edit Plugins DEST VMs V Skeleton V Kinetics Mass Model Editor Units Personal Information Weight N A Walk Bue Jame faker Height Male Female Standard O Zatsiorsky Custom Mass Model
246. ence Manual Chapter 6 Calibration Tab Figure 6 10 Wand Processing Status Wand Processing Status Camera Res Extend Seed Extend Seed Button Note Run Again Button Accept Button Reject Button Stop Button Note 60 61 62 63 64 65 7026 363 133 974 288 875 53 139 28517 930 160 277 4739 449 70 087 3795 558 50 210 7148 751 152 024 18 000 32 967 18 000 31 759 18 000 36 000 18 000 3D Residuals Wand Length Avg 165 262 Avg 521 33 Dev 53 1926 Dev 74 47 This button will seed the cameras that were not seeded during the Seed Calibration based on the wand data After extending the seed clicking Extend Seed all the camera buttons should be yellow Click Run Again to complete the wand calibration for all cameras Not all of the cameras need to see the L Frame Configurations with only 1 2 of the cameras seeing the L Frame work very well provided there is sufficient overlap in the wand data This button continues the refinement of the wand calibration If the num bers in Figure 6 10 continue to change click Run Again for a more pre cise calibration Click this button if the calibration numbers look sufficient Click this button if the calibration numbers are unacceptable Fix the problem then select Run Again A typical fix without having to recollect the data is that you can create a mask in one of the Raw Video Cal Wand vexX files If you need to stop in the middle of a c
247. ency motions motions that are too fast for a person to actually perform while leaving intact the frequencies of motion normal to human movement The user has the choice of selecting how aggressively the fil ter will smooth the motion by choosing a frequency value Lower values will cause a very smooth result while higher values will remain truer to the original data Figure 8 4 An Example of Original Unfiltered Data with Some Unwanted Error Figure 8 5 The Curve After an Application of the Butterworth Filter with an Input Freq of 3 8 7 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Figure 8 7 The Curve After an Application of the Butterworth Filter with an Input Freq of 12 Details of the Butterworth Implementation in Cortex As the previous sequence of images shows the input value to the Butter worth filter noticeably changes the result The first example a frequency input of 3 shows a lot of smoothing applied to the curve while the last ex ample shows very little change to the curve Depending on your needs these might be appropriate levels of change For most purposes however values between 6 and 12 work very well as can be seen in the middle two images In these two examples the noisy part of the data has been re moved while the overall characteristics of motion have been retained The Butterworth filter does have that complexity of having to use extra data at the end points The steps are
248. entations of the reference frames closely match those in the OrthoTrak model Also each body segment in the mocap model is scaled to fit the subject by relating its length to the length of an OrthoTrak seg ment These relations are specified in the mocap model by defining scale segments and scale factors for each body segment If you add delete or modify joints or body segments in the mocap model you should make sure that each segment still properly relates to an OrthoTrak segment Second mocap jnt contains several macros that are used to properly de fine the orientation of the floor and to automatically remove the upper body segments if there are no upper body markers When SIMM reads a joint file it performs these macros but does not save them internally Thus when it writes out a joint file all of the macros have been removed If you make changes to the mocap model in SIMM and then save the new model to a file do not replace mocap jnt with the new file Instead copy the rel evant portions of the new file into mocap jnt using a text editor thus pre serving the macros and comments When you open the mocap model SIMM prompts you for the name of a tracked marker file containing a static pose of the subject This static pose is the same one used by OrthoTrak and for it you can use any of the six marker sets identified by that software package Cleveland Clinic Lower Body Cleveland Clinic Full Body Cleveland Clinic Full Body with Head
249. entral nervous sys tem controls movement For example muscle activation patterns determined from electromyographic recordings can be used to esti mate muscle forces and joint moments generated during a task The computed joint moments can then be compared to experimentally recorded moments e Medical students and residents can use models created with SIMM to study musculoskeletal anatomy and function In addition to visualiz ing anatomical structures students gain an appreciation for the inter play of muscle architecture and joint geometry e Kinesiologists who record and analyze the motion of persons with movement disabilities can use SIMM to create three dimensional ani mations of a person s movement Movements such as walking can be quantitatively compared to normal movement to gain insight into the causes of movement deformities Motion can also be analyzed in the context of optimizing athletic performance e Human factors engineers who need to account for muscle strengths when designing products or work stations can use SIMM to study how posture effects muscle strength Limits on joint ranges of motion can also be taken into account e Biologists interested in animal movement can create models to quan tify limb function Investigating movement strategies in other species can provide insights needed to design machines that move Cortex 2 1 Reference Manual Chapter 1 Introduction KinTools RT e Computer scientists who
250. er For making high quality graphs of all kinds of data that Cortex records or calculates Includes marker data analog voltages force and angle data and calculations based on these data User specifies the number of graphs per page the labels and fonts auto or fixed scaling and other items Pre sentation Graphs can be used in Motion Composer presentations and be printed Graph formats are stored in graph files Leaves a blank space for the selected pane Hides the side panels and dashboards shows only the main graphics pan els Good for eliminating the software controls for presentations or better viewing of your data Also available as a toggle on hotkey 9 Figure 4 12 Graphics Only View ETA Calibrated 4 WG File Layouts PESES Tools Help 0 811 46 0 05 Loaded Capture C ProgramData Motion Analysis Cortex2 Samples Bid 921 Frames 120 FPS Z Up Units mm Analog 600 00 Hz A 4 16 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools Menu Tools gt Settings gt Calibration Tab The Tools menu gives access to various functions within the Cortex soft ware Many of these functions are also available in other sections of the user interface Before collecting your first seed calibration these Calibration Settings must be completed Once the values are filled out press Apply and return to the Calibration window in Cortex Calibration Tab
251. er has experienced an acceleration greater than or equal to the se lected value The indicator appears as a carat V at the top of the XYZ Graphs The PP Settings button opens a form that lets you set the following Tools gt Smoothing filter type Search gaps and or spikes Undo Buffer enable or disable Undo Buffer for data editing Tool Strip Customize Post Process Tool Strip Pons Undo retrieves data affected by the most recent data Edit or ID function and places it back into the data set Cortex supports ten levels of undo This feature can be disabled or cleared on the Post Options form If you get the message that an Undo function may not execute you may need to clean your Undo buffer This can be found in the Tools gt Settings gt Post Process Tools gt Undo tab The Memory Gauge lets you know when you computer is running out of memory to store edits in the undo buffer Hides selected marker s from the 3D view Hidden markers will have an H in front of the marker name in the marker set list Unhides the hidden selected 3D view markers This is always the default setting for new markers Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Rigid Body Rectify L Copy Paste Note Uses the selected markers to ID unnamed markers through the capture se quence For more information on the Rectify functions refer to Rectify Functions What They Do and When To Use Them on page 8 19
252. ere will be an excessive amount of unnamed markers Bring up the Task Manager and monitor the CPU usage You can see this with trials you have already collected by selecting the Raw Video Files you collected click the Run button Change the above Tracking Parame ters press the Run button again and see the difference Check that the Tools gt Settings gt Playback panel and the Real Time speed option is se lected 7 12 Cortex 2 0 Reference Manual Chapter 7 Motion Capture Tab Prop Files Properties of Props in Cortex Cortex has the ability to create and store Prop files for props These were introduced for the animation side software which gave them their name An actor brought a rigid body on set baseball bat hockey stick catcher s mitt etc They wanted to be distinct from the actor s marker set of hierarchically linked segments bones so the Props could be inserted and deleted quickly and easily A new kind of identifying template has been created with an independent local coordinate system specifically used for these Props These are now used by other Cortex users who want a simple bone 3D coordinate system calculated in real time and streamed to their Client SDK program s 1 Assumed to be a rigid body with 4 or more markers which show up as regular named markers They get identified labeled in real time when the Tracking and Identifying boxes are checked in the Motion Capture panel 2 Has an imbedded loca
253. es that changes from one computer to another If that does not fix the problem try to slide the Hardware Acceleration to None Quit Cortex and then re launch If that still does not fix the problem try to change some of the Open GL settings found under the name of your graphics card found under the Properties gt Setting gt Advanced tab Also change the Verti cal Sync setting to On by Default and restart your computer G 4 Appendix H Question Answer Question Answer Question Answer Questions and Answers for Specific Applications Does Cortex require a specific order for markers and linkages For the identification of markers to work swiftly in real time the order of marker definitions is important You should follow these rules 1 Markers should be ordered such that each successive marker builds the character top to bottom through linkages i e Head to Neck down one arm then down the other down the torso to the hips down one leg then the other Do not backtrack 2 If the first markers are linked into a stiff triangle marker identifica tion will be swift For this reason the head markers should always be first Linkage order may affect the rectify process For the head a linkage order of 1 2 1 3 and 2 3 works well How can I prevent ghost markers from appearing 1 Ghost markers may appear if the Max Residual value is set too low This parameter is set in the tracking function in the Motion C
254. es with complete Selected Total frames to use visible O All Include current frame as the Model Pose Show Template Linkages Create Template Extend Template Template Create Button in Post Processing with Template Selected MarkerSet Name This is the name found in the Model Edit Tree View and can be turned on and off in the 3D Display Show Properties check 8 12 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab box MarkerSet Names It is used for the display and for having unique names when you are tracking multiple objects Include Current Frame as the Model Pose The Model Pose can be turned on and off in the 3D Display Show Properties check box It is used functionally for two things in the Cortex software 1 Identifying the template when the Motion Capture gt New Subject dialog box is showing 2 For showing the Model pose when manually fitting the Calcium seg ments within the marker cloud for the Calcium Skeleton in the Model Edit panel Template Create Button in Post Processing with Prop Definition Selected Include Current Frame as the Model Pose Check for display pur poses only not used in the calculations MarkerSet Name A prop file is created when you press Create Prop File in the current data folder The Prop file can be used as an Additional Tracking Object in the Motion Capture gt Objects panel A prop is tracked as a rigid body and the 6 degrees of freedom The pro
255. es you control over how the mass properties of the individ ual body segments are scaled If this option is off then each body seg ment s mass is scaled proportionally with its size If this option is on then each segment s mass parameters are not scaled with their change in size i e the distribution of body mass specified in the model file is pre served In either case after the model has been scaled all the body seg ments mass parameters are scaled up or down by a single percentage so that the total mass of the model equals the number entered into the sub ject mass field Figure F 3 Static Trial Import Dialog Box init1 c3d Options Static C30 file as markers 190 frames 271 Cancel data rate 120 0 Hz croa Mocap Model C Users Simm Resources mocap mocap jnt Save JNT File Save MSL File save MSL file Import Static Pose average from frame 1 to frame 271 subject mass 75 000 IV load personal dat preserve mass distribution read marker names from PO NT DESCRIPTIONS v Export Scaled Model save JNT file ama a These options allows you to specify if SIMM will write out joint and mus cle files containing the musculoskeletal model that is scaled to fit the sub ject After SIMM has loaded the mocap model and scaled it based on the data in the static marker file and personal dat it will write out corre sponding joint and muscle files depending on the states of these check boxes You may w
256. et So what does this mean for your 12 Camera Setup For a 5 person Eagle camera capture with an average data rate for 120 Hz capture per camera it works fine about 1660 Kbps X 12 cameras 19 920 Kbps or about 20 of the available Ethernet bandwidth We used a Gigabit Ethernet NIC and Switch for our 24 camera setup That used about 4 of the 1000 Mbps Ethernet but would have been 40 of the 100 Mbps Ethernet which could result in lost packets The Cortex soft ware is robust enough to deal gracefully with lost packets by ignoring the empty frames and continuing with the capture This also provides another dataset in the Samples folder Dave Face and Body one person 60 Frames sec 400 Frames 300 600 KBytes per cam era average maybe 450 KBytes 450 KBytes X 60 Frames sec X 1 400 Frames 68 KBytes sec or about 680 Kbits sec or about 0 7 of the 100 Mbps Ethernet H 4 Cortex 2 1 Reference Manual Appendix H Questions and Answers for Specific Applications Question Answer Question Answer Question Answer Question Answer Question Answer For your 12 camera setup this would be 680 Kbps X 12 cameras 8160 Kbps or about 8 of the 100 Mbps Ethernet Why is there is a problem displaying the AVI files when a 3D window is displayed on a Windows XP system The AVI file plays in a jerky motion and the screen is sometimes sliced into horizontal blocks This is a problem with Open GL and Direct X displayi
257. ets Lenses Orientation Capture Volume Calibration Up Axis E Calibration Units milimeters Measurements Origin 0 0 0 6 5 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Origin Offsets Tab This allows for translation and rotation from the origin The calibration L frame may then be positioned anywhere in the motion capture area This is useful for two possible reasons 1 All cameras do not see the calibration frame but you want to use it to position the cameras In this case you can move the calibration frame to where it can be seen and enter the Origin Offsets measured from the true origin to the temporary location of the calibration frame 2 You want a different location for an origin for any reason Figure 6 4 Origin Offsets Tab Settings Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins Calibration Frame Lenses Orientation Capture Volume Other Unconstrained follovtthrough iterations Extra wand processing iterations o Include wand metric refinement in calibration Origin Offset Applied at L Frame Calibration Time Property X Translation Y Translation Z Translation 6 6 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab Lenses Orientation Tab This tab is used to set the focal length and positions of each camera as used at the start of the wand calibration p
258. ettings 4 65 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Subject Markers Displays all markers in the 3D View Options for length Links Displays all links between markers in the 3D View MarkerSet Names Displays the prj file name over the marker cloud Marker Numbers Displays the ID numbers for all markers Marker Names Displays the marker names over the marker Trajectories Displays the marker trajectories in PP mode only Virtual Markers Displays the virtual markers Unnamed Markers Displays unidentified markers Skeleton Displays the skeleton segments when they are defined Skin Displays a selected skin Skeleton Axes Displays the RGB XYZ orientation for each bone Forces Displays the force plate and force vectors off the force plates BackCalc Shows the theoretical model pose markers relating to the bone in addition to the actual marker positions in Calcium skeleton bones Model Pose Displays the model pose as defined in Create Template World Cameras Displays the motion capture cameras in the 3D View Camera Rays Displays which cameras can see the selected marker s Cam Field Of View Displays the camera view for the selected camera s based on the focal length as set in the Lenses Orientation tab Floor Displays the virtual floor in the 3D View Volume Displays the capture volume Video Displays the
259. evels of memory and this provides the option to turn it off The Undo Buffer can also be cleared out to lower memory usage by selecting the Clear Undo Buffer button 4 35 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tool Strip Tab Figure 4 28 Tools gt Settings gt Post Process Tools gt Tool Strip Tab Tool Strip Options Display Icons and Text Display Icons Only Display Text Only Tool Buttons V Rectify Unnamed V Create Template RB Rectify Linear Join Virtual Join Make Unnamed Cut Search Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc _ Id Params Plugins Tools Search Undo TIP Use Alt Mouse to rearrange toolbar icons Enable Tool Tips Show PP ToolStrip Quick ID Template ID Marker ID Cubic Join Calc VMs Delete Unnamed Cut Outside PP Settings Unhide Marker SJ S S S S S S S Note Note These Settings adjust the look of the Post Processing Tool Strip Are stored in a User Profile Different preferences can be saved in different profiles using the Profile Manager File gt Profile Manager The buttons in the Post Processing Tool Strip
260. f each computer system with which the Licensed Program is incorporated or used Copyright Protection The Licensed Program is copyrighted by Licensor Copies may be made only as permitted by this Agreement Licensee agrees to reproduce and apply the copyright notice and proprietary notice of Licensor to all copies in whole or in part in any form of Licensed Program made hereunder Warranty Exclusion Any maintenance obligations of Licensor shall be subject to a separate maintenance or update agreement between and licensee LICENSOR MAKES NO WARRANTIES EITHER EXPRESS OR IMPLIED ON ANY LICENSED PROGRAMS AND EXPRESSLY DISCLAIMS ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE Patent and Copyright Indemnification Licensor shall indemnify Licensee against liability for patent and copyright infringement upon the terms and conditions applicable to Licensee s purchase of the Designated System Termination This agreement and any licenses granted hereunder may be terminated by Licensor upon written notice if Licensee fails to comply with any of the terms and conditions of this agreement Upon termination of any license Licensee will at Licensor s option either return the Licensed Program to Licensor or destroy the original and all copies and parts thereof General This agreement is not assignable The rights under this Agreement or any license granted hereunder may not be assigned sublicensed or otherwise tra
261. f freedom and make the two distal joints dependent on the proximal one so that all three joints will flex when the proximal one does Any combination of the optional markers can be used to create a hand model with the desired degrees of freedom All of the op tional hand markers are defined as fixed in the model file This means that the offsets specified in the file are used for solving motions the Mo tion Module does not overwrite them and thus you should place the markers on the subject according to how they are shown in the figure be low F 23 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual Figure F 6 Critical and Optional Markers for Hands R Finger3 M3 R Finger4 M3 R Finger3 M2 R Finger2 M3 9 R Finger4 M2 N wa Oj R Finger5 M3 R Finger2 M2 R Finger3 M1 pe R Finger4 M1 A R Finger5 M2 R Finger2 M1 _ w S Wl i R Finger5 m1 Ay T R Finger5 M1 Ie N NJ R Thumb M3 Co R Thumb M2 O Aiiand R Thumb M1 R Radius R UIna RWRA RWRB R Wrist R Wrist Lateral R Wrist Lat RWRI critical markers for finger modeling Optional markers that add degrees of freedom to the finger joints Starting with SIMM 4 0 support has been added for alternative critical marker sets for use with the Mocap Model For example the sacral marker can be replaced with two PSIS markers and the lateral wrist marker can be replaced with the radius marker It is thus difficult to di
262. ffect When exporting the contents of the form are exported even if they have not been applied Not all data in a force plate configuration can be represented using a for cepla cal file so any unsupported data is excluded Forcepla cal files are still maintained because they are used by the OrthoTrak software Force plate configuration is now stored in your setup file so unless you need it for other reasons like OrthoTrak compatibility you do not need to save the forcepla cal as a separate file 4 47 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Force Plate Configuration File gt Refresh Refresh the form to match the configuration which is currently loaded This is useful if a new Setup file which uses a different configuration has been loaded while the form is open Force Plates List This list displays the force plates that have been defined for the current configuration allows addition removal of plates and displays the config uration status of each plate To add a plate simply click on the green button To remove a plate click on the red X button A plate can be se lected by clicking in the list The input controls will be changed to reflect the selected force plate No changes are made to the loaded configuration until they are saved or applied The force plate list will display the status of a plate compared to the configuration that was loaded into the form If the force plate has a be
263. figures and the reference video images 4 To see the Skeleton blue segments and the PolyBones Skin right click in the 3D View and check both Skeleton and Skin To see these calculated and displayed in simulated real time 1 Select File gt Load Capture Live Walk1 cap This puts the soft ware into the Live motion capture mode and selects the Walk1 cap ture file 2 Click Play What you see depends on which boxes you have checked in the lower left part of the Real Time Dashboard Check Tracking and Identifying to see the stick figure when you press Run Check Skeleton to see the skeleton blue segments and the Skin the brown Polybones that look like the bones in a human skeleton This proce dure will produce a subject with a skeleton and skin as shown in Fig ure 9 3 Figure 9 3 OrthoTrak Skeleton and OBJ Skin Subject Cortex Calibrated cal Walk1 cap W File Layouts DataViews Tools Help Current Directory C Program Files Motion Analysis Cortex2 S amples SIMM OrthoTrak Helen Hayes Marker Set System Calibration Motion Capture Post Process Model Edit Plugins Presentation i a o a 4 amp 4 w O80 WA S Create Template Template Marker ID Exchange Cubic Virtual Cale Smooth Template ID Rectify Join Join VMs Markersets Walk S t Rectify QuickID Rectify Unnamed Browse Markers Segments Click AllNone Ctrl Click Toggle 1 Top Head 2 Front Head 3 Rear
264. folder The System Objects list contains MarkerSet files that can be loaded from the UserFiles SystemObjects folder To load a file just click on it to check the box next to the file name It is important to note that two MarkerSets with the same name can not be loaded at the same time Each object list has three buttons which allow selecting all the files dese lecting all the files and refreshing the file list The red X button allows selected files to be permanently deleted from the hard disk Each list also has an arrow button This is used to copy a MarkerSet from one location to the other After copying the Local Object will always be the one that is loaded This is can be a useful tool in day to day work flows See the Mo tion Analysis Recommended work flow for more information Objects output Open Fusion Object Loader Local Objects lx Select All Unselect All Refresh C Body mars I Club mars SA mars System Objects alx Select All Unselect All Refresh I Static_CC mars I Static_HH mars M Wand500 mars System Objects is a feature used to help track objects that are known to be rigid objects The advantage in using this feature over using a standard objects with a Template is that rigid objects can be more robustly tracked and can have several markers define the 6 DOF Rigid Object coordinate system This is useful for tracking and identifying props such as swords baseball bats and othe
265. force plate number Kistler and other force plates may be included in a single system The proper way to orient the force plate is the 3x3 orientation matrix not the calibration matrix Do not switch the cables to the A D board Keep the Long Term Constant turned off on the charge amplifier Reset the charge amplifier before each test or at least every few tests This re establishes the zero for the charge amplifier The forcepla cal file is unable to distinguish between AMTI Bertec and Tec Gihan As such if you export any of these plate types to a forcepla cal file and re import them they will be imported as AMTI plates AMTI Bertec and Tec Gihan all use the same analog channel naming convention Appendix C Force Plate Configuration Forceplate cal File Setup Cortex 2 1 Reference Manual C 12 Appendix D SDK Software Developers Kit SDK Overview D 1 SDK Programming Example Write your own Streaming D 1 Plugin SDK Overview The SDK is available for the advanced user who wishes to incorporate the output data stream from Cortex into a software application The Software Developers Kit which provides the tools for interfacing your program with Cortex is available by special request from Motion Analysis Corp at Support MotionAnalysis com SDK Programming Example Write your own Streaming Plugin There is a Software Development Kit SDK which is written in the Vi sual C Visual C language an
266. fore its name then it is a newly added plate A indicates that the plate is being removed A indicates that the plate information has been modified and needs to be saved Force Plate Specs These input controls allow some general information about the force plate to be specified The things specified are the type of force plate the scale factor applied to the force plate and the size of the force plate The scale factor and size values should be the same as those in the forcepla cal file Force Plate Calibration These inputs allow you to specify the force plate calibration information This information is the same as that in the forcepla cal file and should be obtained from the manufacturer Clicking on the book icon next to a matrix input region will allow the information to be input using a note pad style control This is useful for copy and pasting from an existing document Entries are delimited by spaces and new lines There is also a button in this panel for running the Kyowa Dengyo cali bration procedure If there are no pending force plate changes and all force plates are of type Kyowa Dengyo then a button will be present to run the Kyowa Dengyo calibration The calibration results will be loaded into the force plate configuration form The results can be treated as any normal calibration edit would be applied saved cancelled Force Plate Position and Orientation These inputs allow you to specify the forc
267. gins Tab within each of the main tabs System tab Calibration tab Motion Capture tab etc The default tab for the X panel is in Plugins Figure 4 31 Settings gt Plugins Tab Calibration Fle Structure Tracking Cameras Playback 3D Display Post Process Tools Misc_ id Params This allows you to specify which tab a plugin panel is available in Select a plugin and then select the tab you wish it to appear in Plugins Available Tab AssistantPanel System XxX Calibration Motion Capture Model Edit Plugins 5 Presentation 4 41 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tools gt Hot Keys Hot Keys are short cuts which integrate simple to complex procedures into single key strokes There are initial default settings and users can also create their own custom Hot Key functions To change a hot key setup right click on the key in the Hot Key layout and select the item you want to do with this hot key Note that you can pick scripts to run from any hot key Put the script you want to use in the UserFiles Skyfiles part of the disk and you will be able to select and run it with a hot key Figure 4 32 Default Hot Keys Setup Custom Hot K and Tr MODIFYING HOT KEYS Key Modifiers Mouse click on a Hot Key to select it Then mouse click on a blank key to move it Right click on a Hot Key to set it using a menu Use the check boxes to select
268. h and focus set to infinity often marked with the co symbol Also some lenses have one focus for zoomed in and another for zoomed out This is sometimes marked t for telephoto zoom in and w wide angle zoom out In a typical full body volume the cameras should be able to be focussed such that all 12 of the discs on the focus card can be seen This is almost always possible with cameras with one million or more pixels but the top line of small discs may not be seen in large volumes Also in volumes with poor ambient conditions where the threshold need to be set high the top line may not be fully resolved This will be more marked with cam eras with less than one million pixels Hawk and Raptor H cameras In these cases try to judge if the large and mid size discs look acceptable If the focus card has been mislaid or damaged then use a selection of markers of various sizes stuck on a matt surface Place the markers sev eral centimeters apart so that their images do not stream or merge when the ring light is bright Most lenses have an aperture which can be made smaller to let in less light and opened to let in more light This is often referred to as the F stop The F stop number is a ratio of the focal length of the lens to the di ameter of the aperture A lens is said to be wide open when it is set on its smallest F stop or with the aperture opened as wide as possible It is very unusual to have to change the F stop on a Mo
269. h complete O Selected Total frames to use O Visible O all Include current frame as the Model Pose Show Template Linkages Create Template Extend Template 20 m tee I M_FRMe m M Purp 30 M fikren If 32 Im oseo 33 M_Fiviethont IEIET Ias mamn 5 M_Lxree 37 M Larkie m Chek Alone CirlvCick Topje A 42 U2 lt tregty gt 43 U3 Enety gt 44 UA sEmgtye 46 US dna 46 US Engt 47 UJ Engty gt 0 000 40 jaaa x eee 100 200 300 aoo 500 600 700 800 soo 1000 1100 1200 1300 1400 Simteton p 7 Faas ie ae f mre Lee vse seice emme 4 e 4 fe Cateusnte Freed md oad on ei 4 75 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Getting Auto ID to If the person who was used to create the template moves some markers or Work Tuning and if a new person comes out with the same marker configuration but in Updating the slightly different locations you will want to update the template to the new marker locations This will make sure that your RealTime tracking and the Template ID and Template Rectify functions in Post Process will be at an optimum performance level Template Activate the Motion Capture tab and then select Connect to Cameras or select the VC files and then select New Subject This will bring up the Pose ID dialog box below and the Model Pose stick figure appears in the 3D View Figure 4 60 New Subject Interface New Subject No pose store
270. h the OrthoTrak algo rithms can definitively locate without knowing anything about the mocap model Then these critical markers are placed on the mocap model and the model is fit to the static pose marker cloud Now the offsets of the other markers can be measured because every body segment in the mocap model is now correctly placed in the static pose F 15 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual Analog Configuration Files Force Plate Data EMG Data Other Data importVariables txt SIMM can include analog data such as ground reaction forces EMG acti vation levels and kinetic data when importing a motion SIMM uses a configuration file named importVariables txt to determine which analog variables to import from an analog file and how the data for each variable should be interpreted This configuration file is used for both TRB TRC import with corresponding ANB ANC analog files and for C3D import where the analog data is contained in the C3D file itself SIMM can in terpret analog data as one of three types These variables specify voltages representing force or moment compo nents as measured by a force plate transducer Given the voltages gener ated by a force plate 6 channels for an AMTI or Bertec force plate 8 channels for a Kistler force plate SIMM can calculate and display a force location and vector for the force plate These variables define activation levels for one or more muscles
271. he Current Frame Zooming occurs more quickly by using the hot keys The best way to zoom into a particular set of frames is to select the frames in the XYZ Graphs by dragging with the middle mouse and then pressing the Zoom In Hot Key Even finer control over zooming can be accom plished by pressing Shift middle clicking to independently set the Low and High Selected Frames and then pressing the Zoom In hot key I The XYZ Graphs also allows you to translate the data vertically and hori zontally This is accomplished by holding the Alt key while clicking and dragging the cursor inside the X Y or Z display It is often helpful to zoom into the data s amplitude Holding the Alt key and simultaneously pressing the left and middle mouse buttons zooms the data s amplitude The marker that was closest to the pixel on the display where zooming began becomes the Target Marker Its data is centered ei ther to the data in the Current Frame or optionally to the data in the frame that the cursor was on when zooming began Data for this marker will re main centered on the screen at all times unless you forcibly translate it off the screen using Alt click and drag Unzoom is a means of resetting the display such that zoom and translate values are equal to zero The default Hot Key is U on the keyboard and it is an XYZ Graphs right mouse pop up menu item Picking a marker out of a crowd of data is done by double clicking di rectly on a marker
272. he OK button to import the mo tion The following list describes each option in the dialog box These fields allow you to specify the range of frames to read from the marker file as well as the increment To use them type into the first two fields the starting and ending frame numbers that you want to import The third field specifies the increment to use when reading frames from the file For example to read every other frame from the file enter an incre ment of 2 The starting frame number field and the increment field are ini tialized to 1 The ending frame number is initialized to the number of frames in the marker file F 3 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual Quick Solve Crop Ends Calculate Derivatives The Motion Module contains two optimization algorithms for fitting the musculoskeletal model to the marker data The default method is fairly robust it is designed to handle cases in which several markers are missing from a frame or in which the markers move large amounts between frames The other method called quick solve is less robust but works up to twice as fast as the default method If speed is an issue and you know that your marker data is well behaved you may want to turn this option on to use the faster optimization algorithm Tracked marker data files often have frames at the beginning and end of a motion that are missing some markers because the subject is outside the camera
273. he WebCam used USB or Firewire If it delivers Mpeg 2 streams over Firewire then it currently would not be rec ognized by EVaRT When evaluating a suitable camera Firewire with DV25 is recommended More types of cameras are scheduled for inclusion into the Reference Video option in the future Please check with support motionanaly sis com for an updated list H 6 Cortex 2 1 Reference Manual Appendix H Questions and Answers for Specific Applications Question Answer When I load a capture with an avi file in Cortex I get a popup error that reads Can not add the atudio renderer It loads the marker data but not the avi file The problem was caused by faulty or buggy device drivers for the sound card Updating the drivers for the sound card may fix the problem H 7 Appendix H Questions and Answers for Specific Applications Cortex 2 1 Reference Manual H 8 Appendix Useful Blank Forms Motion Capture Log Human Body Outline Front Human Body Outline Side Human Body Outline Back The following blank forms may be useful to prepare for and document a motion capture session Feel free to make copies as needed Appendix l Useful Blank Forms Cortex 2 1 Reference Manual Motion Capture Log Date Client Ref Take Cortex Video Filename Seconds Counter Comments Results
274. he capture volume and the position values are in the units used for calibration The file is made up of three parts e the file header e the position data header and e the position data All fields in this file type are separated by horizontal tabs The tre file header occurs on the first three rows e Row one contains the path file type label string path file type number int path file type descriptor string and original direc tory path and file name string E 3 Appendix E Import and Export File Formats Cortex 2 1 Reference Manual Data Header Position Data Empty Fields Example Row two contains the data rate label string the camera rate label string the number of frames label string and the units label string Row three contains the data rate value real the camera rate value real the number of frames int and data units string The data header occupies rows four and five Row four contains the frame number label string the time label string and followed by the marker name labels string There are three horizontal tab characters between each marker name label These names usually correspond to the location where a reflective marker was placed on the subject Row five contains the column labels string for the position data starting on row six For each marker name there is an X Y and Z column These axes labels have the trajectory numbers appended to them Positio
275. he coordinate system is not important the square should be rotated so as many control points as possible can be seen by all cameras e The calibration L frame should be seen by at least half of the cameras to give a good calibration The other half of the cameras can be calibrated using the wand with an Extend Seed menu item You may need to adjust the cameras at this point 3 19 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Figure 3 16 Placing the Calibration L Frame In the Capture Volume Z Up 3 20 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Marker Sizes and Maximum Distances for Motion Analysis Cameras The limiting factor in what size marker works in what volume is the dis tance the marker is viewable and usable from the camera Min 3 lines below is the minimum number of scan lines or pixels to allow in calculating a 2D centroid As a rule the more lines the cleaner the 2D data and resulting 3D data But once you get above 3 lines the data is very clean and going more lines per centroid does not generally make the data any better This setting is found in the Tools gt Settings gt Cameras tab Table 3 2 Marker Size and Maximum Distance for Raptor 4 Raptor E Eagle 4 and Eagle Cameras Raptor 4 Raptor E Distance m Eagle 4 and Eagle Camera Marker Size Min 3 Lines Min 2 Lines 6 mm 1 4 in 4 2m 7 0m 12 mm 1 2 in 8 0m 12 0m 19 mm 3
276. he force plate outlines will not appear in the 3D collection view C 1 Appendix C Force Plate Configuration Forceplate cal File Setup Cortex 2 1 Reference Manual Note Forcepla cal files in the past have been named with a t as force plate Be sure to check that there is no t in forcepla cal Example Forcepla cal files for each type of force plate AMTI Bertec and Kistler can be found in the directory C Program Files Motion Analysis Cortex2 Samples Example Forceplate Configurations Figure C 1 Forcepla cal File Structure for Bertec and AMTI Force Plates Line Description Force plate number 1 through 8 Force plate scaling factor and optional length and width of force plate 25 for AMTI setup with amplifier gain switches set to 4000 6x6 force plate calibration matrix Inverted Sensitivity provided by the manu facturer Xo Yo Zo True XYZ origin relative to the geometric center of the force plate in cm provided by the manufacturer 10 Xc Ye Zc XYZ location of the geometric center of the plate with respect to your video coordinate system the video calibration system s origin measured in cm coordinate system match the laboratory coordinate system 11 12 3x3 force plate orientation matrix to make the force plate 13 C 2 Cortex 2 1 Reference Manual Appendix C Force Plate Configuration Forceplate cal File Setup Figure C 2 Forcepla cal File Structure For Kistler Force P
277. he markers A typical value for a 1 inch marker would be 2 For Raptor 4 and Eagle 4 cameras these values will generally dou ble to 4 lines per marker Max Horizontal Lines per Marker Sets the maximum number of scan lines a marker must occupy on the camera s sensor for it to qualify as a marker Again the value of the pa rameter entered is dependent on the size of the markers and the distance the camera is away from the markers A typical value for a 1 inch marker would be 50 4 23 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Use Per Camera Settings This check box allows the Min and Max lines per camera to be set on a per camera basis These settings are modified in the Tools gt Settings gt Cameras tab This can also be accessed by clicking on the Edit button Shape Analysis Filters out the centroids of blobs that are not round e g a marker is par tially obscured or two markers have merged Tracking Parameters Tracking parameters are used when correlating the images from several cameras to establish marker coordinates in three dimensions Max Residual mm Is the maximum average error when rays from several cameras are com bined to establish the coordinates of one marker If the residual exceeds this amount it is assumed that these rays are not close enough together to be seeing the same marker This parameter value should not be less than 4 times and no greater than 8 times the ave
278. he use of the IEEE 1394 standard also known as a Firewire or i Link connection If your computer does not come with this interface built into it you will need to purchase an inex pensive card that provides the correct port You can run CortexDV on your local machine that has Cortex running on it not recommended as well as with remote machines that are connected to digital video cameras Any standard DV camcorder should be sufficient for use with the Cor texDV software All CortexDV testing and product development was done with a Sony DCR TRV520 NTSC model DV camcorder System Requirements Recommended Minimum Specifications e Microsoft Windows XP Vista or Windows 7 e 256 MB RAM e 80GB or more free hard drive space for captured files CD RW drive e Ethernet card Appendix G Synchronizing Digital Video with Cortex Cortex 2 1 Reference Manual Installation Note Using CortexDV Overview Note Capturing Digital Video Using CortexDV We recommend you install the software into the C Program Files Mo tion Analysis CortexDV directory but CortexDV exe will run from any folder No dongle or license file is required to run this application But to collect synchronized reference video AVI files in Cortex you need the Refer ence Video 3 0 line in your mac_lic dat license file To use CortexDV you will need the Reference Video license entry in your Motion Analysis license mac_lic dat file For m
279. hing 4 33 Snippets 10 2 Socket Error 3 27 Software Installing 1 4 required 1 4 Software Developers Kit D 1 Sound 4 37 Sound Manager 4 56 Square Seed Calibration Index 7 Cortex 2 1 Reference Manual Cameras 6 8 Square Calibration 6 2 Standard System Configuration A 2 static pose see Motion Module Status Bar Messages 4 59 Status Bar Pop Up Menu 4 70 Still Camera 2 4 Studio Preparation 2 1 Subject Preparation 2 6 Synchronizing Video G 1 System 4 58 System Calibrating Process 3 18 System Hardware Interconnection A 1 Overview A 1 Standard System Configuration A 2 System Objects 7 7 System Requirements 1 3 System Tab 5 1 SystemSetup cal 6 18 t B 7 Take 2 5 Talon Plugins 1 14 Target Marker 8 4 Tell Cameras the Network 5 8 Template Building 7 2 Template Create 8 12 Template ID 8 14 Template ID Details 8 20 Template Rectify 8 15 8 19 The 8 17 Threshold slider 5 12 Thresholds Adjusting 5 12 Threshold 4 25 Time Code 4 84 8 3 Time Code Counter 4 80 Time Lines 4 42 8 29 Time Series Files E 12 Time Zoom Method 1 4 82 Method 2 4 82 Time Zoom Slider 8 3 Tool Buttons 4 36 Tool Strip Tab 4 36 tools 4 3 Index 8 Tools gt Settings 4 17 Tools Menu 4 17 Tools Tab 4 33 Track Row Column E 3 Tracked Data Editing 8 1 Viewing 4 63 tracked marker files cropping ends F 4 opening F 2 Tracking 4 72 With More Than 8 Cameras 3 13 Tracking mode 4 81 Tr
280. hould be set on range 3 for the X Y and Z range settings X and Y are set to gether This is the 10 000 pC setting This setting can be changed if desired but the forcepla cal file will have to reflect the change A gain 1 on the A D board should be used since the Kistler outputs 10 V full scale The Kistler force plate requires an 8x8 calibration matrix The matrix only contains non zero data on the main diagonal upper left to bottom right All non diagonal cross talk elements are zero To calculate the values to use on the main diagonal of the matrix assum ing nominal sensitivity values of 7 8 and 3 8 pC N X and Y Scaling 10000 pC 7 8 pC N 10 V 128 2 N V Z Scaling 10000 pC 3 8 pC N 10 V 263 4 N V Figure C 6 shows an example 8x8 matrix in a forcepla cal file This is a measure of the X Y and Z distances to the piezoelectric trans ducers used to generate the signals in the Kistler force plates These num bers are supplied by the manufacturer Figure C 6 Example Forcepla cal File For a Kistler Force Plate N N oo 0 1 0 0 0 0 0 0 2 0 0 i A T ee N OSOOONOCOOCO OONOCOOOCOCO ONOCOOOOCO NOOOOOOO 1009o o og A o t C 10 Cortex 2 1 Reference Manual Appendix C Force Plate Configuration Forceplate cal File Setup General Notes On Kistler Force Plates Notes Note Since the Kistler force plate format is flagged with a K after the
281. ht or more cameras effectively in a relatively small volume if there is sufficient height We suggest placing half the cameras at a moderate height and the other half as high as possible You may need to experiment to obtain the optimum camera adjustment for your lab or studio 3 14 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Adjusting Camera View for Increasing Height Note If your capture volume is too high for your cameras you may turn the cameras on their side just as photographer may turn their camera on its side for increased height Note that your camera width coverage will de crease You may turn the cameras on their side up to 89 without having to make any changes to the software settings If you turn the camera 90 or greater you will need to select the Alternate setting for the particular camera s This is done in the Calibration gt Calibrate panel Select De tails gt Lenses Orientation then change the setting from Normal to Al ternate These settings are also available by using the Tools gt Settings gt Calibration gt Lenses Orientation tab If the camera is hanging upside down you will need to use the Alternate position It is recommended to not leave the cameras set too close to 90 i e 85 to 95 since it may appear Normal or Alternate and result in non repeatable calibrations Figure 3 13 Lenses Orientation Window Settings Calibration File Structure Tracking C
282. icitly requires that the wand capture procedure of having the wand oriented in all three coordinate axes x y z is followed The result ing calibration calculation converges much faster and is a little more ac curate Origin Offset This allows for translation of the capture volume s origin from the L frame s coordinates The values are specified in the units that the system is calibrated in see Calibration Frame The calibration L frame may then be positioned anywhere in the motion capture area This is useful for two possible reasons 1 All cameras do not see the calibration frame but you want to use it to position the cameras In this case you can move the calibration frame to where it can be seen and enter the Origin Offsets measured from the true origin to the temporary location of the calibration frame 2 You want a different location for an origin for any reason 4 20 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Settings gt File Structure Tab Figure 4 17 File Structure Settings Settings amp Tracking Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins Folder Naming Settings Single MarkerSet legacy file naming enabled C Supress HTR writing when saving Captures VCFiles YC VCFilesi capture i lt capture gt ee VC files an TC files AMI CGY files y ANB files ane AVI files CGY WAN files Tc e
283. ics File 4 11 Export Prj File 4 15 Export SIMM Motion File 4 12 Export Skeleton mod File 4 11 Export ts Time Series File button 8 32 Extending the Seed Calibration 6 20 Extra Stretch 9 20 Falcon Camera Settings 5 11 FIFO slider 4 61 File Cleanup 10 7 file management 4 3 File Menu 4 3 File Structure Tab 4 21 Filters 8 5 Flash Drive Software Installation 1 4 Floor Calibration 6 14 Folder Naming Settings 4 21 Force Plate 3x3 Orientation Matrix C 4 6x6 Calibration Matrix C 9 Calibration Matrix C 4 Channel Order E 11 File Data C 4 Forces 4 49 Number C 4 Optional Length amp Width C 4 Scaling Factor C 4 C 6 True XYZ Origin C 4 XYZ Location in Video Coordinate System C 4 Force Plate Calibration 4 48 Force Plate Configuration 4 47 Force Plate Position and Orientation 4 48 Force Plate Specs 4 48 Force Plates List 4 48 Force Vectors 4 31 Forcepla cal Index 3 Cortex 2 1 Reference Manual File Format C 1 Forceplate Configuration Forceplate cal File Setup C 1 Frame Counter 4 80 Frame Number 8 3 Frame Offset 10 5 Frame Offsets 4 30 Frame Rate 5 2 Frames Selecting 8 5 gait analysis 3 2 gait lib C 2 Gauss Newton 9 24 General C 1 ghost markers H 1 Global Marker Data Adjustments 10 4 Global Scale 9 23 Going Live 5 11 Greyscale Calculation Floor 4 28 H Hardware 5 11 required 1 3 Hardware Masks 5 11 Hardware Sync 5 3 Hawk C
284. if you record your VC files at 60 Hz the VC frame advances twice for every single frame advance in the Refer ence Video when you play it back or step through the data The SMPTE time code is visible on the Real Time Dashboard Motion Analysis digital cameras can use the Time Code Reader PCI ver sion card installed into the Cortex Host computer It reads the LTC Longitudinal Time Code from the RCA audio connector on the Time Code card creating a trialN tc file time code when you collect a tri alN veX dataset It is automatic if you have the Time Code Reader option card installed in your Cortex computer There is a BNC type connector on the card as well it appears that the Time Code Reader will genlock to the black burst video signal but that is not needed Cortex reads the cur rent time code when the data collection is started and time stamps it into the TC file The current time code also displays on the Post Process Dash board A simple test program called TimeCodeReader exe is distributed with the latest Cortex releases It is a stand alone program which launches and in a small window reads the current value of the Time Code Reader in the Cortex Host computer It is useful for testing to see if the Time Code reader is working Without a card installed it just leaves a blank display With a time code reader card installed it displays the current time code static or not When the time code starts to advance you can immediately
285. ignal applied to the camera This is done using the BNC connector of the 2 meter long Eagle Test Cable that came with the Motion Analysis system It connects to the master camera using the AUX connec tor on the back of all the MAC digital cameras Failure to connect the video signal to the Master camera will show up when you press the Run button The slave cameras will send data but the Master camera will not This feature is available on all Motion Analysis digital cameras and can be set to any multiple of the NTSC or PAL frequencies that your mocap camera will allow So you can capture at 59 94 NTSC frequency or 119 88 2X NTSC or 179 82 3X NTSC or higher if your motion cap ture camera will allow it For NTSC genlock sync you need to set the camera frame rate to 59 94 Hz on the Cameras sup panel For PAL gen lock sync set the camera frame rate to 50 Hz or 100 or 150 or 200 or so on The slave cameras will follow the master camera without any extra wiring Displays the selected camera number and its corresponding IP address software version number along with the date and time the camera soft ware was compiled Sets the selected camera as a master camera A master camera generates synchronized pulses to the rest of the cameras within the system so that all camera shutters are opening and closing at the same rate Only one master camera can be set for each system 5 3 Chapter 5 System Tab Cortex 2 1 Reference Manual
286. ile gt Save MarkerSet or Save MarkerSet As if you want to give it anew name MarkerSets can also be selected moved between the Local folder and the System folder in the Motion Capture gt Objects panel 9 1 Chapter 9 Model Edit Tab Cortex 2 1 Reference Manual Markers Panel The Markers panel is intended for building and modifying marker sets Figure 9 1 Markers Panel Markers TreeView Clear MarkerSet Create Linkages for Template LID BEE Marker Names N 1 M_TopHead 2 M_L_Head 3 M_B_Head 4 M_R_head 5 M_F_Head 6 M_RShould TEA 7 M_LShoulg diac 8 M_TopSpit Delete 10 M_FLShoulder 11 M_FChest 12 M_RBicep 13 M_RElbow 14 M_RForearm 15 M_Rvrist 16 M_RPinky 17 M_RThumb 18 M_LBicep 19 M_LElbow 20 M_LForearm 21 M_LWrist 22 M_LPinky 23 M_LThumb 24 M_Midback 25 M_ShoulderOffset 26 M_LowBack 27 M_RootOftset 29 M_BRHip 30 M_BLHip 31_ M_FRHip E 32 _ M_FLHip 33 M_RThigh 34 M_RKnee 35 M_RShin 36 M_RAnkle 37 M_RHeel 38 M_RMicfoot 39 M_RToe 40 M_LThigh 9 2 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab Clear MarkerSet This button clears out the capture s marker set linkages and skeleton defi Button nitions Create Linkages for This button must be clicked prior to creating linkages on the 3D View Template Button Linkages can be built by connecting the dots Linkages should reflect the rigid
287. ime Refer to Real Time Dashboard on page 4 71 pag Dashboard Information The Information Center gives the following information for the current Center capture from left to right e Cell 1 Number of frames in the current data set e Cell 2 Frame rate in frames per second e Cell 3 Up axis e g Y up Z up e Cell 4 Calibration units e g mm e Cell5 Analog sample rate samples sec If you leave the mouse pointer over the message its definition will pop up Figure 4 47 Information Center 500 700 800 900 1000 1100 1200 121 1434 1434 t Oooo SY veie 2 e a 1434 Frames 120 FPS Y Up Unitsimm _ Information Center Cells 1 through 5 4 59 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Setup Files cal Extensions Important Note Setup files are the main files used to set up and save all the variables in volved with capturing data in Cortex Every motion capture session must have a Setup file containing all system settings equipment parameters and other information related to the capture This file contains both equip ment parameters common to many different setups and calibration values unique to one particular session Among the data found in a capture file are e the camera setup e calibration setup and results e camera type and parameters e tracking parameters Data trials are stored in separate captures and their associated files In most cases you wil
288. ime analog data is processed frame by frame without the benefit of the full data set This has the following implications To set the baseline for the force plates the first frame of force data is used as the zero level Thus when you first connect SIMM to Cor tex you should make sure that nothing is on the force plates F 8 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module e Ifno MVC levels have been specified for some of the muscles a run ning tally of each muscle s maximum level will be kept and used to scale the EMG signals into the range 0 0 to 1 0 Thus if you want to accurately scale EMG levels throughout a real time SIMM motion import you should either specify MVC levels or have the subject perform MVCs just after connecting SIMM to Cortex Using the Mocap Model The Mocap Model SIMM has the ability to read tracked marker data and convert it into a mo tion by fitting a musculoskeletal model to it For this to work well the body segment lengths marker names and marker locations in the model must exactly match those for the subject whose motion is being recorded Because it is time consuming to measure and scale the body segments and measure and record the offsets of all of the markers the Motion Mod ule has the ability to automatically scale a pre made model the mocap model to fit the subject To use the mocap model select Open Mocap Model from the File menu SIMM will display a Windows
289. in the 3D view Marker ID is the same as Quick ID without the auto incre ment feature Exchanges the 3D positions of two selected markers Exchange requires that exactly two markers are selected The data is ex changed between the markers within the selected frames Calculates the values to place in the gaps with a cubic spline If you man ually select the endpoints of the gap before executing the join the func tion will fill the gap with a linear interpolation because the second deriva tive at the endpoints equals zero Selecting this will automatically fill a gap in selected frames of the XYZ marker data with linearly interpolated data The assigned Virtual Join definitions will be applied to XYZ marker data for the selected markers over the selected frames For all information re garding Join Virtual refer to See Join Virtual on page 8 24 8 15 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Calculate Virtual Markers 2 oN w Smooth E a Make Unnamed Sy Rectify Unnamed Cr Delete Unnamed Cut a This calculates the locations for all assigned virtual markers over the se lected frames For more information refer to For complete information on Calcium software and Calcium segment definitions please reference the Calcium for Cortex Quick Start Guide p n 651 1920 010 on page 9 24 Smooths data within the set frames with the selected filter type A Butter
290. in any program modes that reference this MarkerSet Additionally if this MarkerSet is part of a Capture loaded in Post Process ing the Capture will now refer to the new file name Loads only the calibration from a setup cal file or legacy project prj file 4 10 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface File gt Load Analog Setup File gt Select Raw Video File File gt Export File gt Skeleton Definitions Loads only the analog setup from a setup cal or legacy project prj file Analog setup includes forceplate channel names EMG channel names and other analog data to be digitized by Cortex during data collec tion Allows you to select the legacy camera 1 file vc1 for re tracking or re cording a new capture For Cortex 2 captures you should use File gt Load Capture Live for the same function Export HTR File Exports a file in HTR format which is commonly used in the animation software packages Export C3D File Exports marker positions and analog data in an open sourced file format viewable by many different software packages Export CRC File CRC Centroid Row Column data are the 2D data points in ASCII text format Usable by advanced users who want to reconstruct 3D positions of markers using their own software in post process mode only Export Kinetics File Exports Kinematics joint angles and Kinetics forces and moments data into
291. in the SIMM full body model SIMM rectifies smooths and scales EMG data so that it can be plotted and used to control the width and color of mus cles during an animation Any variables that are not force plate or EMG data are classified as other data SIMM does not perform any calculations on these data variables but they may be included in SIMM plots The importVariables txt file located in SIMM Resources mocap misc contains a list of variable names and attributes When SIMM processes an analog data file or an OrthoTrak XLS file it consults the importVari ables txt file to decide which variables to import and how to interpret them Each row in importVariables txt defines a variable to be imported The first column in a row specifies the name of the variable as it appears in the analog or XLS data file Since certain analog files support variable names with spaces in them the first column of the importVariables txt file must be terminated by a tab character SIMM considers all characters from the beginning of a row until the first tab character to be the name of the im port variable SIMM does a case insensitive comparison when matching variable names defined in importVariables txt with variable names in an analog data file Therefore the name Rt Tibialis would be considered the same as rt tibialis The second column in a variable definition specifies the type of the vari able It must be one of the following keywords f
292. ing any breaks in the stream of data for all markers Figure 8 20 Time Lines Time Lines DER Tracks to draw Named Only Unnamed Ony Both 1 M_TopHead 6 M_RShoulder 7 M_LShoulder 8 M_TopSpine 9 M_FRshoulder 10 M_FLShoulder 11 M_FChest 12 M_RBicep 13 M_REIbow 14 M_RForearm 5 SE Ries CS a tak 2 a 16 M_RPinky 17 M_RThumb 18 M_LBicep 19 M_LElbow 20 M_LForearm 21 M_LWrist Re an ae 25 M_ShoulderOffset 26 M_LowBack 27 M_RootOffset 28 M_Root 29 M_BRHip 30 M_BLHip 31 M_FRHip 32 M_FLHip 33 M_RThigh a _l ft C es a E eE E E C ee _ _ _ _____A7A EEE C ee _ _ _ SSD Ee Le CE eee 24 M_Midback ee ee Gd DT ET SS a SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSlF Fy D EA J T P ee eT _ _ ___ O EEE Xz CL T CE C b _ _ _ _ _ _ _ _ _ _ _ _ __ _ 47 U 1 lt Emptv gt 8 29 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Analysis Graphs Position Velocity and Acc
293. ing is not checked 4 33 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Search Tab Figure 4 26 Tools gt Settings gt Post Process Tools gt Search Tab Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc _ id Params Plugins Undo Tool Strip Min Size of Spikes mm Q Min Acceleration Gs Q Markers All One Auto Center 3D Display while Searching Gaps These settings change the functionality of the Search tool in Post Pro cessing Search For This setting indicates what should be searched for The things that can be searched for are Gaps in the data Spikes in the data and big accelera tions in the data Min Size of Spikes mm This specifies how big a data jump must be to be considered a spike Min Acceleration Gs This specifies how big an acceleration must be to be considered big Markers This specifies if the search should be performed on one marker or all markers 4 34 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Undo Tab Figure 4 27 Tools gt Settings gt Post Process Tools gt Undo Tab This tab allow the user to turn on and off the Undo function for post pro cessing data editing The Undo function can use high l
294. ing tools Any sub folders added to the Global Sky Files folder will appear in the list as sub folders This allows for the organization of scripts by category This contains a list of all the Sky files in a common network directory This location is intended to be a shared network folder accessed by users on different computers When you click a new file name any changes you made to the currently loaded file are saved automatically if the Autosave flag is set under the Options menu The currently loaded file name will continue to be highlighted for as long as that file is current The Cloud button to the right of Network Sky Files label brings up the Windows Explorer for the network folder This makes for easy access to all the standard Windows file system browsing and editing tools The Input Text area displays the currently loaded script This is what will be run when the Run button is pressed Right clicking in the Input Text window brings up a menu of editing tools e Undo One level of undo is available in the Input Text window e Cut Standard text operation e Copy Standard text operation e Paste Standard text operation e Delete Standard text operation 12 6 Cortex 2 1 Reference Manual Chapter 12 Sky Scripting Interface Output Drag And Drop Sky Functions e Run Runs the script Same as the Run button in the Toolbar e New Script Same as New Script operation in the Toolbar e Open Script
295. ion Calculations Binary Files ANB TRB and C3D E 14 Overview The files generated by Cortex fall into two main categories ASCII and binary ASCII files contain data in a text form that can be read by any text editor They usually have descriptive headers that indicate the nature of the data that follows Often these files are in a row and column format that allows data to be read and manipulated by spreadsheet programs such as Excel ASCII files are not compact and can be quite large Binary files contain raw binary data and are more compact than ASCII files They cannot be read by a text editor In general binary files are not meant to be read by the end user E 1 Appendix E Import and Export File Formats Cortex 2 1 Reference Manual mac_lic dat All Motion Analysis software requires a valid license to run The license is keyed to a particular dongle supplied by Motion Analysis which can be tranferred from one computer to another The license file is ASCII and has the unique name mac_lic dat It is lo cated in the Motion Analysis directory Only one license file is used for all Motion Analysis software Each additional software application be yond Cortex is given a separate line in the license file with the license type enclosed in square brackets followed by two license codes If you acquire new Motion Analysis software you must use a text editor to enter the new line in your license file to enable your
296. ions where details matter and looks are everything you will be glad to have your Calcium Solver skel etons under the skin of your final characters Cortex Skeleton Engine Selection The Engine Selection sets the method of calculating the optional skele ton model that can be calculated in Cortex There are two main skeleton engines available from Motion Analysis Skeleton Builder and Calcium Solver Cortex will run any skeleton engine that has been previously defined without any additional licenses To define or edit the skeleton def initions you need the Skeleton Builder or Calcium license items The skeleton model is saved with your marker set information in the MARS file The File gt Add MarkerSet menu item will load the skeleton along with all the other markerset information Post Process Skeletons can also be calculated in the Post Processing tab from your cur g y Skeletons rent XYZ data that is visible in the 3D and XYZ data views SkB Skeleton Skeleton Builder SkB skeletons are always calculated if the SkB Skele Builder Skeletons ton Builder option is selected You can see the Skeleton by selecting Show Skeleton from the right mouse menu in the 3D data view If you are using one of the streaming plugins like the Maya Talon plugin or the MotionBuilder plugin both the marker data and the calculated skeleton is available to drive your animated character from either the Real Time or Post Processing mode Chapter
297. ions of six different graphical panes which include Displays the live action in a capture volume or a replay of an AVI file You will need to have a DV Digital Video camera connected to the Host computer s 1394 Firewire port to see the live video in this window Displays a 2D image of the markers and their centroids Displays a moving 3D stick figure showing named markers virtual mark ers linkages and or a skeleton Displays graphs depicting the marker s positions in each frame Displays analog data graphs representing the force plate s output Displays the following data graphs for selected skeletal segments e Kinematics e Forces e Moments e Linear Movement e Angular Movement Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Analysis Graphs F7 Doc View F8 Web View F9 Presentation Graphs F10 Empty View F11 Graphics Only Ctrl G e Solver Stats Calculates and displays angles between markers distances between mark ers and position velocity and acceleration of a marker or groups of se lected markers Results can be saved as ASCII Time Series ts files For more information Provides an interface to open and edit most text based files and display them within the Cortex software Used for making Presentations with Motion Composer Provides an interface to open display and edit HTML files within the Cortex software Used for making Presentations with Motion Compos
298. itive offsets are allowed It is meant for visual ization of multiple data sets in the 3D window The first trial that is loaded must have enough frames to wholly accommodate the additional trials as 10 4 Cortex 2 1 Reference Manual Chapter 10 Plugins Tab Frame Offset Moving the X Panel to a New Tab additional memory for any additional frames is not allocated and can cause unpredictable results You can make one trial that has enough frames to fully accommodate all of the merged data frames and load that track data set first with the File gt Load Capture menu item The merged data does not get marker names or linkages unless you have a capture and marker sets defined for the additional tracks This offsets the first tracks file with respect to the second The first tracks file loaded must have enough frames to accommodate all additional tracks files If not unpredictable results may occur This is intended for viewing multiple trials To see the stick figures multiple marker sets must exist in your current marker set You can move the X panel to a different tab System Calibration Motion Capture etc with the Settings gt Plugins tab This provides a custom function that may help improve workflow Figure 10 5 Settings gt Plugins Tab Settings Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc This allows you to specify which tab a plugin panel is available in
299. jects panel select your new MarkerSet from the System Objects panel use the blue UP arrow to copy that to the current Local Objects folder Note You can also make a skeleton for this MarkerSet which can be either a Skeleton Builder or Calcium type skeleton and that can have a Mass Model associated with it Capture Outline Live Mode Figure 2 2 Capture Outline Live Mode Interface W File Layouts DataViews Tools Help Current Directory C Program Files Motion Analysis Cortex2 5 amples BioFeedT rak GolfS wing Calibration Motion Capture Post Process Model Edit Plugins Presentation Capture Outline Capture Outline Live Mode Club mars Golfer mars Markers Links Segments Segment Hierarchy Unnamec gt Click All None Ctrl Click Toggle 2 10 Cortex 2 1 Reference Manual Chapier 2 Planning a Motion Capture Session How to Rename a Capture in Cortex If you have made a mistake in the naming of the capture the easiest thing to do is to save the capture with a new name Trying to rename all of the files associated with the capture is laborious and error prone But if you use the Save Capture As dialog Cortex does not re write all of the files with the new capture names It will re write the tracks file s but not the Raw Video Camera VC files or the AVI files To be sure all files are rewritten use the File gt
300. ke notes and to fill in the Motion Cap ture Log A sample of this log is found in Appendix I Useful Blank Forms The take number Cortex file name and the duration of the take and any comments from the director or subject should be recorded The scribe can also do a time check using a stop watch to get the length of data capture for each new move The Cortex operator must make certain that the motion capture data is clean and trackable The Cortex operator must make sure the camera cal ibration is good and that raw calibration data is collected at various times throughout the session as insurance This is particularly important when there are several people around and a camera might get bumped acciden tally The operator should watch for reflections changing light conditions such as sunlight coming through a window or other external variables which may affect a capture 2 3 Chapter 2 Planning a Motion Capture Session Cortex 2 1 Reference Manual Additional Equipment Props Camcorder Still Camera Slate Board Markers Tape Pre tape Liquids Rubberbands Backup Media If the motion capture session requires the use of props this must be known to all parties well in advance The type of prop and its use are very important because reflective markers may have to be attached to the prop as well as the subject One marker may be used to track position but as many as three markers may be required to show all rotations
301. kerSet is added to the MarkerSet list for which ever mode Cortex is in Live vs Post Pro cessing Figure 4 9 New MarkerSet Interface File gt Add MarkerSet File gt Remove MarkerSet File gt Replace MarkerSet File gt Save MarkerSet File gt Save MarkerSet As File gt Load Camera Calibration ioixi M MarkerSet Type Identifying Template MarkerSet Prop MarkerSet OK Cancel Prompts the user to select a MarkerSet file mars and adds the Marker Set in the selected file to the MarkerSet list for the current program mode Removes the selected MarkerSet from the MarkerSet list for the current program mode In Post Processing and identified marker data for the MarkerSet is made unnamed Prompts the user to choose a MarkerSet file that replaces selected Mark erSet in the MarkerSet list for the current program mode The replace ment MarkerSet must have the same number of marker definitions as the MarkerSet that is being replaced All skeleton and event data for the MarkerSet is cleared This can be useful for switching between versions of a MarkerSet or the same template with different skeleton types Saves the selected MarkerSet into the mars file that it was loaded from If the MarkerSet is not yet associated with a file then the Save MarkerSet As prompt is displayed Saves the selected MarkerSet into a new mars file This is the file that now is referred to
302. l Loading Objects If you use zin group files they contain multiple objects in a group Mov ing the zin file from the left to the right expands the list to the individual objects in the zin file These group files are created by using the Save As Group and Save Selected As Group buttons on the right side of the Fu sion Object Loader window These buttons save all the objects or the se lected ones from the staging list on the right into the group file so you can preserve the list and the ordering in one group that you can re use You may find that the order will affect the speed and accuracy of Identify ing during the motion capture session You may use the Up and Down ar rows to move objects up or down in your staging list if necessary Refer back to Figure 7 3 You will find an example of a group of objects staged and ready to load Note it includes both prop and prj type objects Once your staging list is complete all the objects contained in it can be loaded into the Additional Tracking Objects list at the press of a button Since you cannot load objects while capturing data there are Pause and Run buttons in the Fusion Object Loader to allow you to control the cap turing state of the system Next to the Pause and Run buttons are the Load Objects and Unload Objects buttons These are used to move the objects into and out of the Additional Tracking Objects list From the paused state press Load Objects You will then see tha
303. l The Output panel is used when the motion capture recording is initiated It is set by the following procedure Choose the output file type at least 1 Enter a file name Set the file length in time If necessary set the external trigger mechanism Pons Figure 7 5 Output Panel Objects Output Output Files C Raw Video c C Analog anb C Reference Video avi C Reference Audio wav C Cyber Glove cgv C Tracked ASCII tre C Tracked Binary trb C Events evt Settings Capture Name olfSwing_ Trial ean eM Auto increment Min Trial Digits 1 Duration seconds 20 C Enable COM port trigger C Post Trigqger Mode Load Last Capture Generated Files Setup WithE vents cal Golfer mars Club mars 7 9 Chapter 7 Motion Capture Tab Cortex 2 0 Reference Manual Output Files Settings Note OK to Overwrite Enable COM1 Trigger Post Trigger Mode Load Last Capture The Output files are the files generated during a motion capture session This section of the Output panel allows you to choose which files are to be produced and saved in the capture file directory Settings allows you to provide the specifics for your generated output files This includes the name of your files the trial number and the dura tion of the trial The duration lets you set the length of the motion capture so there is little wasted time in the session VC ANB
304. l time making Cortex a suitable engine for a number of widely used 3D an imation packages as well as custom applications created using the sup plied Software Developers Kit SDK Being a real time application the results of a motion capture session can be viewed instantly while simulta neously saved in several file formats In addition you can graphically edit data with a complete suite of tools without resorting to other off the shelf software packages Cortex handles image data from systems comprised of up to 250 cameras System setup and calibration is fast and simple with immediate feedback and a high degree of accuracy and precision Motion capture sessions are managed using directory and file access tools and the motion data gener ated is of the highest quality Post Processing data is accomplished graph ically using intuitive controls integrated with mouse and keyboard func tions for fast and easy editing Model Edit features give you access to the properties of the current set of named markers virtual markers linkages and skeletal segments Cortex combines three major functions into a single software package 1 Calibration of your capture volume Tracking and identifying marker locations in your calibrated 3D space 3 Post processing tools for tracking editing and preparing the data for other packages The advanced calibration procedures calibrate the 3D volume with ease and accuracy Options for using the software inc
305. l Center of Mass alus ri ack 4 U_4 lt Empty gt cae 5 U_S lt Empty gt 6 U_6 lt Empty gt Additional 3D Display Settings m en lt Empty gt 0 704 4140 2 28 En __y T i T T T T T T T T T ray 100 200 300 400 500 600 700 800 900 1000 raies 00 0 00 mma 4 BI bee 12 Loaded Capture C Program Files Motion Analysis Cortex2 Samples 16 Camera Calibration Face Bady DaveROMI cap 1080 Frames 60 FPS Y Up Unitsimm 10 Set the shutter speed in the Cortex software so the markers are bright and have a good threshold setting usually about 500 11 Place the calibration L frame in the center of the taped area Note The cameras need at least 20 minutes to warm up before collecting cali bration or trial data Tracking With More As the subject moves from one region to the next in a multiple region cap Than 8 Cameras ture volume Cortex has no problem as the subject leaves the view of some cameras while entering the view of others The only requirement is that at least two preferably three or four cameras can see the subject at all times Chapter 3 Camera Setup Cortex 2 1 Reference Manual Using Many Cameras in a Small Volume For additional cameras to be effective they must be sufficiently far apart so that the rays from a given marker to the two adjacent cameras subtend a large enough angle to yield good positioning data It is possible to use eig
306. l begin a session by loading an existing setup file editing it as necessary and saving it in the directory where the motion data is to be saved Any time you calibrate the system or edit capture pa rameters you should save the setup file to disk to retain the new informa tion Cortex can read project files from older EVaRT and Cortex software ver sions for backwards compatibility Setup files contain ASCII data and it may be useful to view them using any text editor however you should not edit them in a text editor as that can result in a corrupt file MarkerSet Files mars Extensions MarkerSet files contain the following elements e the markerset names and colors e linkages and colors e template information e skeleton types and skeleton definitions 4 60 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Viewing Sample Data Sample Data Set Note To become familiar with Cortex we will start by replaying some sample data This is done by loading a sample capture found in the Samples di rectory 1 In live real time mode select File gt Load Capture Live Navigate to Program Files Motion Analysis Cortex2 Sam ples BioFeedTrak GolfSwing 3 Double click on GolfSwing_1 cap to load the Capture file Click the Run button on the Real Time Dashboard At this point the ac tion on the screen is a simulation of a live motion capture session Cortex is processing the data from the stor
307. l coordinate system LCS with origin at the geometric center of mass of the markers and initial orientation defined by the placement of the prop in the field of view when the prop was created Local coordinate system will show if Show Skele ton and Show Skeleton Axes boxes are checked with the XYZ gt RGB convention of showing a coordinate system 3 The single bone Skeleton is calculated using the Global Optimization method which is the same method as is applied to the generally more complex multi link Calcium models Translations and Rotations are reported with respect to the global coordinate system as defined by the placement and measures of the L frame 4 The Quick Prop button generates a prop from the selected un named markers in the 3D view Default marker and prop names are used which can be edited by selecting the prop in the Model Edit view If marker ordering is important these can also be edited in the Model Edit Tree View with the Prop selected 5 Props are saved in their own file with the unique prop extension They can generally be used where ever a MarkerSet is used including objects selectable in the Motion Capture gt Objects panel under the Open Fusion Object Loader button 6 If you use a Prop and a MarkerSet more than an single object the trb and tre files you generate will have a file name that includes the Prop or MarkerSet name which is different from the anb avi or other files associated with the capture
308. l fix a bumped camera all within 60 seconds It is one of the most powerful tools in Cortex To use it check the Refine Camera Positions check box press the Run button when con 6 14 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab Modify Only the Selected Cameras Camera Position and Properties nected to your cameras Have a subject move about in the capture volume Like with wand calibration you must cover the entire capture volume and field of view for each camera with any marker data If you get good cov erage then refined calibration will be very good If you get only partial coverage then you the results may be worse than not doing the refine When checked the seed wand and refine calibrations will only affect the cameras that are selected on the dashboard The panel on the bottom of the Calibrate panel displays the details of the selected camera in the 2D view You can move and rotate the cameras in the 3D View by changing the X Y Z coordinates and the Elevation Azi muth and Roll angles This can be helpful to see if moving the cameras will help with seeing the volume better Once you have finished posi tioned the cameras select File gt Save Setup As to save this camera configuration for viewing at a later time Figure 6 11 Selected Camera Information Refine Procedure Property Camera No 1 2470 197 2514 597 2939 508 Elevation 32 12 Azimuth 132 15 Roll 19 02 Principal Pt
309. l when talking to Motion Analysis Customer Support staff a Unplug the network cable from the back of the computer and plug it back in b Do the same for the connectors on the EagleHub You should hear an audible Click when inserting it back into the jack If Windows Updates has been recently run they may be running in the background there may be a possibility that the Microsoft Win dows Firewall was either installed or turned on This will need to be turned off as well as any other Firewall software installed on your motion capture computer Because of the nature of the digital cam eras it is required that the network coming in to the computer on a particular IP address is open for streaming data If your facility requires a Firewall to be installed for their network it will need to be configured to leave the camera network untouched and open You can turn off the Windows Firewall by going to the Start gt Set tings menu in your Windows desktop and then selecting Control Panel gt Security Center This is a feature in Windows XP Service Pack 2 and later software 3 23 Chapter 3 Camera Setup Cortex 2 1 Reference Manual 4 Double check to make sure the Network Address that is set in Cortex is the same as the Network Address that is assigned to your Network Interface Card NIC To do this follows these steps a From your desktop select Start gt Settings gt Control Panel gt Network Connections You should
310. lates Line Description Force plate number followed by K to indicate a Kistler force plate Force plate scaling factor and optional length and width of force plate 8x8 force plate calibration matrix created by the user 1 2 3 4 5 6 7 8 9 1 0 11 Xo Yo Zo position of the force plate transducers in cm provided by the manufacturer 12 Xc Ye Zc XYZ location of the geometric center of the plate with respect to your video coordinate system the video calibration system s origin measured in cm 3x3 force plate orientation matrix to make the force plate coordinate system match the laboratory coordinate system C 3 Appendix C Force Plate Configuration Forceplate cal File Setup Cortex 2 1 Reference Manual Force Plate File Data Force Plate Number Force Plate Scaling Factor and Optional Length amp Width Force Plate Calibration Matrix True XYZ Origin XYZ Location in Video Coordinate System 3x3 Orientation Matrix A unique number is assigned to each force plate in the system The scaling factor depends on the force plate manufacturer and the gain setting Length and width are optional and are measured in cm Length and width orientation is also dependent on the force plate manufacturer Refer to later sections specific to the manufacturer of your force plate The calibration matrix transforms the output of the force plate into forces and moments Refer to the section later in this a
311. layed in the Message Bar indicating recorder filename stop time and any available statistics ND G 2 Cortex 2 1 Reference Manual Appendix G Synchronizing Digital Video with Cortex Capturing Digital Video in CortexDV from Cortex Note Note Note Note Cortex indicates the action needed on the Cortex computer CortexDV indicates the action needed on the CortexDV computer 1 Ensure the CortexDV host and the Cortex host are connected to each other via a TCP IP network connection 2 CortexDV Launch CortexDV on the video capture host 3 Cortex Launch Cortex on the Cortex host Note launch order is unimportant however if Cortex grabs the camera capture device first i e displays Reference Video window CortexDV will not have access to the camera Cortex will grab the camera when you press the F1 key in a capture window and release it when you select another key F2 F3 etc 4 CortexDV Select the desired camera capture device from Camera dropdown If there is a single video camera connected to the host sys tem CortexDV connects to this camera automatically 5 Cortex Activate the Reference Video avi checkbox in the Motion Capture gt Output panel Press the F1 key to show video and grab the DV camera 6 Cortex Press the Record button 7 CortexDV On Record CortexDV will record the file specified by Cortex to the directory specified by Cortex or if not present to the lo
312. le Host Computer Eagle Hub Ethernet Cable USB Cable Before you plug the NI USB device into the host computer you must first install the NI Acquisition software For using the NI USB 6218 A D de vice you need to have the NIDAQ software version 8 3 or later in stalled Run the National Instruments software installation accept all the defaults then let it finish and re boot your computer This may take 10 15 minutes The remainder of the process takes less time For more informa B 5 Appendix B Analog Input Hardware and Software Cortex 2 1 Reference Manual tion please refer back to Installing NIDAQ Software on an Cortex Com puter on page B 3 Second Install 1 Plug in the A D device NI USB 6218 will be used as the example the Hardware below l 2 You will then automatically go through the Found New Hardware Wizard operation for a USB device Figure B 2 NI Measurement and Automation Explorer USB 6218 Configuration Interface X NI USB 6218 Dev1 Measurement amp Automation Explorer DER File Edit Yiew Tools Help Configuration i GSfProperties X Ebself Test MH Test Panels gt Pride Help Ey My System ala Data Neighborhood Name value Geack ral R PJserial Number OxESAE 4 Devices and Interfaces NI DAQmx Devices NI ANI USB 6218 Dev1 DAQmx Device F Ports Serial amp Parallel PX PXI System Unidentified G3
313. lean up data will vary significantly from one user to another These tips are guidelines that outline a general approach to successful editing sessions e It is best to start identifying from Frame 1 forward Then identify from the last frame backwards This entails naming unnamed markers using the Marker ID and Quick ID tools e Use of Rectify over small frame ranges may help in cleaning the data by taking unnamed data into named tracks e After identifying the Post Process tools can be used to fill gaps and cut out unwanted data sections fix abnormalities and smooth anoma lies and can be used to exchange switched markers Note It is recommended to save your files often especially when perform ing heavy edits e Many users will select all markers and all frames and execute a Join Linear or Join Cubic and possibly a Smooth as a very last editing step e Learning and using Hot Keys is critical to high productivity 8 33 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual 8 34 Chapter 9 Overview Note Model Edit Tab Overview Markers Panel Tree View Panel The Model Edit tab provides tools to build and modify the model parame ters that are mandatory for the MarkerSet file These parameters include markers names and colors virtual markers linkages between markers skeleton types and segment names It is important to save your MarkerSet after building the model by select ing F
314. lect Network Connections gt Local Area Connection right click Properties gt Con nection and use the following items e Internet Protocol TCP IP Use the following IP Address 10 1 1 199 e Subnet Mask 255 255 255 0 e DNS Server settings do not matter e Other addresses will also work as long as you are consistent with the camera addressing and do not overlap IP addresses The default camera addresses as configured when they are built start at 10 1 1 201 for camera number 1 with ascending numbers For example e Camera 1 10 1 1 201 e Camera 2 10 1 1 202 e Camera 3 10 1 1 203 All have sub net masks of 255 255 255 0 It is not necessary for the cameras to have ascending numbers When you Connect to Cameras in Cortex the software polls the network camera network and reports the number and the kinds of digital cameras A 7 Appendix A System Hardware Interconnections Cortex 2 1 Reference Manual A 8 Cortex 2 1 Reference Manual Appendix A System Hardware Interconnections A 9 Appendix A System Hardware Interconnections Cortex 2 1 Reference Manual A 10 Appendxs Analog Input Hardware and Software Overview Installing NIDAQ Software on an Cortex Computer Analog Signal Naming Conventions 32 Channel 16 Bit NI USB 6218 Configuration NI USB 6259 Analog Channel Connections Overview The Cortex system can accept analog data from external devices and syn
315. lected Frames can be independently picked by pressing the Shift key and middle clicking on the XYZ Graphs Select All Frames default Hot Key is the A key displays and selects all frames in the data set This is also a right mouse menu item on the XYZ Graphs All Motion Analysis digital cameras generate extremely clean noise free data For the majority of data captures it is never necessary to modify the data by filtering or smoothing Occasionally however it is useful to re move artifacts in the motion capture data This can happen in the case of captures which contain a high number of marker occlusions or a large amount of marker merging as it frequently happens with face tracking for example For these purposes Cortex provides 3 different smoothing filters that can be applied to tracking data Each filter affects only the currently selected markers over the currently selected sample range All three dimensions X Y and Z of each marker are smoothed To access the options dialog select the Post Process gt Options button 8 5 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Figure 8 3 Tools gt Settings gt Post Process Tools gt Tools Tab Settings 8 6 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Butterworth The Butterworth filter is a low band pass filter with excellent mathemati Filter cal characteristics for biomechanical motion The purpose is to remove high frequ
316. les F 6 opening C3D files F 2 opening TRB C files F 2 opening XLS files F 6 real time import F 7 Motion Trails 4 32 Move 2 5 Move 1 Frame Button 8 3 Move to Lowest Highest Frame 8 3 Moving Force Plate Options 4 48 mport Skeleton mod File 4 11 Muscle Name Selection EMG 5 14 N Network Configuration A 7 Network Interface Card NIC A 7 New MarkerSet 4 10 New Subject Button 4 74 New Subject button 4 74 NI PCI 6071E B 1 NI USB 6218 B 1 B 5 NIDAQ Software B 3 NRSE 5 16 Number of Cameras 4 38 Index 5 Cortex 2 1 Reference Manual OBJ skins 9 6 Objects Panel 7 4 Offset X Y Z RX RY RZ 9 10 Open Fusion Object Loader 7 4 Optional False 9 13 True 9 13 Options to Change 8 19 Orient Body 9 24 Origin Offsets Tab 6 6 OrthoTrak 1 15 Intended Use 1 15 Other 4 20 Outline 4 22 Output Files 7 10 Output Panel 7 9 P3D E 11 Package Capture 4 5 Panel Buttons 4 58 Paste 8 18 Pinging a camera 3 25 Play Backward Button 8 2 Play Speed 8 2 Playback Tab 4 29 Plugins 4 58 Plugins Tab 4 41 10 1 pop up menu 4 64 2D Display 4 67 3D Display 4 64 Analog Graphs 4 68 XYZ Graphs 4 69 Pop Up Menus 4 64 Position Velocity and Acceleration Tab 8 30 Positioning Cameras 6 9 Post Process 4 58 Post Process Dashboard 4 81 Post Process mode 4 62 4 81 Post Process Tool Strip 4 81 8 11 Post Process Tools Tab 4 32 Post Processing 8 1 Square Data 6 2
317. lfS wing_2 anb Video Data RawFiles GolfSwing_2 GolfSwing_2 avi Audio Data Timecode CyberGlove Data E MarkerSets Body mars Club mars E Trb Marker Data GolfSwing_2 Unnamed trb GolfSwing_2 Golfer trb GolfSwing_2 Club trb Trc Marker Data Htr Skeleton Data Event Data M Load Setup Setup WithE vents cal File gt Save Capture Saves the Capture currently loaded into Post Processing All MarkerSets and data files associated with the capture are loaded The Setup File asso ciated with the capture will also be saved File gt Save Capture Save the Capture currently loaded in Post Processing under a new name As New processed files trb trc htr evt are generated for use by the new Capture The new Capture will refer to same raw files vc anb tc avi wav cgv that the original one referred to Since the raw files are not du plicated when doing a Save As it is important to be careful when deleting raw files Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface File gt Package A capture is often composed of several files not necessarily in the same Capture amp Package folder Package Capture provides the user with an interface that collects Capture gt With files in the Post Process capture so that they can be moved to a new loca Options tion computer There are options for selecting which files should be col lected This is useful since e mailing tran
318. lick on the color property and select from the drop down menu Extra Stretch The Extra Stretch factor is the amount in percent refer to Figure 9 11 that a link is allowed to stretch beyond the measured template The tem plate is usually measured from a Range of Motion capture and that motion is not always an adequate representation Data captures often push the body closes to its limits The Extra Stretch gives an appropriate margin to allow real captures to go beyond the template Figure 9 11 Link Property Values Markeri M_TopSpine Marker2 M_LShoulder Color m1 Extra Stretch 0 What confuses the user most is that rigid body parts the head is a good example will not have their markers move around much no matter what data you use to create the template So almost any template will work to give you values with high confidence Conversely if you have links that are stretchy it s easy to not get a good template for it and so your confi dence in the template will be less Because of this many users think that the Extra Stretch factor is a state ment about the elasticity of the link which it isn t A link could be put be tween a hand marker and the toe marker but as long as it had sufficient data for the template Extra Stretch could be set to 1 the lowest and have it work just fine Multiple Link Selection Multiple links can be selected by pressing the Ctrl Shift buttons on the keyboard and clicking on the individual links
319. ll be file per mission issues when running and closing Cortex Use the search function in the Control Panel and search for UAC and then turn it OFF You can keep both Public and Private firewalls turned ON in Win dows 7 and still collect data from your Motion Analysis cameras From the Control Panel you can specify which programs will be allowed to ac cess the Ethernet on a per program basis You need to allow all versions of Cortex that you will use for data collection Note that you must press the OK button for any changes to take place 1 7 Chapter 1 Introduction Cortex 2 1 Reference Manual Software Packages within Cortex The following are software products offered by Motion Analysis that are integrated within the Cortex user interface These files will require a li cense file update Calcium Calcium is the graphical user interface to the Solver engine Solver is a powerful numerical tool for calculating skeleton motion from marker data The Calcium interface in Cortex is what allows you to correlate the positions of a marker pose to the initial pose of a skeleton The skeleton is usually created in an outside animation package such as Maya 3D Studio Max or Kaydara and then exported to an HTR file by a Motion Analysis file IO plugin for that package Figure 1 4 Calcium Interface in Cortex Cortex Jodi cal Jodl_TwontyTwo2 cap Y E Me Layouts Dataviews Toos Heb Queri Dreciory C Prog am Files Motion Anal
320. log displays become static graphs rather than having the oscilloscope style seen during collection and replays of raw data The 2D Display and Skeleton Graphs become entirely unavailable but the XYZ Graphs become available 3D stick figure images can be rendered for all of the data set rather than just the 256 frames available in Real Time mode Post Process mode allows you to edit the tracked data generated during a motion capture session Editing can be performed upon groups of markers or one marker at a time From the Menu Bar select File gt Load Capture Double click on GolfSwing_1 cap Leave the 3D figure currently in the top pane in the 3D view From the Menu Bar select Layouts gt 2 Panes Top Bottom Left click on the bottom pane This action will select this pane Press F4 on the keyboard or choose Data Views gt Marker XYZ Graphs Select marker 15 on the MarkerSet panel right side OarPenn N 4 62 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface The two Graphics Panes used often simultaneously during a Post Process editing session are the 3D View and the XYZ Graphs shown here Notice that the Post Process Dashboard has replaced the Real Time Dashboard The data shown in the XYZ Graphs represents the X Y and Z coordinates of the selected markers throughout the capture period Figure 4 49 Viewing Tracked Data in Post Process Mode iW I Fie Layouts DataViews Tools Help Curent Dire
321. long a line or relative to a plane can be accomplished in real world measured values using the units of calibra tion as the units of measurement or as a ratio In the case of a line the ratio is based on the distance between the two markers defining the line In the case of the plane the ratio is based on the distance between the two markers defining the Y axis of the plane Figure 9 7 Example Virtual Marker Setup Virtual Marker Definitions Three Marker Value Three Marker Ratio Two Marker Value Two Marker Ratio EMR Enter Name of Virtual Marker enterHead Origin Marker Long Axis Marker Plane Marker 5 M_F_Head 3 M_B_Head 4 M_R_head Snap to this Marker optional 0 00 0 00 Perpendicular mi 0 00 E SS PS SS PS See Calculate Virtual Markers New Marker Definition Delete V Marker Definition Ee mt Degrees of Freedom A segment s movement characteristics can be expressed as having various degrees of freedom For example if a single marker placed on the right shoulder is used to define the origin of the right upper arm and we track this marker through space creating a trajectory we will express the move ment of the right upper arm origin as having 3 degrees of freedom trans lations in X Y and Z If we add another marker to the right elbow and track it along with the marker on the right shoulder we can now express movement of the right upper arm segment as having 5 degrees of freedom translations in
322. lude 1 Reference video capture synchronized with the CortexDV software either on your capture computer or on one or more auxiliary comput ers 2 Synchronized analog channels capable of collecting from 32 to 192 channels of analog data at any frequency between 60 and 5000 Hz 3 Genlock to your studio camera with the Motion Analysis cameras 4 Calcium Solver for generating constant bone length skeletons for high quality animation 5 OrthoTrak clinical gait evaluation module 6 SIMM Software for Interactive Musculoskeletal Modeling 7 KinTools RT a Real Time kinetics and kinematics calculation engine 8 Motion Composer used for producing packaging and presenting data reports 1 2 Cortex 2 1 Reference Manual Chapter 1 Introduction System Requirements for Cortex Table 1 1 Required Minimum and Recommended Specifications Required Minimum Specifications Recommended Specifications Dual 2 0 GHz CPU up to 12 cameras Quad Core 3 2 GHz CPU 4 GByte RAM 8 GByte RAM Windows XP Pro with NET 2 0 or later operating system Windows XP Pro with NET 2 0 or Windows 7 64 Bit operating system OpenGL video card with 128 MByte RAM capable of 1280x1024 resolution OpenGL video card with 256 MByte RAM capable of 1280x1024 resolution 19 inch or larger monitor capable of 1280x1024 resolution Dual 20 inch or larger monitors capable of 1280x1024 resolution
323. markers segments background foreground Real Time floor and post floor for your capture Marker Color 1 Marker Color 2 Marker Color3 Marker Color 4 Marker Color 5 Marker Color 6 Marker Color 7 Marker Color 8 Marker Color 9 Marker Color 10 i Marker Color 11 Marker Color 12 i Marker Color 13 il Marker Color 14 Marker Color 15 Marker Color 16 Background Foreground Real Time Floor Post Floor 3D Background Synthetic Data Segments AG b gt eee Invert Colors Defaults Close To change the color for any item just click on the colored box and a color palette window opens up This lets you choose the color blend for that marker The colors are remembered the next time you launch Cortex 4 43 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tools gt Misc Note These are functions that are not a part of the normal operation of Cortex or need a place in the menus so that a hot key can be assigned Tools gt Misc gt Replace Loaded Analog Channel Names Occasion ally there are situations where an incorrect analog channel name can oc cur Examples of this can be seen when analysis software like OrthoTrak requires specific muscle names for the analysis In these cases the ability to go back and rename the problem analog channel is required To Rename Analog Channels follow these steps 1 Load the Capture or with legacy data Loa
324. me time in two different Graphics Panes Click Post Process from the Mode Buttons From the Menu Bar choose Layouts gt 2 Panes Top Bottom Left click in the Top Pane to select it Activate the 3D View by pressing F3 on the keyboard of by choosing Data Views gt 3D View from the Menu Bar Left click on the bottom pane to select it Activate the XYZ Graphs by pressing F4 on the keyboard of by choosing Data Views gt XYZ Graphs from the Menu Bar It will dis play X Y and Z tracked position data and optionally residuals and the cameras that triangulated the markers Ponsa on 8 1 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Viewing Your Data The XYZ Graphs will display none any or all markers you have selected in the Post Process tab Selection of markers from a marker list is done with standard selection methods including Shift click Ctrl click and click drag over the marker names In addition the top row of the marker list acts as a special selecting button Markers can also be selected by sim ply clicking and Ctrl clicking on markers in the 3D view The Post Process tools heavily utilize the Post Process Dashboard con trols These controls are itemized and described as follows from left to right in Figure 8 1 Figure 8 1 Post Process Dashboard Move to Active Play Pause Play Speed Frame Lowest Highest Frame Frame Selectors
325. mera at any time You Camera s IP need to make sure that you do not use duplicate numbers though It is rec Address ommended that you use the same IP address number scheme as used when the cameras are first shipped 10 1 1 xxx The last three digits should be any number between 1 and 250 In the event that your local area network is set to a 10 1 1 xxx IP scheme you can also use 10 1 2 xxx for the camera network Eagle Host computer EagleHubs cameras etc 5 4 Cortex 2 1 Reference Manual Chapter 5 System Tab Loading New Camera Software Note Loading New Eagle Hawk Camera Software Note Note Raptor camera systems will update all of the cameras all at once when loading the new camera software Eagle4 Eagle and Hawk cameras must have the new software loaded one camera at a time The software loaded into the camera must be of the form rom_filename_date bin for non Raptor cameras and file name date cam for Raptor series and Hawk M cameras The specific date in the file name may vary Hawk i cameras require a different version of the rom bin software from the other digital cameras Loading of incorrect software may cause your Hawk i camera to cease functioning The rom bin file for the Hawk i cameras is found in a folder of its own under the Camera Software direc tory Install the new software as follows 1 Obtain the latest camera software file from the Camera Software folder associated with this Co
326. meras must be increased when e the motion of the subject becomes less constrained e the number of subjects or objects increases e the capture volume increases 2 As more cameras are used each camera should view only a portion of the capture volume to achieve higher accuracy and prevent too many cameras from seeing any one marker For large capture volumes with a large number of cameras 10 it is recommended that all 4 mark ers on the calibration L frame are seen in only 1 4 to 1 2 of the cam eras You can then use the Extend Seed function see Extending the Seed Calibration on page 6 20 to calibrate the remaining cameras Note When more than 5 or 6 cameras see the same marker the accuracy of tracking is not increased and computation time increases 3 Camera views should not include areas outside the capture volume to ensure the highest possible spatial resolution The number of cameras in a typical motion capture setup can be as few as 2 or as many as 250 The following provides some guidelines for deciding on the number of cameras to use In the following figures all measure ments are in meters 6 Cameras For motion capture involving only one subject where the occlusion of markers is not a problem six cameras may be adequate This configura tion is often used for gait analysis and other similar biomechanical appli cations The two end cameras are often tilted so that the long axis of the view areas is vertical For optim
327. milli meters measured from end marker to end marker 1 In the Wand Calibration box on the right hand side set the wand length to your wand size Make sure that you are using only a three point wand 2 Set the duration of the trial The duration should be sufficiently long enough to wave the wand through most of the volume that you want calibrated Smaller volumes take less time to complete 3 Click the Collect and Calibrate button and start waving the wand side to side and up and down through the volume You want to spend about 1 3 of the data collection time with the wand parallel to each of the three X Y amp Z axes It is recommended that you view the wand movement through the volume at least for the first few times To do this you must select Layouts gt Top Bottom One window should reflect the 3D view and the area where it is possible to see the wand waving through the volume The other is the 2D view where the individual camera coverage of the wand in the volume is seen To show all cameras press the All On button In the 2D view the display is automatically smeared in showing the wand data This shows the volume coverage for each camera A good wand calibra tion will fill most of the 2D view for each camera 6 11 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Figure 6 9 Seeded Cameras 3 D and 2 D View all cameras on EVa RealTime File Layouts View Tools Help a fa Setup Il Calibration Motion
328. mined from the marker locations Velocity Calculation is done with a central difference Let FR represent the Frame Rate of the camera Time difference between frames 1 FR in the below calculations Velocity Calculation for frame i with a Frames Factor of 3 vX1 i FR X itl X i 1 2 vY1 i FR Y itl Y i 1 2 vZ1 i FR Z itl1 Z i 1 2 Velocity Calculation for frame i with a Frames Factor of 5 vX1 i FR X i 2 X i 2 4 vY1 i FR Y i 2 Y i 2 4 vZ1 i FR Z it2 Z i 2 4 Cortex 2 1 Reference Manual Appendix E Import and Export File Formats Velocity Calculation for frame i with a Frames Factor of 7 vX1 i FR X i 3 X i 3 6 vY1 i FR Y i 3 Y G 3 6 vZ1 i FR Z i 3 Z i 3 6 Velocity Calculation for frame i with a Frames Factor of 9 vX1 i FR X i 4 X G 4 8 vY1 i FR Y i 4 Y G 4 8 vZ1 i FR Z i 4 Z i 4 8 Resultant velocity scalar vRI frame i SQRT vX1 2 VY1 2 vZ1 2 Accelerations for Frame i are calculated as the differences in velocity as A frame i Velocity frame I gt frame i 1 Velocity frame i 1 gt frame 1 Time difference between frames 1 FR Acceleration Calculations sing the Frame Rate FR of the camera for a Frames Factor of 3 aX1 i FR FR X i 1 2 X i X i 1 aY1 i FR FR Y 1 2 Y i Y i 1 aZ1 i FR FR Z Git 1 2 Z i Z i 1 For
329. mities will likely differ This can result in the character s feet not touching the ground Enabling the Apply Inverse Global Scale to Global Segments skin option will cause the char acter s position to be scaled to match the scale of the skin This adjust ment will change the character s position in the X Y and Z dimensions so the skin may no longer sit exactly on top of the skeleton data being dis played in Cortex To make a Collada skin for Cortex in Maya you will need a Collada ex porter for Maya If you have a Collada exporter installed you would In Maya 1 Load character for which you will be making a skin Export HTR using MacFileIO to create a basepose skeleton to be used in the Calcium setup 3 Export dae file from Maya using the Collada export plugin 4 Place the dae file in the Cortex2 UserFiles Skins folder In Cortex 2 1 1 Load cap file to be used for character setup usually an INIT or ROM capture 2 Create a skeleton using the HTR basepose Setup the Calcium model 4 Set the skin to a matching dae model in the Calcium setup panel bot tom right when Calcium is selected and segments tab selected 9 9 12 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab Tree View gt Markers Name Index Size Color Optional False default Optional True Selecting Markers in the Treeview allows you to make changes to any of the markers associated with the current captur
330. move 3 Enter an Cortex filename the duration of data capture the trial num ber and trigger the Event button 4 Update the slate and the Motion Capture Log 5 The director should ask if everybody is ready and then say Roll video Slate video 6 The Cortex operator presses the event trigger button and the subject begins the trial When the trial is finished the event trigger button is pressed again to complete the capture 7 Comments on the quality of the trial should be entered into the Motion Capture Log and on the audio of the camcorder 8 The Cortex operator quickly reviews the raw data and looks for any problems 9 This process is usually repeated for 3 trials of each move that is scheduled Usually only one trial is tracked The other trials are there for insur ance and to allow the end user to pick the best trial For insurance it is a good idea to periodically collect raw calibration data whenever there is down time As the number of people increases in the capture studio the chance for bumping a camera if tripods are being used increases and insurance calibration data suddenly becomes very valuable After all the trials have been collected perform the following to wrap up the process 1 Collect the last calibration trial 2 Backup all the Cortex trials on a CD ROM external hard drive or other backup medium Label and store the tape in a safe place 2 8 Cortex 2 1 Reference Ma
331. n 7 5 DOES NOT WORK with any version of Cortex Shutdown power OFF the computer and remove the A D unit Power ON the computer go to START Settings Control Panel Add Remove Programs select NI_DAQ and then select Remove 3 When complete shutdown power OFF the computer wait 10 sec onds power ON the computer let the system boot up and then log in when prompted It is necessary to have the computer boot without the A D card or software Proceed to the next step N 1 Install the NI DAQ software version 9 0 or later Note that NIDAQ version 9 1 does not work with Cortex 2 0 or earlier versions on 64 bit Windows Cortex 2 1 release works on all Windows platforms Install all of the default entities that are checked then shutdown power OFF the computer 2 Power ON the computer and let it boot completely without the A D card installed This will complete the National Instruments software installation Once the computer is completely booted Shutdown power OFF the computer once again 3 Install the A D unit and power ON the computer It should come up with the Hardware Wizard and the Found new hardware pop up window At this point the computer will automatically install the NI DAQ drivers correctly 4 Shutdown power OFF the computer one last time and then power it back ON 5 Go to the National Instruments Test and Measurements software and select Traditional NIDAQ devices and then right click and select test panel
332. n be changed in the Raptor Specific sub tab of the Cameras settings area pictured above Some of the advanced settings can be displayed hidden using the Advanced button These settings available for Raptor cameras are 2D Centroid Calculation Greyscale Visualization Greyscale Calcu lation Floor Greyscale Calculation Margin Asymmetry Limit Each of these settings can be changed for All cameras or the Selected cam eras based on the setting of the Edit These Cameras radio button at the bottom of the Cameras tab 2D Centroid Calculation Raptor series cameras have two ways to calculate centroids in the cam era s 2D view They can be calculated the same as the non Raptor cam eras i e send edge information to Cortex and have them calculated in the Cortex software In addition the Raptor cameras have the ability to apply data analysis algorithms to the greyscale camera image and calcu late the centroid on board the camera sending the final result to Cortex To have the greyscale images calculated by the camera select the On board Camera greyscale radio button To have them send edge data to Cortex select the In Cortex edge based radio button Greyscale Visualization The Raptor series cameras can send their greyscale image to Cortex for visualization This setting is used to change the visualization method 4 27 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual
333. n data begins at row six Column one of the data fields contain the frame number int Column two contains the time real and columns from three on contain the X Y and Z position data real for each trajec tory There are three columns for every trajectory An empty frame of position data missing data is represented as three consecutive horizontal tab characters Shown below is a portion of a file with the following attributes captured rate 60 frames per second total frames 90 total reflective markers 33 units of measure mm Data for only the first 3 markers is shown the remaining markers would appear in columns to the right Also data for only the first 12 frames is shown the remainder would appear in rows below frame 12 E 4 Cortex 2 1 Reference Manual Appendix E Import and Export File Formats Figure E 2 An Example of a TRC File PathFileType4 X Y Z DataRate 60 0 Frame Time 1 0 000 2 0 017 3 0 033 4 0 050 5 0 067 6 0 083 7 0 100 8 0 117 9 0 133 10 0 150 11 0 167 12 0 183 CameraRate 60 0 Head_Top 234 235 235 235 235 235 235 235 235 236 235 235 X1 5437 2399 2361 0781 0781 0781 3844 1416 4312 0334 7562 5336 1673 1673 1673 1673 1673 1673 1673 1673 1673 1673 1673 1673 Yi 7619 4542 4926 4376 4376 4376 4179 4447 4882 42
334. n either side of it 4 54 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Tools gt Reference This function sets the 3D Display including marker cloud skeleton Video Calibration skins forces etc to match the orientation of the Reference Video This is Wizard useful when overlaying the two perspectives The interface provides in struction as you work your way through the process Figure 4 40 Tools gt Reference Video Calibration Wizard Reference Video Calibration E a Initial Setup Reference Video 1 The Main Markerset should be tracking the wand 2 The Video Backdrop display should be visible If these are showing in the 3D display then press the Next button Number of Frames Average Residual Note You must start by loading the 3 marker wand capture file This can be done by creating a wand capture with a template or selecting it from the Motion Capture gt Objects gt Select Markerset gt System tab Note The wand template must be set so that marker 1 is on the end marker 2 is closest to marker 1 and marker 3 is on the opposite end of marker 1 ref erence Figure 4 41 Figure 4 41 Wand Marker Order for Setting Up Template Marker 1 Marker 2 Marker 3 o_ _ _ _e _____YY _ 4 55 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Tools gt Sound The Sound Manager is used to configure the sound files associated with Manager BioF
335. n page F 4 For example if 12 frames of data are cropped from the beginning of the motion and the data frequency is 60 Hz the starting X value will be 0 2 seconds for units of time and 13 for units of frame number If you want the X values to start at 0 0 or 1 for frame number even if frames are cropped turn on the start at zero option When this box is checked SIMM will look for and automatically load any analog ANB ANC or XLS data files with the same base name as the TRB TRC file If SIMM did not detect the presence of any analog files when the TRB TRC file was selected this option is grayed out If you selected a C3D file with the file browser then this box controls whether or not the analog data will be read from the C3D file If an analog file is present and the auto load analog data box is checked see above then this box is active and gives you control over the calibra tion of the force plate data When this box is checked SIMM determines the baseline of each force plate channel and automatically subtracts these baseline values from the data thus zero ing out the force data In order to display force plate data that is in the analog file SIMM creates graphical objects in the model window representing the force plates Each time you load a tracked marker file with corresponding analog data SIMM creates a new graphical object for each force plate in the file In most cases you will want to remove the existing force
336. n take several seconds to minutes depending on the length and complexity of the skeleton If you are using one of the streaming Talon plugins the skeleton data is available after the calculations are finished You can scrub back and forth in the Post Processing mode or press the Play button and both the marker data and the skeleton htr type data are available to the streaming Talon plugins like Maya Skeleton Option Details as selected from Tree View The type of skeleton is chosen from the attributes section of the top level of the TreeView Figure 11 3 The Top Level of Tree View a Treeview Markers 40 VMarkers 0 l Links 134 SkB Segments inactive Calcium Segments 23 H Root H Spine H Spine2 H Spine3 X MarkerSet Name Matt Skeleton Engine Calcium Solver 1 5 0 Rotation Order ZYX Bone Axis Skin File 25 _Bones_Male_obj Skin Transparence 0 Chapter 11 Skeleton Types Cortex 2 1 User s Manual Skeleton Builder SkB Engine Figure 11 4 The Top Level of Skeleton Builder Markers TreeView E Dave_SkB Markers 41 H VMarkers 25 Links 98 fee SKB Segments 24 DaveRoot LHip LUpperLeg LLowerLeg LFoot LToes RHip RUpperLeq Fill Gaps False m Bone segments are defined from one marker to another typically virtual markers that represent joint centers The advantage to this method is the fast and direct calculations from markers to joint
337. n those set for the number display LEDs This indicates a standard operating camera Camera Ready for rom bin Download This display code with the active LEDs in a Slash through the display number indicates that the Eagle camera is ready to accept a new rom_date bin file This display code will be go away after the new software has been installed and the camera is rebooted x w i ve Chapter 5 System Tab Cortex 2 1 Reference Manual Table 5 1 Camera Display Codes Code Press Download Image Description This display code with active LEDs in an arrow and rectangle pattern indicate that the Download button in the Download FTP window is ready to be pressed Progress Rom bin Download in This display code indicates the progress of the download process The number of activated LEDs will increase as the download process nears completion 5 10 Cortex 2 1 Reference Manual Chapter 5 System Tab Creating and Clearing Masks Hardware Masks Going Live Masks are rectangular regions in the 2D View that you designate to re ceive no marker information Masks allow you to block out fixed light sources that cannot be physically removed from a camera s view Masks are created on the 2D Display by clicking and dragging the middle mouse button and appear as hatched regions Masks can be cleared by using the right mouse pop up menu item in the 2D
338. nalog Data as 4 45 Save Capture 4 4 Save Capture As 4 4 Save MarkerSet 4 10 Save MarkerSet As 4 10 Save Setup 4 9 Save Setup As 4 9 Save System Setup 4 9 Scaling 8 4 SDK D 1 Search 8 17 8 19 Search Tab 4 34 Seed Calibration Extending 6 20 Segment Selecting 4 83 Select All Frames 8 5 Select Raw Video File 4 11 Selected 8 13 Selected Markers Radial Button 8 14 Selecting Frames 8 5 Buttons 8 3 Selecting Linkages 4 83 Selecting Markers 4 83 Selecting Segments 4 83 Selecting Virtual Markers 4 83 Set as Master 5 3 Set Master Camera button 5 4 Setting Up Cortex 2 1 Reference Manual Cameras 3 10 Settings Output Panel 7 10 Setup Files 4 60 Setup Panel 5 1 Shape Analysis 4 24 Show 4 64 6 17 Show Camera Field of View 3 11 Show Camera Volume 6 17 Show Kinetics Options 4 32 Show Residuals and Cameras 8 4 Show Template Linkages 8 13 Shutter Speed 5 2 SIMM 1 16 SIMM Calcium Model 11 9 Simulated Calibration 6 19 SKB 1 9 SkB Segments 9 22 Skeleton Builder 1 9 Skeleton Builder SkB Engine 11 6 Skeleton Definitions 4 11 Skeleton Engine 9 4 Skeleton Graphs 4 15 Skeleton Types 11 1 Skin Configuration 9 9 Skin File 9 6 9 9 Skin Offset 9 9 Skin Tranparency 9 6 Sky 4 42 Sky Scripting Compiled Script Reference 12 8 Sky Scripting Interface 12 1 Sky Writer 12 1 Sky2 Scripting GUI 12 4 Interface 12 1 Slate Board 2 4 Slave Sync 5 3 Smooth 8 16 Smoot
339. nce Analog Display With Right Click Pop Up View Options and Channels Table Visible Channels Shift the Data Corrects for time match problems between analog and video data 0 4 68 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface XYZ Graphs Pop Up Menu Post Process mode allows you to edit tracked data The XYZ Graphs dis plays the positions of each marker in each frame It also lets you select and edit those markers in any frame A complete discussion of editing tracked data can be found in Chapter 10 Post Processing Panel To see the XYZ Graphs and the pop up menu of tools and view options 1 Press F4 on the keyboard or choose View gt XYZ Graphs 2 When in Post Process mode right click on the XYZ Graphs Figure 4 54 Post Process XYZ Graphs With Pop Up View Options and Tools Zoom Frames In Zoom Frames Out UnZzoom Auto Scale Uniform Scale Select All Named Data Zoom into the current frame range Zoom out from the current frame range Reset the amplitude display Auto scale to visible channels Applies uniform scale to all three X Y and Z panels Select all frames in the data set Show Residuals Camera Show Residuals and Cameras plots Quick ID MarkerID Template ID Rectify Hide Markers Unhide Markers Make Unnamed Create Template Quick ID the markers sequentially Marker ID the selected marker ID marker s based on current tem
340. ndance of data slowing the system down Try to have no more than three cameras see any given area of the capture volume from one direction and 10 to 12 cameras total 2 Calibration Tracking residuals should be below 2 0 mm If not try raising the Max Residual value Too low a value may cause ghost markers to appear 3 Template Verify that marker identity is being performed quickly Click the Reset IDs button several times while the actor is in the cap ture space and see if there is a lag in acquiring marker identification If there is a lag you may need to create a better template Verify that the first three markers are the head markers and that the first three links form a rigid triangle Finally verify that remaining link defini tions flow down the body following the marker definitions 4 Frame to Frame Rectifying This is mainly influenced by your 3D data quality and tracking parameters Too many extra stretchy link ages can cause problems here Can I use MoCap Solver Si 2 0 or Calcium in Cortex Yes Export a MOD file from Si Calcium and name it the same as the cap ture file Select Model Edit gt Tree View and then select Calcium Solver in the Skeleton Engine field What is the order of the data in the TRC or TRB files when you use MTOs for tracking The resulting tre file from MTO tracking should match the marker order of the resulting Merge MarkerSets operation If I have a Solver skeleton setup from EVa
341. new software This line can be typed in or entered by cutting it from the file you receive and pasting it into the existing license file The order of the licenses in the file is not important and only those lines that start with a left bracket are read by the software Note Make sure that file extensions are not hidden which is the default This makes the mac_lic dat look like mac_lic which might be renamed to mac_lic dat dat If this happens the system will not recognize the license file Figure E 1 An Example of a Motion Analysis License File Motion Analysis License File Customer MAC Customer Platform NT SystemID 19c Created 9 15 20xx 1 42 26 PM Sales Order 05 xxx Entered By Support Cortex 2 0 aed50167 873b2d56 Analog Input b9806c31 d1567841 OrthoTrak b2d 5e69 8964274a Animation Plugins b1a46160 805b5c49 Director Sequencer ela04e65 85745819 RT2 Animation Plugins e3 f05340 a069081b Analog Input b9806c31 d1567841 Calcium 4 e7ed5923 c363151f Skeleton Builder 4 a3 44279 99780c5b Reference Video 3 0 eb92592 cf636a13 Talon Streaming 4 ecb36136 d65b4b14 Talon Viewer 4 86 b0714 43d037e Motion Composer c7 00e25 c534083f This license has no expiration Cortex 2 1 Reference Manual Appendix E Import and Export File Formats PRJ Legacy Cortex Project File Important For earlier versions of Cortex prior to Cortex 2 every motion capture session uses a project file co
342. ng any direction e e 2 Turn the lens focus ring in the opposite direction 3 Turn the lens focus ring in the opposite direction again should be the same direction as step 1 G0 Oe Oe Oe Ge Ge Oe Oe 4 Focusing in progress about 50 e e e e eo Li ee ee Lal G2 Ge Ge Ge GF GF Ge or o Oe 00 Oe OF Ge Ge Oe Oe Ge Oe Oe Oe Oe Oe Ge Oe Os Os oe O G0 Oe Oe OF oF OF Oe OF Oe 00 08 OF 0o Oe Oo os os osos o 02 0o oe oo bo oe oo Gegutnbbartnteanants 5 Focusing progress continues about 75 Oe Oe G2 Oe Oe oeoo O0 Oe Oe O O OF OF Oe Oe oe Ge oe oe O G2 Oe oo BF OF OF Oe Oe O Oe Oe Oe O O Or G OF or 6 Focusing progress continues about 90 7 Focusing complete 100 3 30 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Focusing with the Camera Focus Card Figure 3 22 Camera Focus Card A Camera Focus Card ships with newer systems If you do not have one contact support motionanalysis com or you can make one that works for you with cardboard and some retro reflective tape The Camera Focus Card is a simple piece of card that unfolds into an A shape On the front surface are 3 rows of 4 flat disc markers of 3 different sizes with instruc tions for use In brief 1 Place the card in the middle of the volume so that the face is roughly square on with the camera 2 Choose a 2D view of that camera and connect
343. ng at the same time Right click on your desktop then select Properties gt Settings gt Advanced gt Troubleshoot Slide the Hardware Acceleration down a few points Quit Cortex then re launch See if that fixes the problem The set tings depend on what your graphics card does and has for features that changes from one computer to another If that does not fix the problem try to slide the Hardware Acceleration to None Quit Cortex and then re launch If that still does not fix the problem try to change some of the Open GL settings found under the name of your graphics card found under the Properties gt Setting gt Advanced tab Also change the Verti cal Sync setting to On by Default and restart your computer We came across a problem while in a two person w prop motion capture session Whenever we recorded a motion the recorded trc file would be missing a good portion of the marker data Any idea why the data would just disappear This is most likely cause by insufficient marker slots The default marker slot setting is 192 In your case you should increase the value The marker slot setting maybe adjusted under Tools gt Settings gt Misc We are only using 93 markers 40 per actor 5 per prop and 3 for the ball Shouldn t 192 marker slots be enough Not necessarily You should always have at least twice as many marker slots then actual markers The number of slot is dependent on the tracking parameters settings Each sni
344. nimation 9 11 When the skin represents Biomechanics 9 11 the mocap actor X X Panel 10 2 XYZ Graphs 4 69 pop up menu 4 69 Z Zoom amplitude 4 83 Zoom In Zoom Out 8 4 Zooming 4 82 2D Centroid Calculation 4 27 Cortex 2 1 Reference Manual AVI Frame Offset 4 30 Brightness 4 26 Calc Without Forceplates 4 38 CPU Speed 4 29 Data Specific sub folders 4 22 Empty View F11 4 16 Forces w o Forceplates 4 38 Greyscale Calculation Margin 4 28 Greyscale Visualization 4 27 Import C3D File 4 13 Marker Slots 4 38 Markers 4 34 Max Horizontal Lines per Marker 4 26 Min Horizontal Lines per Marker 4 26 Min Acceleration Gs 4 34 Min Size of Spikes mm 4 34 One Foot Off Forceplate 4 38 Origin Offset 4 20 Presentation Graphs F10 4 16 RealTime 4 29 SDK2 Streaming 4 37 Search For 4 34 Single MarkerSet legacy file naming enabled 4 21 Standard Forceplate Usage 4 38 Time Code 4 37 Tool Strip Options 4 36 Tracking Parameters 4 24 Unconstrained Followthrough Iterations 4 20 Validate Joins with Template 4 33 WAV Frame Offset Mocap frames 4 30 XYZ Graph Zoom Options 4 38 Centroid Parameters 4 23 Index 9
345. ns Export Prj File Export Trb File Export Tre File 4 6 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Quick Loader The quick loader allows one click loading of legacy project files and tracks files When a project file is selected all post processing data is un loaded The Setup contained in the project file is loaded and any Marker Set contained in the project file is loaded into Live Mode and Post Pro cessing When a tracks file is selected the named and unnamed data it contains is loaded into Post Process along with any associated data files anb htr etc just as was the case in EVaRT and Cortex 1 After this data is loaded it can be saved into a Cortex 2 capture using the Save Capture As File menu option Figure 4 6 Quick Loader Interface C Documents and Settings ben ahiborn My Documents CortexD ata Samples Calcium Tutorial ExampleD ata x Browse Refresh File Importing fi Batch Importer l Project Import click to load Tracks Import click to load Matt prj MattPickup1 tre MattRoll1 tre MattROM1 tre MattRunt tre MattSwan tre MattT pose tre File Exporting Export Prj File Export Trb File Export Tre File Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Batch Loader The batch loader is used for converting groups of files into captures This is accomplished by creating a list of project tracks file pairs Each pair is then loaded
346. nsferred without the prior written consent of Licensor Except as otherwise specified herein this is the entire agreement between the parties relating to the subject matter hereof and may only be modified in writing signed by each party This agreement is governed by the laws of the State of California For further information regarding this Cortex 2 1 Reference Manual or other products please contact Motion Analysis Corporation 3617 Westwind Boulevard Santa Rosa CA 95403 USA tel 707 579 6500 fax 707 526 0629 info motionanalysis com P N 665 1200 021 www motionanalysis com Copyright 2010 Table of Contents Chapter 1 Introduction KONOW een en eee Peet PRR wer et ee ee Re CaD esas ee a meta eter ne etter 1 1 System Requirements for Cortex ccccccsceeeeeeeeeeeeeeeneeeeeeeneeeeeeees 1 3 Installing the Software and LICENSES ccseeeeceeeeeeeeseeeeeeeeeeeeees 1 4 Software Packages within Cortex ccessceeeesseeeeeeeeeeeeeeeseeeeeeneaes 1 8 Software Packages Used with Cortex cccseeeeseeeeeeeeseeeeeeees 1 13 F r More Informati ccssccs ccesetiecasicemcetecileciaesinisomeRneladedes 1 18 ACkKNOwedgmMmeEM S enasna anean 1 18 Chapter 2 Planning a Motion Capture Session PE a A E E A E E E E 2 1 Ss ems gle Preparations eaaa 2 1 Prior to the Capture Session aces ses ccescaciceeccceaeeateoieucidkeancted 2 2 Job Assignments and Tasks During the SeSSION ceeeeeeeeee 2 3 Addi
347. ntaining all system settings equipment pa rameters and other information related to the project This file contains both equipment parameters common to many different setups and calibra tion values unique to one particular session Among the data found in a project file are e the system setup e the marker set e calibration setup and results e linkages between markers e SkB segment definitions coordinate systems and hierarchies e optional MoCap Solver segment definitions joint types and hierarchies e camera type and parameters In most cases you will begin a session by loading an existing project file editing it as necessary and saving it in the directory where the motion data is to be saved Any time you calibrate the system or edit project pa rameters you should save the project file to disk to retain the new infor mation Project files contain ASCII data and it may be useful to view them using any text editor however you should never edit them in a text editor TRC Track Row Column File Header The tre file contains X Y Z position data for the reflective markers This is an ASCII file in a Row Column horizontal tab delimited format that can be easily read into a spreadsheet program such as Excel and Lo tus The position data for each marker is organized into 3 columns per marker X Y and Z position with each row being a new frame The posi tion data is relative to the global coordinate system of t
348. nual Appendix A System Hardware Interconnections Power Consumption The maximum power consumption you can expect for normal system configurations are shown in Table A 1 The actual power consumed de pends on the video frame rate and the intensity of the ring lights and is usually less than that indicated For the most reliable system operation it is recommended that all camera assemblies and computers be powered by an uninterrupted power supply UPS If you want to save your data when power is lost altogether you will also need to power the tracking computer monitor from the UPS Table A 1 Power Consumption of Typical Systems 8 Cameras 12 Cameras 16 Cameras Power Hub E Net Switch with 265 W 400 W 530 W Cameras 21 SVGA Monitor 125 W 125 W 125 W Dual Processor Computer 200 W 200 W 200 W TOTAL 580 W 725 W 855 W Basics of There is a difference between the older Ethernet hubs and the newer Ethernet Ethernet switches even though they look alike and are functionally simi Switches and Hubs lar The difference is in the performance Ethernet switches guarantee the full rated Ethernet bandwidth between all ports simultaneously whereas the older Ethernet hubs share the bandwidth for all ports We call the Ea gleHubs hubs to indicate that they are the center connection point for a block of cameras but inside the EagleHub resides a switch This perfor mance difference is important and neces
349. nual Chapter 2 Planning a Motion Capture Session 3 Remove the video tape from the camcorder and set the safety tabs on the tape to prevent being recorded over 4 Consolidate and make copies of the motion capture logs and forms 5 If necessary give the video tape and Motion Capture Logs to the director so the best trials of each move can be indicated 6 Place logs and offset forms in a binder Clear plastic inserts can be added to hold the still photos The binder along with the video tape will provide important information to both the Cortex user tracking and editing the data and for the artists who will apply the final data to the model Creating a New The following steps are to give the MarkerSet a name input the marker MarkerSet in Cortex names capture a trial identify and edit the data create linkages create a template and finally save the MarkerSet name 1 Click on Post Process gt MarkerSets Tab gt New and give the MarkerSet a name Check Identifying Template MarkerSet Props are for single rigid objects like tennis rackets or golf clubs Figure 2 1 MarkerSet Tabs System Calibration Motion Capture Post Process Model Edit Plugins Presentation Cre a OT VHRREDS S Rectify QuickID Rectify Create Template Template RB Marker ID Exchange Linear Cubic RB Virtual Calc Smooth Unnamed Template ID RectiFy RectiFy Join Join Join Join VMs 2 Select Model Edit gt Markers and type in the new marke
350. o see the 3D View options 1 Choose the cascading Show item and another pop up list will appear Several of the view options will have check marks next to them indi cating they are active All of the Show items in the Show list are con 4 64 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface sidered User Preferences and get stored to the Cortex ini file when you exit the program or in your own custom preferences file from the File gt Profile Manager function Choose items from the Show options menu and see the effects These options are saved in profile settings and are reloaded when you launch Cortex Figure 4 51 3D View Right Click Pop Up View Options Refer to the following page for descriptions of these options 3D Display Show Properties Subject Markers Links C MarkerSet Names C Marker Numbers C Marker Names Trajectories C Virtual Markers Unnamed Markers Skeleton Skin C Skeleton Axes Forces C BackCale C Model Pose Kinetics Segment Center of Mass C Linear Velocity C Linear Acceleration C Angular Velocity C Angular Acceleration C Gravity Vector World Cameras C Camera Rays C Cam Field Of View Floor C volume C video C Camera Coverage View C Keep Centered C Mirrored C Auto Rotate C Relative Perspective View Orthographic View Joint C Forces C Moments C Global Center of Mass C Down Events Additional S
351. ody motion The model has 41 body segments 41 joints 40 degrees of freedom and 88 lower extremity muscles It represents an adult male ap proximately 175 cm tall with a mass of 78 kg The model is scaled to match the size of the motion capture subject using algorithms described in Section 5 3 4 The model s joints have been carefully constructed to rep resent normal joint motion as closely as possible To load the mocap model into SIMM the software looks for the MOCAP_ MODEL variable in the preferences file SIMM Resources prefer ences to get the name of the joint file that comprises the mocap model The default setting for this variable is SIMM Resources F 9 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual The Static Pose mocap mocap jnt This joint file includes the file mocap msl to get the definitions of the muscles You may change the mocap model however you wish For example you can add or remove muscles from the model or change the tendon and fiber parameters of existing muscles You can also add degrees of free dom to the model in order to more accurately represent a particular mo tion e g adding toe joints and gencoords to examine toe motion in greater detail If you modify the mocap model however you should keep in mind two things First the model has been set up to correspond to the skeletal model that OrthoTrak uses when processing gait data The lower extremity body seg ments and ori
352. of frames each represent ing a snapshot of the subject s motion at a particular instant in time Each frame contains the X Y and Z coordinates expressed in a global coordi nate system of all the identified markers A frame of marker data can thus be thought of as a marker cloud because the coordinates are not orga nized by body segment The Motion Module imports tracked marker data and fits a SIMM model within the marker cloud for each time frame If the SIMM model contains markers whose names and positions match those of the markers placed on the subject the Motion Module can adjust the model s gencoord values to determine a best fit of the model to the marker cloud The quality of a fit is determined by how closely each of the model s markers is to its cor responding marker in the marker cloud It then uses this best fit as the starting position for solving the next frame of data The result is a SIMM motion that matches the tracked marker data The model that is used to fit the data can either be one that you create or the pre made model the mocap model that comes with the Motion Module F 1 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual The Motion Module has two primary components The first component reads files containing tracked marker data in the TRC TRB or C3D for mat and creates SIMM motions from them as described above For more information on how this process works and the various
353. of the process is to collect both an init pose and a ROM range of motion for the actor Do a manual identification of the makers in the init pose T pose or A pose Use this to create your tem plate You should next be able to ID the first frame of the ROM which should be a T Pose and do a Rectify through the whole ROM Once the ROM has been completely identified save the changes and then use Extend Template from the Create Template Dialog box The next step is to process all the easier motions This way you can use these motions to extend your template further which will allow you to have a more complete template by the time you need to track the harder motion files I m in the process of setting up Cortex to collect video data and I have a question about compatible video devices The manual indicates that a Sony camcorder with Firewire output was used in testing Would it be ac ceptable to run for example a surveillance camera through a capture de vice with a Firewire output Currently Cortex looks for DV format streams over Firewire IEEE 1394 only using those devices designed to operate with the Microsoft DV driver MSDV A device delivering data over Firewire will likely use the MSDV driver if the data is in the DV format which refers to a specific compression codec DV25 which is what most consumer handycams deliver WebCams as a counter example tend to deliver compressed Mpeg 2 streams So it would not matter if t
354. of the prop Many props that would ordinarily seem simple become very difficult to deal with during a motion capture session A good example is the use of a ball as a prop If a small ball is only being held one marker may be used to track position If a large ball is being bounced three markers may be required to show all rotations Reflective or glossy material should not be used in the construction of props and very large props may occlude the subject s markers Remem ber the design of the prop and how it affects the subject s movement are more important than the prop s physical appearance Props may also be assigned separate templates Used to completely document each trial a camcorder will allow the pro ducer to rank the trials of a move and will also give the animation artist something to use as a reference for the completed animation See also Digital Reference Video Option CortexDV Software on page 4 70 Photographs of the subject with markers attached will help the artists un derstand the correspondence between the marker data and the actual fig ure A slate board and chalk or grease pen board will provide an easy way to relate the camcorder record to the Cortex data An adequate supply of reflective markers double stick tape paper tape and Tuff Skin or New Skin should be available For rough and tumble sessions the best method to adhere markers is by using Velcro on a skin tight motion capt
355. oftware Packages within Cortex Software Packages Used with Cortex For More Information Overview Figure 1 1 Cortex User Interface Motion Coriex SetupWithtvents cal GolfSwing_1 cap GH Fe Layos Ostavews Took ap Ciment Directoy C Progam Fles Mohon Anaiys System Calibration Moton Capture Pos t a 0 QAD Retiy Cose Tomite Tengiste Tengist D Batty fodel Edt Plugrs Presentan as ee TA Annan Cheick Tope Were si O a a S Leete Ot CA Search 3 M Teptgee Mother ID Exchange G k Wiwi Cok Smooth Mie Jon on Ve tensed Mattenete New Adi Gore Os EJ 0 887 4541 ine Ove fie 200 300 ao 500 500 706 800 ES ae Cee ee EE Do o0 00 oe e can _ x dat kiil ies Frames i0 FPS Tup unesem anaog 600 00 re 7 Unable to locate oki Video Rarxdarer for removal This instructional Reference Manual provides a complete description of the Cortex software and its capabilities along with many step by step procedures critical to a successful motion capture project Motion capture theory is separated from the body of this manual in the form of appendi ces so that the tutorial approach does not become cluttered Chapter 1 Introduction Cortex 2 1 Reference Manual Cortex is a complete package capable of meeting the most demanding re quirements of the motion capture industry Output is generated in rea
356. ogether be sure the connections are secure and snap firmly into place Figure A 4 Rear Panel Connectors Power Connector Ethernet Connector Aux Connector Future Connector Future Ethernet The power connector powers the camera with a 48 Vdc source from the EagleHubs through a CATS cable The Ethernet connector is set for a 4 wire full duplex 100 Mbps Ethernet The Aux connector can be used for testing VGA and diagnostics and is generally not needed for normal customer use An Aux cable is supplied with each Motion Analysis system which has three connectors on one end VGA COM 1 and BNC for use in various applications and diagnostic testing The Future connector is reserved for future use A 6 Cortex 2 1 Reference Manual Appendix A System Hardware Interconnections Network Interface Cards and IP Addresses Configuring a Network with Your Motion Analysis Digital Cameras Note Ethernet Camera Addressing It is recommended that a Motion Analysis system have two Network In terface Cards NIC 1 Single port for your own LAN connection 2 4 Port dedicated to the system The IP addressing for the camera system is initially setup in the following manner e Digital Network Interface Card NIC 10 1 1 199 e Subnet Mask 255 255 255 0 This will need to be set in the Camera Network IP Address box in the System gt Cameras panel The NIC address is set from the Windows Control Panel Se
357. om Previously Collected Files 6 19 Refining 6 14 Simulated 6 19 Calibration Frame Required Settings 4 17 Calibration Frame Tab 6 5 Calibration L Frame 3 18 Placing 3 19 Calibration Panel 6 1 Calibration Settings Window 6 5 Calibration Settings Window Tabs 6 5 Capture Volume 6 8 Origin Offsets 6 5 Calibration Tab 4 17 Calibration Wand 6 1 Calibration with Wand 6 11 CalSeed vcX 6 10 Calwand vcl 6 1 CalWand vcX 6 13 Camcorder 2 4 Camera Aiming 6 4 Camera Aiming check box 4 18 6 7 Camera Buttons 4 80 camera buttons Index 2 Real Time Dashboard 4 71 Camera Connections A 6 Camera Coverage 4 31 Camera Depth of Field 4 31 Camera Software 5 5 Loading New 5 5 Camera System Configuration A 2 Cameras Optimum Number 3 2 Properly Seeded 6 10 Setting Up 3 10 Square Seed Calibration 6 8 Cameras Panel 5 1 Cameras Tab 4 25 Capture 2 5 Capture Inspector 10 8 Capture Outline Live Mode 2 10 Capture Volume Sizes 3 5 Capture Volume and Marker Size Relationship 3 27 Capture Volume 4 19 Centroid Parameters 4 23 Channels Table 4 68 Check Template 4 72 Clear All Segment Mappings 9 11 Clear MarkerSet Button 9 3 Clearing Masks 5 11 Close Capture 4 6 Collada 9 6 Collect and Calibrate Button 6 10 Collecting Captures 2 7 Colors 4 43 Colors Form 4 43 Connect Cameras Button 4 79 Connect to Cameras 5 1 Connections Analog Input Channel B 10 B 12 Analog Input Hardware B 1 Control Poin
358. on Tab gt Lenses Orientation Required Settings Figure 4 14 Lenses Orientation Settings These settings are used to set the focal length and orientation of each cam era as used at the start of the wand calibration procedure After the wand calibration the actual focal length of the lens is calculated exactly and can be stored in your capture file The focal length should be set to something fairly close to the actual focal length of the lens e g 6 for 6 mm lenses The positioning for the camera should be Normal if the camera is up right top if the camera is within 90 degrees of perpendicular to the floor Otherwise the camera positioning should be set to Alternate If you use the Camera Aiming check box in the Calibrate panel the focal length entries should first be set to be nominally correct values e g 6 for 6 mm lenses When using the Show Camera Field of View flag in the 3D display the value from this table is used to compute the view frustum of the camera 4 18 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Calibration Tab gt Capture Volume Figure 4 15 Capture Volume Tab Calibration Fle Structure Tracking Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins Calibration Frame Lenses Orientation Capture Volume Other Z Minimum Z Maximum
359. on co teo O L VHVEDE ogent CL FE e Delete Coy Gt Gt Unnamed Outside T 2 LHi 3 B jesa 4 R josi Topspne 7 Stender 9 Proar 10 SheuaderOttaet 11 Rticep 13 Rrit 14 Rory 17 Likeep Volume C Angie Acceleration C Gobsl Center of Mass ud 4 U4 text gt C orevey vector 5 U5 Engey 6 US eety gt 7 UJ egty gt Adana ID Derpiny Settings Hai 0 704 4140 sus te Ow 100 200 200 400 500 600 700 800 800 1000 O taton gt i T ECHE ma visioi seice e 12 Looded Capture C Program FlesiMation Analrsis Cortex2 semeleril6 Camera Calibration Facet BodyiDeveR OMI cap i000 Frames cores Yup Untsime The Volume display is used as a visual aid when aiming the cameras in real time during setup There is an option to delete all marker data outside of the volume in the Plugins gt X panel 3 12 Cortex 2 1 Reference Manual Chapter 3 Camera Setup 9 To See the camera coverage in the volume select the Camera Cover age check box in the 3D Display Show Properties window See Fig ure 3 12 Figure 3 12 Show Camera Coverage i Fie Layouts DataViews Tools Help 8 MotionAnalysis Current Directory C Program Files Mation Analysis Cortex2 Samples 16 Camera Calibration Face Body v Browee i P System Calibration Motion Capture Post Process Model Edit Plugins Presentation Cre a OF VHVEDPY SL ABLA Markers Segments Click Alon
360. on marker that has data for that frame field 6 Repeat step 1 through step 5 for all problem markers in your data set You may also setup the Virtual Marker definitions for as many mark ers as you feel will be needed prior to capture 8 24 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Real Time Streaming with Join Virtual Fill 7 Selecting File gt Save Capture will save all Virtual Marker definitions you have set into the capture file If you will be continuing to capture motion using the same template the Virtual Marker Join definitions are now resident with the capture files and template The Join Virtual check box can now be activated on the Real Time Dashboard allowing for Virtual Markers to be created in Real Time where data is missing for the markers you have set definitions Thus streamlining the editing process or post processing tasks Figure 8 17 Join Virtual Check Box Origin Marker Long Axis Marker Long Axis Marker Example 0 878 51 E V Tracking Events kal v Join Virtual ic Skeleton Check Template GolFSwing_t cap aron 1 2 3 Connect To Cameras Disconnect Use Raw 23 Stopped The concept behind the Join Virtual and the Virtual Marker definitions are the same and are much more stable and more useful than the classic Rigid Body data filling mechanisms The reason is that you get to choose
361. on to colla tion and presentation with a minimal learning curve For current users this integration leverages their existing knowledge of Cortex Presenta tion output can be as simple as redirecting a Cortex capture to presenta tion format Motion Composer ships with Motion Viewer a freely distributable inter active player that enables customers to distribute their presentations quickly and easily When it s time to send research data to a colleague or take it on the road authors can simply pack and go turning their presen tation into a single packaged ZIP file for quick burning to CD or emailing to a friend With the interactive player inside presentations are ready for launch on any Windows operating system In addition to displaying capture data from Cortex Motion Composer supports text and web based media formats This allows users to present data from third party applications Examples would be text based clinical notes Microsoft Word documents and HTML files The following is a list of file formats which Motion Composer supports e Text TXT RTF HTML XLS e Reference Video MPG AVI e Images JPG GIF BMP e Cortex Captures CAP e User defined data types views e Presentation Graphs Cortex 2 1 Reference Manual Chapter 1 Introduction Presentation Tools The Motion Composer authoring interface provides a simple interface to easily manage a user s disparate files offering views of referenced files
362. on will read Calbrate and you can process the data in the simulated realtime mode as above The software starts with the cur 6 1 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual TrialN cal rent state of the calibration which is normally the results of the seed cali bration but can be otherwise and refines the calibration The calibration includes the exact location and orientation of each camera with respect to the origin the lens distortion parameters for each camera and other de tails about the cameras When the user accepts the calibration the result is automatically saved to the file SystemSetup cal This System Setup cal file is automatically loaded each time you start Cortex so you always start with the most recent calibration already loaded Every time you collect a trial in the Motion Capture gt Output panel the system writes out the current calibration to a file that has the same name as your trial name but with a cal extension This file is the default cali bration that will be loaded when you load a capture you must also have the Load Calibration checkbox active What is the Square and Wand Calibration Note In Cortex a four point square and wand calibration has proven to be very robust and is extremely accurate This method requires only four markers on the L frame and three markers on the wand If using an L frame orient your markers in the same directions as illus trated Care
363. on with Square section 2 In the Calibration with Square section of the Calibration panel click Calibrate 3 Select Raw Files in the Real Time Dashboard and then select Cal Wand vc1 or CalWand cap Select your CalWand data set in the data capture folder You can create a mask to eliminate unwanted markers or reflections Re select the CalSeed vc1 or CalSeed cap file again and press the Cali brate button in the Calibration with Square section 4 In the Calibration with Wand section of the Calibration panel click Calibrate 5 Complete the wand calibration as described in Calibration with Wand on page 6 11 If you are having trouble getting the system to calibrate due to the wand images being blocked by some cameras things to try in increasing diffi culty for the user are as follows Simplest method Using the existing Calibration Check Protect Lens Correction in the Calibration Panel and 1 Select the problem cameras use Refine Selected cameras by waving the wand to cover only those cameras The un selected cameras are not affected Or 2 Use Refine ALL cameras by waving the wand to cover all cameras This has often worked better than refine selected cameras Or 3 Do a new wand calibration with Protect Lens Correction CHECKED This will keep the lens corrections and other internal camera parameters alone and establish only the camera locations This takes less data and should be accomplished with many fewer w
364. ond frame If the number is set too small tracking will slow down as the software tries unsuccessfully to find continuations of markers This af fects the first to second frame tracking time especially If the number is set too big you will see markers switch identities After a marker has a history of 2 or more frames of continuous identity in time a track history allows the software to predict where the marker should be based on a 2nd degree polynomial prediction The software looks in a search radius of the Max Predictor Error about the predicted lo cation for a continuation of each marker being tracked The Max Predic tion Error is usually set to about one half of the Max Speed parameter 8 23 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Join Virtual Join Virtual is an extremely powerful editing tool used to fill gaps in r marker data with simulated data based on the relationship positional in l terpolation with other markers on or near the particular problem seg ment This accurately simulated information is a result of making four passes over the data in both Real Time and Post Processing modes To use the Join Virtual function 1 Find a gap within the position data of a marker It is easiest to use the Search function right click in XYZ Graphs and select Search If you are not using the Search function select the gap area in the XYZ Graphs middle click and drag for the problem marker
365. ool Strip on page 8 11 4 81 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Zooming Rotating and Translating in the 3D View Time Zoom Method 1 Time Zoom Method 2 Zooming and translating a display can occur in both the 3D View and the XYZ Graphs Rotating only occurs in the 3D View Choosing Help gt Hot Keys and Tips from the Menu Bar will bring up an online table describing how these features work Zoom lIn the 3D View zooming is accomplished if you 1 Hold the Alt key down 2 Hold both the left mouse and middle mouse buttons down 3 Move the mouse forward or left to zoom out and backward or right to zoom in Rotate In the 3D View rotating is accomplished if you 1 Hold the Alt key down 2 Hold the left mouse button down 3 Move the mouse in any direction Translate In the 3D View translating is accomplished if you 1 Hold the Alt key down 2 Hold the middle mouse button down 3 Move the mouse in any direction In the XYZ Graphs time zooming is done in terms of frames time or amplitude If you want to zoom in frames there are two methods 1 If one or no frames are selected zooming is done relative to the current frame 2 If two or more frames are selected zooming is done relative to the selected frames Click on the Post Process button among the Mode Buttons Press F4 or choose View gt XYZ Graphs from the Menu Bar 3 Left click on None in the lowe
366. op files or zin Fusion Group files Depending upon your selec tion that type of file from the current capture directory is displayed in the list below on the left Any or all of the files listed can be moved into the list to the right using either the right arrow button for any selected files or select and drag and drop into the window from the left to the right The right list is a staging list for objects to be loaded into Cortex when the list is ready Additionally you may use the File Manager to drag and drop these files into the right list The files you use should be from the current capture directory If you leave the Fusion Object Loader window open while working and happen to change capture directories you need to select the Refresh but ton on the Object Loader to get a correct list of files in the new directory Figure 7 3 Fusion Objects Loader Interface with Prop and Capture Files EE Fusion 70 Objects File Types M MarkerSet Files mars V Prop Files prop V Project Files pri V Object Group Files zin Club mars Golfer mars Refresh Button Recently Used Groups Pause Load Objects Clear History Quick Load Run Unload Objects x Club mars Golfer mars g Save As Group Save Selected As Group Select All Unselect All Select All Unselect All Clear All 7 5 Chapter 7 Motion Capture Tab Cortex 2 0 Reference Manua
367. or Specific Applications Cortex 2 1 Reference Manual Question Answer Question Answer Question Answer Is there a way to have two templates for two people in the capture that identify them both in real time at once rather than using one huge tem plate that includes everything This is the MTO Multiple Tracking Object item Refer to Multiple Tracking Objects on page 9 7 What does the extend template option do Extend Template adds new linkage stretch to the existing template if you need it For example you can make a one frame template ID some mo tion then you can extend the template so that it knows about the new mo tion linkage stretches as well as the old ones What are the latest specifications for the Motion Analysis system perfor mance From the 5 person Eagle camera data included in the Cortex release pack age under the Samples folder e Trial FivestarsAgainandAgain VCX 1800 Frames 120 Frames sec per the Cortex software e Biggest VC file 3900 KB highest data rate Smallest VC File 1100 KB Avg VC size about 2500 KBytes e Data rate per Eagle camera Max size file 3900 KBytes X 120 Frames sec X 1 1800 Frames 260 KBytes sec or about 2600 Kbps kilobits sec or 2 6 Mbps or about 2 6 of the 100 Mbps Ethernet or about 0 26 of the 1000 Mbps Ethernet e Avg size file 2500 KBytes X 120 Frames sec X 1 1800 Frames 166 KBytes sec or about 1660 Kbps or about 1 6 of the 100 Mbps Ethern
368. orce_ plate mus cles or other_data These keywords must be lowercase Following each keyword is information describing the variable This keyword specifies a ground reaction force variable It must be fol lowed by three values 1 The force plate number 1 2 3 etc then 2 The keywords force or moment then F 16 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module forcepla cal Note 3 The channel component x y or z for AMTI or Bertec force plates or x12 x34 y14 y23 z1 z2 z3 24 for Kistler force plates This keyword specifies an EMG variable It must be followed by one or more SIMM muscle names The keyword mvc may optionally appear after the last muscle name If mvc appears then it must be followed by an integer number that SIMM uses as the voltage for the maximum voluntary contraction when scaling that EMG channel If no MVC value is speci fied then the channel is scaled such that its maximum value is 1 0 EMG scaling is performed after the EMG channel s data has been smoothed and resampled to the motion s frequency This keyword specifies a data channel that exists simply to be included in SIMM plots This keyword may be optionally followed by a single word that will be used to label this channel in SIMM plots If no name follows the other_data keyword then the name of the imported variable will be used When importing analog data from ANB ANC files SIMM uses the same calibration file as C
369. ore information on this license please contact Motion Analysis Customer Support support mo tionanalysis com You must also activate check the Reference Video avi check box in the Motion Capture gt Output panel for CortexDV to work Cortex sends an Ethernet packet to CortexDV to start and stop the cap ture It also tells the name and number of the current capture Systems that have more than one Ethernet port must specify which Ethernet port to use Using the same Ethernet port that the cameras use works fine for most systems You can designate which Ethernet port to use with the AVI Re mote Signal Output function in the Tools gt Settings gt Misc tab This has a pull down list of the Ethernet ports known to Cortex when it was launched Launch CortexDV Select the desired camera capture device from Camera dropdown If there is a single video camera connected to the host system Cor texDV connects to this camera automatically 3 Select a Capture Folder to indicate where captured files should be stored 4 Select a Capture File to indicate the name of the file that will be cre ated 5 To begin recording press the Record button red circle A red RECORD will display next to the player control panel indicating the system is recording and a message will be displayed in the Message Bar indicating record start time 6 To stop recording press the Stop button The red RECORD will dis appear and a message will be disp
370. origin off sets It will use these parameters to determine joint center locations and segment lengths using the same algorithms that OrthoTrak does If there is no personal dat file present in the folder this option will be grayed out If it is checked and you do not want to load personal dat click the box to turn it off For C3D import only This option allows you to choose from which pa rameter field in the C3D file to read the names of the tracked markers Be cause the POINT LABELS field in a C3D file is limited to four characters some software packages e g Cortex store the full marker name in the POINT DESCRIPTIONS field Since the marker names in the tracked file must exactly match the names used in the mocap model if your C3D file does not contain full marker names in the POINT DESCRIPTIONS field you may have to edit the mocap model so that the marker names match the four character names stored in the POINT LABELS field This field allows you to specify the total mass of the model after it has been scaled to fit the size of the subject After the scaling is done all the body segments mass parameters are scaled up or down by a single per centage so that the total mass of the model equals the number entered into this field This field has no effect if mass properties are not specified in the model file F 11 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual preserve mass distribution This option giv
371. ortex and OrthoTrak for processing force plate data Therefore you can simply copy the forcepla cal file from your Cortex folder into the Resources mocap misc folder For users who need to create a forcepla cal file to describe their force plate s refer to Appen dix C of the OrthoTrak manual forcepla cal is not used for C3D import since C3D files contain the nec essary calibration information for the force plates SIMM Motion Module Guide to Mocap Model Markers Definitions This guide describes the markers used by the Motion Module in SIMM to load each Mocap Model scale it to fit the subject and import recorded motions For details on how the Motion Module processes the marker data and the model see Chapter 5 of the SIMM User Guide For a tutorial of the Motion Module click on Help gt SIMM Tutorials gt Motion Mod ule Demo in the SIMM menu bar This document focuses on the names and locations of the markers and when they are needed by the Motion Module Static Trial A TRC TRB or C3D file of a motion capture subject in a static pose usually the T or scarecrow pose Motion Trial A TRC TRB or C3D file of a subject performing an activity such as walking or throwing F 17 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual Mocap Model A SIMM musculoskeletal model that can be loaded into SIMM scaled to fit a subject using a static trial and used to animate motion trials of that subject
372. ortex first if it is running This will guarantee that Cortex is using the same mocap model and the same scaling algorithms as SIMM uses F 7 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual Each motion capture session Note 10 Open the Model Viewer window 12 11 13 14 Open the text file SIMM Resources preferences in a text editor such as Notepad or Wordpad Locate the line that reads Cortex MACHINE lt hostname gt and change the hostname to the name of your Cortex machine Save and close the preferences file make sure that the file is saved as ASCII text with the name prefer ences Wordpad likes to surreptitiously append a txt extension when it saves files that don t already have a filename extension If your motion capture system includes force plates copy the file for cepla cal from your Cortex computer onto your SIMM computer and put it in the folder SIMM Resources mocap misc Copy the folder containing the motion data from the Cortex computer to the SIMM computer or make it shared If there is a personal dat file for this data make sure it is in the folder too Launch Cortex Load the appropriate capture Select File gt Load Capture and select the tracked marker file corre sponding to the static trial for the subject Under System gt Misc click on the radio button for SIMM OrthoTrak Solver located in the Skeleton Options area Launch SIMM Select File gt Open
373. ost Process Dashboard is available when Cortex is in Post Process mode as opposed to Tracking mode After you have generated and saved tracked data this becomes available to help manage a data editing ses sion It controls the range of visible frames and the range of selected frames to be edited It also provides several controls for playing through the tracked data and choosing a current frame This dashboard is de scribed further in Chapter 10 Post Processing Panel Figure 4 64 Post Process Dashboard Move to Active Play Pause Play Speed Frame Lowest Highest Frame Frame Selectors Sick i F T ah T T T T T T T T T T T T ah T T T T T T T T AS apy coe 497 497 gt sso 539 Kinetics RO Si gt 4 Bl gt ime Calculate 23 Stopped 964 Frames 120 FPS Up Units mm Analog 600 00 Hz ce Selected Frames Low Move 1 Frame Selected Frames High Visible Frames Low Time Code Visible Frames High Post Process Tool Strip Figure 4 65 Post Process Tool Strip t D O Vee i amp amp FCORKIAB QuickID Rectify Create Template Template Marker ID Exchange Cubic Virtual Calc Smooth Make Rectify Delete Cut Cut Search PP Template ID Rectify Join Join Ms Unnamed Unnamed Unnamed Outside Settings Post Process For a listing and description of all Post Process Tool Strip Icons reference Tool Strip Icons Post Process T
374. ot recommended at this time While Cortex 32 bit runs fine with the same memory limits as WinXP stability problems have been ex perienced with Vista that is unrelated to Cortex Vista 32 bit seems to degenerate over several weeks has trouble booting and eventually re quires reformatting the disk drive and reinstalling Vista again In Win7 the font size in Control Panel gt Appearance and Personal ization gt Display needs to be set to Smaller 100 the default is Medium 125 Pros on Using WinXP x64 64 bit Version of WinXP 1 Allows the user to run Cortex 64 which runs 20 faster than WinXP 32 bit on the same computer Motion Analysis supplied Time Code Reader is supported and is frame accurate Firewire Digi tal Video cameras collect data and run to specifications WinXP x64 and Win7 x64 are solid and runs both Cortex 32 bit and Cortex 64 2 For machines that support 64 bit Windows the user has the option to utilize more RAM This is beneficial when you are dealing with large TRB files Testing has exposed memory problems on WinXP 32 bit with 130 MByte TRB files that have 4 persons recorded at 120 Hz for 4 minutes The same files run smoothly without memory problems on the 8 GByte WinXP x64 computer Only Known Problem In Using WinXP x64 WinXP x64 does not support analog data collection National Instruments drivers will not install on WinXP x64 Users can do all Post Processing and editing tasks run Calcium Sk
375. ote after you apply the configuration the Setup file is not updated until it is saved Figure 4 37 Force Plate Configuration Interface Force Plate Configuration File Note Each force plate s channels must be configured in the System gt Analog panel in order for that force plate s data to be collected Noise Filters Use Force Threshold Force Threshold N 5 Require COP on Force Plate Margin Cal Units 0 Calibration Matrix o P o Lo P o Force Plates Force Plate Specs Type Kistler v AMTI AccuGait Width 4 AMT AccuGait 232 Bertec Length fy Tec Gihan Kyowa Dengyo Motek Gait Drigin o 6 o o0 0 a Position in Yolume o o Lo H o o o f o opopo eo of of o o o em m Orientation in Yolume ojojo o W o o eo of o o o Llo o Lo ff o Moving Force Plate Options C Track Position Orientation Tracking Object Kristina o o W o W o Lo foo g o o Rotation Offset p Position Offset mil o J o f o em Tracking Segment o N Lo E o E o Lo g o f o OK Cancel Apply Force Plate Configuration File gt Menu Import forcepla cal and Export forcepla cal Reads or writes legacy forcepla cal files When importing the force pla cal file s contents are loaded into the form and must be applied via the OK or Apply buttons before they will take e
376. ou create when you make a template The result is that if you use the same marker set repeatedly you will not have to ID the new person each time the marker set is used The marker identification is automatic and instant saving you time The Model Pose has its own kind of generalized template that is used to automatically identify a new person when they appear in the field of view This generalized template depends on the person facing the same direc tion as the stored Pose ID and having the markers in the same general lo cations with respect to each other You save the Pose ID from one frame of data and is saved in your capture file It saves you the steps of using the Quick ID feature to identify a new person in order to make a template for them The Auto ID feature works in the RealTime mode when you are connected to cameras or it works when you are tracking the data from VC files after the collection The following are basic steps on how to use the Pose ID function The Connect Cameras button will activate all the cameras used in a mo tion capture session A pop up message announces the number and type of cameras A D units Reference Video cameras and time code reader if present The Raw Video button will tell the program to simulate a live motion cap ture session from previously captured Video Camera VC files It also al lows you to tack and record to TRB or TRC trials for which you have raw VC files This button opens the Se
377. our computer is too slow for the number of markers being tracked For single person captures you may connect the DV Cam era directly to the Cortex Host computer In this case the CortexDV soft ware is not needed as it is built into the Cortex software You can run CortexDV on one or more computers and then capture multiple AVI files multiple views You may experience a small delay in frames from the Cortex software and the CortexDV software when capturing This can be easily reconciled using the Adjust Frame Offset function found in Tools gt Settings gt Playback which allows for time matching data streams It is recommended that you start your digital video collection from pause mode not in run mode to minimize the potential for frame offset be tween the AVI and TRB files Cortex 2 1 Reference Manual Chapter 1 Introduction Software Packages Used with Cortex The following are software products offered by Motion Analysis that are used in conjunction with Cortex These files will require a license file and a separate installation package Animation The MAC Animation Plugins also known as the File IO Plugins are used Plugins to read and write Motion Analysis motion capture files TRC into all of the major animation software packages including e Maya e 3DS MAX e Softimage XSI e Lightwave e Alias Motion Builder The Motion Analysis HTR file format is used for skeleton motion capture data The Animation Plugins can t
378. overwrite the original mocap jnt file In stead after editing the marker set save the model to a new file name and copy the altered markers into mocap jnt All of the markers in the mocap model have X Y and Z offsets that put them in realistic locations given the dimensions of the generic model Thus if you load the unscaled mocap model into SIMM using the File gt Open command not the File gt Open Mocap Model command which will scale it the markers will appear in positions corresponding to where they are placed on the subject These offsets are purely decorative to help you view the marker set They are not used by the Motion Mod Cortex 2 1 Reference Manual Appendix F SIMM Motion Module ule to process any marker data To explain why this is so we must first introduce the concept of critical markers and non critical markers Critical markers are ones that must be present in the static trial in order for the Motion Module to load and scale the mocap model For the lower body these markers are V Sacral R ASIS L ASIS R Knee or R Knee Lateral R Ankle or R Ankle Lateral R Heel R Toe L Knee or L Knee Lateral L Ankle or L Ankle Lateral L Heel and L Toe If any of these markers is missing from the static trial the SIMM model of the lower body will not be loaded For the upper body the critical markers are V Sacral R ASIS L ASIS R Shoulder R Elbow R Wrist L Shoul der L Elbow L Wrist Note that the ASI
379. p in the Analog panel 6 channels per plate e Channel 1 connects to the F1X signal e Channel 2 connects to the F1Y signal e Channel 6 connects to the M1Z signal If there are two plates it connects to Channels 7 through 12 The reserved names for OrthoTrak and KinTools RT are PLATE 1 F1X F1Y F1Z M1X M1Y M1Z PLATE 2 F2X F2Y F2Z M2X M2Y M2Z See the OrthoTrak Reference Manual for OrthoTrak muscle name con ventions The OrthoTrak muscle names are built into the analog display They can be selected in the same manner as with the force platform man ufacturer and channel B 4 Cortex 2 1 Reference Manual Appendix B Analog Input Hardware and Software 32 Channel 16 Bit NI USB 6218 Configuration Note Note The following has been tested on Windows XP Pro Windows Vista and Windows 7 with the latest web based updates from Microsoft The Cor tex software will support up to 6 USB devices and up to 192 channels of analog input USB 2 0 ports work best USB 1 0 ports have not been tested Up to 6 A D devices can be installed into the host computer The Sync Cable must be connected to all devices A single pull up resistor is needed for legacy cameras Eagle Hawk Figure B 1 32 Channel 16 Bit A D Hardware Setup for the USB 6218 A D Master Camera Master A D Sync Cable 600000000 000000000 000000000 000000000 NI USB 6218 or NI USB 6259 First Install the Software Eagle Hawk Camera Cab
380. p is dis played in the 3D Display window and streamed to the SDK interface as a 6 DOF segment that is reported with respect to the Global Coordinate System defined by the L frame calibration Show Template Linkages This option selects all linkages and displays them in the following man ner e Black parts represent measured linkage information for use with the Identifying Template for Template ID and Template Rectify This is set or extended when you Create or Extend the Template e Grey Parts represent the Extra Stretch used by the Template ID and Template Rectify This is set in the Model Edit gt TreeView Links You can set individual links or groups of links e When you create a new link in the Model Edit gt Markers Panel the default values for the Extra Stretch is 15 can be changed in Model Edit gt TreeView e For compatibility with previous versions of EVaRT software project files with undefined templates were always given extra stretch values of 0 30 30 which is larger than is now optimal Reading older project files with undefined links will be given Extra Stretch value of 0 30 and can be changed by the user selecting those links setting the Extra Stretch and saving the file 8 13 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Figure 8 13 Show Template Linkages Cortex Matt prj MkattCartwheelt tre E e Lots Dataview Toos Heb IMotionAna System Calbration Moton Captu
381. paced when viewed from the center of the capture area e Beware of making the capture area too large The resolution and the quality of the data may be compromised 5 Place cameras in lower positions Good results can come from adding cameras or positioning the cameras low on the floor looking up at the capture subject This is also effective for capturing markers as the subject is stooped over or lying on the floor Opposite camera ring lights can be masked out if necessary 3 10 Cortex 2 1 Reference Manual Chapter 3 Camera Setup 6 One by one adjust each camera so it sees as much capture area as possible 7 To see the camera view right click in the 3D view and then select Show gt Show Camera Field of View See Figure 3 10 Figure 3 10 Show Camera Field of View File Layouts Data Views Tools Help seg otionAnalysis Current Directory C Program Files Motion Analysis Cortex2 Samples 16 Camera Calibration Face Body Browse System Calibration Motion Capture Post Process Model Edit Plugins Presentation Markers ents Ess 4 Sree Of VWHOEDP SES amp ADL
382. plate Rectify marker s over the selected frame range Hide selected marker s from view Show selected marker s Make selected marker s unnamed Create Template Cut Cut Outside Exchange Smooth Join Cubic Join Linear Join Virtual Cut data in selected frames from the selected marker s Cut data outside of the selected frames from the selected marker s Exchange data between two markers over the selected frames Smooth selected marker s over the selected frames Join selected marker s over selected frames using cubic splines Join selected marker s over selected frames using linear interpolation Create a temporary virtual marker to fill in missing marker data Undo Undo last edit on marker data Search Search for spikes and or gaps as defined in the Search tab 4 69 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Status Bar Pop Up Menu Figure 4 55 Status Bar Pop Up Menu Enabled View History Allows the StatusBarLog ixt file to collect new messages Same action as double clicking StatusBar line Pops the Status Bar history into a text window This is sometimes useful in tracking down problems especially if you are having data collection problems in real time Digital Reference Video Option CortexDV Software Reference Cameras Supported Note The color Digital Video option allows you to record a time matched Ref erence Video along with your mo
383. ppendix specific to the manufacturer of your force plate This is the offset of the origin of the force plate XYZ coordinate system relative to the center of the top surface of the force plate Each manufac turer provides this offset value This tells the Cortex system where the center of the top surface of the force plate is located relative to the Cortex video coordinate system Once this is established the video calibration frame must be placed in the same location each time you calibrate The center of the top surface can be found by measurement or drawing diagonal lines from opposite corners The units of measurement are centimeters cm This matrix describes the orientation of the force plate relative to the lab oratory or room coordinate system It is a matrix of direction cosines of the angles between the force plate coordinate system and the laboratory coordinate system Using the terminology cos Xplate Xlab to indicate the angle between the force plate X axis and the laboratory X axis the matrix takes the following form Xplate Yplate Zplate Xlab cos Xplate Xlab cos Yplate Xlab cos Zplate Xlab Ylab cos Xplate Ylab cos Yplate Ylab cos Zplate Ylab Zlab cos Xplate Zlab cos Yplate Zlab cos Zplate Zlab Since in real situations the force plate should be aligned with the room coordinate system the numbers in this matrix will always have one of three values Angle 0 cos 1 Angle 90 cos 0 Angle 180 co
384. ppet of trajectory requires its own slot and different parameter values will create different sets of trajectories How will I know if I need more marker slots After loading the file trb trc In Post Processing Mode scroll down the unnamed marker list u_marker If the all the slots are filled then you should increase the number of marker slots I just made some changes to my capture file but I do not want to recap ture the entire motion list over again Is there any way to rebuild the trb trc data from the VC files Yes You can re record the tracks files using the updated set of parameters in Cortex First load the VC files Then go to the Motion Capture gt Out put panel Select to export a trb or tre file you have to select the option OK to Overwrite if the tracks file already exists Click on Record The recording will automatically stop at the end of the VC file as long as the option Loop Raw Files is not checked in the Tools gt Settings gt Play H 5 Appendix H Questions and Answers for Specific Applications Cortex 2 1 Reference Manual Question Answer Question Answer back tab If it is checked then you will have to stop it by pressing the Stop button same as the Record button it changes name during the re cording Our templates in Cortex are always either extremely good or extremely poor Can you give us some time so we can get a consistently good tem plate each time The first step
385. presentation graphs Enabled For Live Enables Disables the Event in Live Mode Enabled For Post Enables Disables the Event in Post Processing Cycle Properties Name The name of the Cycle All Cycles must have unique names Description A description of what the Cycle represents 4 51 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Color The color in which the Event is illustrated which shows up on the presentation graphs Start Event The Event that triggers the beginning of the Cycle End Event The Event that triggers the end of the Cycle This can be the same as the Start Event More on Event Scripts The Event script specifies what feedback will be provided for an Event The Sky functions that are used for setting the Event flags are swEvents_SetUserEventOnFrame and swEvents_GetUserEventOnFrame For more information on writing Event scripts see the BioFeedTrak tutorial in Help gt Tutorials Scripts Area The lower portion of this area contains a grid that lists all scripts when they were compiled and any runtime errors that were encountered while executing the script The scripts must be compiled in order for the Event detection engine to make use of them This is done in advance so that run time resources are not consumed by the task There is a check box to Auto Compile the scripts when a new Setup is loaded If the script is modified while Cortex is running it must be re compil
386. r functions found in the Cortex dll Any call you make is immediately passed on to the corresponding core function in Cortex These are the same functions that the Cortex GUI uses at runtime so again for the most part you can do just about anything through the scripting interface that Cortex does interactively All the script functions have the same name as the corresponding dll function call except a sw has been added to the beginning sw stands for Sky Writing Online help for all functions is found from the Sky Functions list on the right also clicking on a highlighted Sky function in side the Input Text window will display help for a function The Sky Functions filter box will display only those Sky functions which contain the text in the filter This makes it easy to search for functions that contain a particular name such as Camera or Marker or Load A drop down menu retains previously typed in filters Only those names shown in the Sky Functions list are highlighted in the Input Text window The Sky Functions list is generated automatically from the internal script ing objects so the list is guaranteed to display all available Sky functions 12 7 Chapter 12 Sky Scripting Interface Cortex 2 1 Reference Manual The functions are organized in sub folders by category to make finding functions easier Status Bar The status bar at the bottom of the window displays messages regarding operations going on in the
387. r E folder 5 6 Cortex 2 1 Reference Manual Chapter 5 System Tab Do need to update camera software Old Camera New Camera Compatibility Issues Note Dedicated Interface for Cameras The Download Progress window in the Download New Camera Software box will show the status of each camera 7 After the firmware has been downloaded on each camera a message saying File download completed X X seconds now writing flash will appear in the Download Progress window 8 Once the firmware has been installed on each camera a message say ing Successfully wrote new image into flash will appear in the Download Progress window and the ringlight on each camera will turn off Also each camera will have a red R showing on the cam era display board DO NOT touch the cameras until the R appears on the display board 9 Once all cameras have R on their display boards power cycle turn on off power each power hub 10 Once all cameras have rebooted select Connect To Cameras The camera firmware date on each camera can be checked by going to System gt Cameras and verifying the date is June 30 2010 You can continue to use the same rom bin software Reasons to upgrade to the new camera software include 1 Displays camera numbers greater than 99 2 Mixed camera environment with all cameras including Eagle Hawk and Raptor Cameras with different revisions of the CPU board installed may exhibi
388. r Samples SkyExamples 12 2 Cortex 2 1 Reference Manual Chapter 12 Sky Scripting Interface Updating Old Sky Files The Sky scripting language based on Visual Basic is pretty much the same as previous versions the first version for EVaRT was called Sky and this section is mostly meant to describe how the current version is dif ferent from that The second version of Sky for Cortex 1 was called Sky2 to avoid confusion with the EVaRT version the most recent ver sion of Sky for Cortex2 is back to being called Sky and is almost identi cal to Sky2 with the exception of new commands added to implement Cortex2 features but there are a few small differences based on how Sky invokes the Script object The most important difference is that the main execution of the script is contained within a subroutine named SkyMain Other subroutines can be defined and used within the script but the ac tions of the script need to be contained in a SkyMain subroutine The first version of Sky required a Main subroutine this is now reserved for the compiler and using Sub Main will cause a compiler error For example FindAutoIDFrame 1 Increment frames and keep calling AutoID until a marker gets identified This assumes no markers were identified before being called 1 sub SkyMain swPopups SetQuietMode 1 iHi swhoadedTracks GetNumberOfFrames 1 for i 0 to iHi swLoadedTracks SetFrameNumber i swPost_AutoID iResult
389. r names Order them so that the highest markers are at the top of the list Cap ture a trial then load the last capture 3 Quick ID to Identify the markers edit if needed use caution to avoid any marker switches or mistakes in making the Template 4 In the Model Edit gt Markers tab create linkages for the template Click and drag in the 3D views to make the linkage lines between the markers For best automatic identification use rigid triangles where possible Connect things that are close and don t move much with respect to each other 5 Click on Create Template Check Show Template Linkages Use a frame range as large as possible where there are no mistakes Check Include current frame as the Model Pose if you want to use this as the New Subject identifying template for new persons 6 Select Save MarkerSet As and give it a name It will be saved as a mars MarkerSet file Save it in the current folder 2 9 Chapter 2 Planning a Motion Capture Session Cortex 2 1 Reference Manual 7 Copy it to the System Objects folder If you want to use the Marker Set in other folders make a copy as follows In the Motion Capture gt Object panel select the MarkerSet name and use the blue DOWN arrow You will see a copy in the System Ob jects folder 8 Using the new MarkerSet in a new folder Load an existing Setup from your last Capture Select Save Setup As and make a new folder From the Motion Capture gt Ob
390. r right corner below the marker list Now no frames are selected 4 Left click anywhere on the XYZ Graphs to set the Current Frame which is indicated by the red line 5 To zoom in press the Zoom Frames In hot key default is I or by right clicking in the XYZ Graphs and selecting Zoom Frames In from the pop up menu 6 To zoom out press the Zoom Frames Out hot key default is O or by right clicking in the XYZ Graphs window and selecting Zoom Frames Out from the pop up menu 7 Unzoom time Double click on the Time Slider on the Post Process Dashboard to zoom out completely making all frames visible The Post Process Dashboard Visible boxes will now have a 1 and the highest frame number displayed N The second method of zooming in frames is described as follows 4 82 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Amplitude Zoom 1 Hold the middle mouse button down in the XYZ or the Analog Graphs 2 Drag the mouse to the right or left to select any number of frames 3 To zoom in press the Zoom Frames In Hot Key default is I or by right clicking in the XYZ Graphs window and selecting Zoom Frames In from the pop up menu Zooming amplitude is done relative to the closest data point and frame nearest to the location you initially click on You can optionally zoom into the data in the Current Frame regardless of where your mouse cursor is on the screen This op
391. r set the MOCAP_MODEL variable in SIMM Resources preferences to that file or choose that file using the Options Choose Model Model com mand in the SIMM menu bar Table F 1 Combinations for Model Components lower upper movable fingers muscles file name extremity extremity yes yes yes legs only mocap jnt yes yes no legs only mocap jnt yes no no legs only mocap jnt no yes yes none mocap jnt no yes no none mocap jnt no right arm only yes none rightArm jnt no right arm only no none rightArm jnt no left arm only yes none leftArm jnt no left arm only no none leftArm jnt yes yes yes legs only 3D mocap3D jnt yes yes no legs only 3D mocap3D jnt yes no no legs only 3D mocap3D jnt It is important to note that the critical and semi critical labels for markers are relevant only for the static trial For motion trials all markers are op tional That is after recording the static trial you can remove any of the markers from the subject before recording motion trials Generally how ever you will want to keep all of the markers on the subject for the mo tion trials with the possible exception of the medial joint markers Also once the static trial has been recorded you must be careful not to move any of the markers on the subject except for removing them completely SIMM uses the static trial to calculate the coordinates of each marker rel ative to its body segment so if you mov
392. r sport accessories To use this feature 1 Create a capture file with just the marker names of the prop Each prop should have its own marker set and associated capture file There must be three or more markers for rigid bodies to work five or more markers is recommended Marker names do not matter when they become tracked as Rigid Objects Linkages are not needed as Rigid Objects have implicit linkages between all markers on the 7 7 Chapter 7 Motion Capture Tab Cortex 2 0 Reference Manual object You can create linkages to help you visualize the prop when it is tracked if you wish but when a rigid object is identified as such both the markers and the linkages are shown as a purple color Create a Prop file Record some number of frames of the prop maybe 2 5 seconds and then load the Tracks into Post Processing Identify the markers and click the Create Template button Select Rigid Object as the template type The Create Template changes words to Create Prop File A message pops up telling you that you created a prop file in your current capture folder A second message informs you that The type will become rigid when selected on the Objects panel and that a Rigid Object Template has been created Using the prop file in you local folder the prop file can be selected as any Tracking Object in the Motion Capture gt Objects panel Props can be selected as normal tracking objects and they take up one of the tracking object
393. rage residual value The aver age residual value is found in the lower left corner of the screen when the cameras are running A typical parameter value is 4 mm Max Target Speed mm frame Sets a speed limit on the markers A marker s track is eliminated when it surpasses this value When tracking the tip of a golf club or other object with fast moving markers it is possible that this value will need to be in creased A typical parameter value is 100 mm frame Make it larger if the tracks break into small pieces when tracking fast objects Marker Size mm Limits the size of the markers so that higher residual cameras do not see more than one centroid for the same marker This parameter should be set to the physical size of the markers in use 25 4 millimeters 1 inch This parameter will also set the size of the markers that appear on the 3D View Max Prediction Error mm Is is used to identify a marker in the next frame While the software is tracking a marker it is assumed that it will not deviate by more than this amount along its path Otherwise the marker will not be identified in the frame A typical parameter value is 30 mm Make it larger if the tracks break into small pieces when tracking fast objects Min Cameras To Use Tells the software what the minimum number of camera s rays are re quired to triangulate track a marker during a frame Some users will benefit by setting this value to 3 if spurious data points
394. rate the system you must first decide on the location of H the origin and orientation of your object reference frame This is deter Coordinate mined by the calibration L frame All results generated by the tracking System process are referred back to this reference frame The selection of an object reference frame is arbitrary However judi cious selection is advised In most cases it is advisable to align one axis of the frame with the axis of gravity and another with the predominant di rection of motion Remember that all targets will be tracked with respect to the object reference frame and that the units used to locate the control points mm cm inches etc will be the same units used in the tracking process For computer animation users a commonly used coordinate system con vention is called Y up with the Y axis pointing up the Z axis normal to the direction of motion and the X axis oriented from the person s right side to left side Looking at the frontal view you would see a normal X Y plot Y up X right and the Z coordinate sticks out of the screen For biomechanics applications it is common to use a coordinate system with Z up X in the direction of forward motion and Y toward the subject s left side The coordinate convention you use is your choice Be sure that e The coordinates of the calibration L frame are entered into your project file s correctly Cortex 2 1 Reference Manual Chapter 3
395. re Post Process Model Edt Plugs sak MOR Ee BM Py Ss QUID Rectty Tempie Temoiste Template Marber ID Exchange Cub Crone 5 Rectty den In We 100 200 3o awo soo soo zoo soo s00 1000 100 1200 1300 1400 iene Ce oo 00 00 mma E Bote J oe F Create Template ii Frames izo res Yup Urea This feathered stick figure can be used to look for possible problems in the template such as e Asymmetry Unless the person is doing asymmetric activities the template should be fairly symmetric in both the black and grey bands e Black lines that are too long This can be caused from a mis identi fied marker or a marker switch that got measured and stored in the template with the Create Template or Extend Template functions Template ID Uses the template to ID all markers in the current frame a A All Markers Pull Down Selection Allows you to select all markers at once for Identifying Selected Markers Pull Down Selection Allows you to select specific markers for Identifying Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Template Rectify gt Marker ID o Exchange Vy Cubic Join Join Linear co o Virtual Join 4 I Uses the defined template and identified current frame to ID markers over the selected frames Option All or selected markers The user selects a marker in the marker set list to identify that marker
396. re 5 5 5 7 Local Objects 7 7 Loop Raw Files 4 29 Low and High Selected Frames 8 4 Low and High Visible Frames 8 2 mac_lic dat 1 5 E 2 Make Slide 4 45 Make Unnamed 8 16 marker cloud defined F 1 Marker ID 8 17 Marker Size 3 27 4 24 Marker XYZ Graphs 4 15 Markers Identifying 8 11 Selecting 4 83 Unnamed 8 10 Markers Panel 9 2 Clear MarkerSet Button 9 3 Create Linkages Button 9 3 MarkerSet Name 8 13 9 4 Masks Clearing 5 11 Creating 5 11 Mass Model Editor 4 50 Master Sync 5 3 Matrix Method 9 23 Max Frames 4 39 Max Horizontal Lines per Marker 4 23 Max Horizontal Lines per Marker 4 23 Max Prediction Error 4 24 Max Residual 4 24 Max Residual mm 4 24 Max Speed mm frame 8 23 Max Target Speed 4 24 Max VC File Size 4 39 Max Prediction Error mm 8 23 Menu Bar 4 3 Merge Captures 4 56 Min Cameras To Use 4 24 Min Horizontal Lines per Marker 4 23 Misc 4 44 Cortex 2 1 Reference Manual Misc Tab 4 37 mocap model F 15 joint center calculations F 13 marker set F 14 scaling F 13 static pose F 10 Mode Panel Buttons 4 58 Model Adjustments 10 4 Model Edit 4 58 9 1 Overview 9 1 Motion Analysis Corp Contact Information 1 18 Motion Analysis License File Example E 2 Motion Capture 4 58 Overview 7 1 Motion Capture Laboratory Setting Up 3 1 Motion Capture Panel 7 1 Motion Capture Terminology 2 5 Motion Composer 1 10 Motion Module F 1 F 17 opening analog data fi
397. reated for rigid objects with 4 or more markers per segment For rigid or semi rigid objects such as swords spears head markers torso markers multiple markers on a basketball it is convenient to use this feature to join across missing marker data You must select a starting frame where all markers that you select are all present and part of a rigid body You then select a range of frames on which you wish this to operate Select Rigid Body Join and it automati cally joins across the missing marker data There are three main Rectify tools for naming markers and propagating the names through time Rectify Rectify Unnamed and Rigid Body Rec tify They are not for generating XYZ data from the 2D camera views which we call Tracking but they are very useful for Identifying the tracks or markers Rectify means to make right or set right All of the Rec tify functions start at the Current frame and go forward in time first then backwards from the current frame For more information reference these functions in the Post Process Tool Strip section starting on page 8 11 Template Rectify In Post Processing use this when you have a reasonably good template Work from known good frames into unknown and difficult frame ranges Uses the template from the Create Template item A template can be of one or more frames should represent characteristic motions to be seen be tween markers and is a measure of the min and max linkage length
398. rkers from the trial and sets the values of the model parameters so that the appropriate portions are in cluded For example if the critical markers on the right hand are present then the degrees of freedom in the fingers are activated If they are not present the hand is modeled as one rigid body segment with movement only at the wrist The Mocap Model that you will most likely want to use is mocap jnt This is a model of a full body with lower extremity muscles and option ally movable fingers in each hand There is also a right arm model and a left arm model rightArm jnt and leftArm jnt These should be used if you want to capture motion of one arm without any torso or pelvis mark ers Lastly mocap3D jnt is similar to mocap jnt but it includes 3D mus cle surfaces for 18 key lower extremity muscles rather than the lines of action for all 86 muscles These muscle shapes look more realistic but they do not have force generating parameters so you cannot calculate the lengths or forces in these muscles during the recorded motion F 18 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module Table F 1 on page F 19 shows the available combinations of model com ponents To determine which Mocap Model you should use find the row that best describes the model you want then locate the filename in the last column All of these files are located in SIMM Resources mocap Once you have determined which one to use you can eithe
399. rocedure If you use the Camera Aiming check box in the Calibrate panel to position and orient your cam era the focal length entries should be nominally correct e g 6 for 6 mm lenses In the Camera Aiming and Calibration with Square functions the Show gt Show Camera Field of View cone is determined only by what you put in this table After the wand calibration the actual focal length of the lens is calculated exactly and can be stored in your capture file Note The Calibrate Wand option calculates the actual focal lengths but does not update the table Figure 6 5 Lenses Orientation Tab Settings Dak FocalLength Positioning Normal Normal Normal j Normal Normal Normal Normal ze Normal 6 7 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Capture Volume Tab This displays the rectangular capture volume according to your measure ments and helps to provide a visual reference of the volume to the opera tor It does not affect the tracked data in any manner It is for display pur poses only in the 3D view In the Plugins gt X panel the Delete Outside Volume feature will delete any marker data outside of the capture volume Figure 6 6 Capture Volume Tab Square Seed Calibration of Cameras Settings EER Calibration Cameras Playback 3D Display Post Process Tools Misc Id Params Plugin
400. rred to as the root of the skeleton Skeleton Builder as the name im plies is a tool that allows you to construct a skeleton by creating bones and arranging them in a hierarchy Each bone is defined by the motion of three markers used to construct its rotation data The Skeleton Builder in terface is incorporated with the Cortex interface Skeleton Builder is typi cally used in the Movement Analysis Biomechanics applications Skeleton Builder bone definitions are stored in the Cortex capture file Any time you wish to save the definitions you have created simply save out a capture file Various capture files are stored in the sample directory which contain the example skeleton at various stages of construction 1 9 Chapter 1 Introduction Cortex 2 1 Reference Manual Motion Composer Integrated Authoring Interactive Player Rich Media Support Motion Composer is a component of the Cortex interface which provides a seamless workflow for the user to package and present a motion capture session This is done by loading data into Cortex and using Motion Com poser to generate snap shot slides of the data The slides are stored and can be retrieved and interacted with at a later time Some of the key fea tures to be found in Motion Composer are described in the following sec tions Motion Composer is an integrated part of Cortex This integration allows new and existing users a seamless pathway from data collecti
401. rsion of Cortex from the CD Install the Sentinel Drivers after the Cortex installation is finished Insert the Dongle into the USB port Insert the Motion Analysis USB Flash drive into a USB port Double click on the program Install Mac License and follow the instructions Press Y or Enter and the license will be installed onto your hard drive in the C Program Files Motion Analysis directory 5 On the Task bar left click the Green arrow icon and select Stop USB mass Storage Device 6 Unplug the USB Flash Drive and store it in a safe place Pens If you need any further information please consult the readme txt file lo cated on the Motion Analysis USB Flash Drive If You Already Have If you have Motion Analysis software already installed you will need to Software Installed add a new line to your Motion Analysis license file provided by Motion Analysis Customer Support 1 4 Cortex 2 1 Reference Manual Chapter 1 Introduction Launch Notepad Wordpad or your favorite ACSII text editor Navigate to C Program Files Motion Analysis Open the mac_lic dat file Add the new line beginning with Cortex 2 from your new license to the bottom of your current license as shown below Pons Figure 1 3 Sample Motion Analysis License File If You Install a Dongle Operating Systems in Different Languages Motion Analysis License File Customer MAC Customer Platform NT SystemID 19c Created 9 15 20xx 1 42 26
402. rtex 2 1 Reference Manual Chapter 4 The Cortex User Interface 8 Press the Export Trimmed Capture button and type in the filename you want or keep the current one 9 If you have more files that need to have the analog channel names replaced you will need to repeat steps 2 through 9 Tools gt Record tThe record function under the Tools menu item starts the recording of a data capture It is the same function as the Record but ton found on the Motion Capture gt Output panel and the F12 function key Tools gt Misc gt Replace Loaded Analog Setup There have been rare instances where the analog channel setup was not correctly recorded dur ing a capture This function allows you to Load a capture or an Imported legacy trb anb file and REPLACE the analog setup with the setup cur rently loaded and seen in the System gt Analog panel This was found to correct some files that were recorded with an incorrect analog setup for unknown reasons The steps are like the Replace Loaded Analog Channel names function above in that you need to use the File gt Trim Capture W Options to force the analog file to be re written with the updated channel names and or other analog setup information Tools gt Misc gt Save Analog Data as After importing new or differ ent analog channel data with the File gt Import ANC menu item you can save the analog file out again with the new or modified channel or data Tools gt Misc gt Make Slid
403. rtex software release 2 Copy the rom_ date bin file into the following directory C Program Files Motion Analysis Cortex2 Release 2 1 Camera Software Figure 5 3 Camera Software Directory amp C Program Files otion Analysis Cortex2 Release2 1 CameraSoftware File Edit View Favorites Tools Help ay pak BL Search Ey Folders E Address C Program Files Motion Analysis Cortex2 Release2 1 CameraSoftware v Ed Go Folders B Motion Analysis 4 CellTrak Cortex 5 Cortex2 DirectX Licensetility 6 Release2 1 x Name Size Type Date Modified a QEagle_Eagle 4_Hawk File Folder 9 14 2010 2 05 PM O Hawk i_ONLY File Folder 9 14 2010 2 05 PM SHawk M File Folder 9 14 2010 2 05 PM Raptor 4 File Folder 9 14 2010 2 05 PM Raptor E File Folder 9 14 2010 2 05 PM S Raptor H File Folder 9 14 2010 2 05 PM H O CameraSoftware O Help 3 Motionview Plugins 9 Return to the Calibration panel in the Cortex user interface 4 Select the camera on the Real Time Dashboard you wish to load the new rom_ date bin software into and click on the New Camera Software button in the Cameras panel Chapter 5 System Tab Cortex 2 1 Reference Manual Figure 5 4 Download New Camera Software Dialog Download New Camera Software Download Type Raptor Series Digital Cameras Download Progress Download To Selected Cameras All Cameras NOTE Non Raptors will be skipped
404. run immediately when selected from any of the Sky file lists e Set Network Folder Set the folder location for the Network Sky Scripts file list This value is saved in the registry e Autosave When on checked this mode causes the Sky interface to auto save the currently selected Sky file when ever the Sky file is changed refreshed or run This is the default mode When off the file is not saved at any time so the user must use Save Script As to save the file e Reset Sky Script Object This clears the VB Script object of all variables and functions so it is just like when the Sky interface was first opened e Colorize Text When on checked the text in the Input Text window is colorized This is the default When this flag is off no colorization is done All Sky functions are shown in blue comments are shown in green and strings are shown in red e Set Startup Script Specify the startup script used by Sky This script is automatically run whenever Sky is first opened This is where Sky buttons are saved so they can be regenerated when Sky is opened e Save Startup Script Save the current state of the Sky interface to the specified startup script Currently this only saves Sky button information e Clear Startup Script Delete the startup script 12 5 Chapter 12 Sky Scripting Interface Cortex 2 1 Reference Manual Local Sky Files Global Sky Files Network Sky Files Input Text e Run Startup
405. ry TRB file has been generated in the current directory and is ready for editing Next the markers must be hand identified according to the marker list built for the subject s marker set assuming that the marker list was already defined prior to the motion capture 11 Choose Post Process from the Mode Buttons 12 Click Quick ID and identify the unnamed markers according to the conventions described in Appendix C Marker Sets 13 Click Rectify This applies the naming convention across all the frames of data 14 Manually cleanup and identify all tracks in this range of the motion file The template should be defined as at least 75 of the visible frames selected 15 Select Template 7 2 Cortex 2 0 Reference Manual Chapter 7 Motion Capture Tab 16 Click Create Template for more information on the Create Template Interface refer to Template Create on page 8 12 17 Select the appropriate Frames Range e Current the current displayed frame e Selected tframes highlighted in blue low to high in dashboard e Visible what is displayed across the screen as a function of the time zoom e All Frames all frames 18 Click Create Template Figure 7 1 Create Template Interface Create Template MarkerSet Name Template Prop Definition Golf Person Frames Range Frames Used Current Frames with complete Selected Total frames to use Visible All Include current frame as the Model
406. s 1 Example matrices are shown in the following figure c 4 Cortex 2 1 Reference Manual Appendix C Force Plate Configuration Forceplate cal File Setup Figure C 3 Force Plate Coordinates System Forceplate Orientation Connector for AMTI plates is always on Y axis of forceplate lt J LJ pr 3x3 Orientation Matrix for Forcepla cal O oO oo oOo SG o oO O Oo oon oko 32oo0 Note The video lab coordinate system is determined from the L Frame orientation i X Normal direction of walking for OrthoTrak C 5 Appendix C Force Plate Configuration Forceplate cal File Setup Cortex 2 1 Reference Manual Force Plate Scaling Factor X Width and Y Length The scaling factor depends on the force plate manufacturer and the force plate amplifier gain setting and the voltage range Table C 1 Sample Force Plate Scaling Factors Force Plate Manufacturer Scaling Factor AMTI For Gain 4000 Use 25 0 Bertec Use 0 25 if using AM6501 Analog Unit output 5V Kistler 10 Volt Amplifier Use 1 0 5 Volt Amplifier Use 0 5 The x width and y length are the force plate measurements in centimeters as measured in the force plate coordinate system Check the manufac turer s specifications If no x width and y length values are used AMTI and Bertec force plates default to 18 inches by 20 inches and Kistler force plates default to 50 centimeters by 50 centimeters
407. s PRT Calibration Frame Origin Offsets Lenses Orientation Capture Volume Property X Maximum Minimum Y Maximum Z Minimum Z Maximum Selecting Tools gt Settings gt Calibration gt Calibration Frame Tab or Calibration Panel gt Details will bring up a window as shown in Figure 6 3 on page 6 5 The calibration L frame should be laid out on the floor exactly as is in this figure This can be done with four separate loose markers or it can be done using the wand and a single loose marker placed at the end of the wand handle The distances from the origin are measured and are entered into the Measurements spaces Observe the right hand rule and make sure that you enter the data correctly In the Z Up example in Figure 6 3 points 1 2 and 3 would be at X and point 4 would be at Y coordinates but adjust accordingly to your Calibration Up Axis The vertical distances are the distance from the center of the markers centroid to the floor Click on the other tabs and fill in the val ues accordingly The Lenses tab should reflect the type of lenses you have in your camera e g 6 mm 17 mm 20 mm etc The values for the lenses need only be approximations within a factor of two The actual focal lengths are calculated when you process the wand data Once you have completed filling in the details press Apply and return to the Calibration window in Cortex 6 8 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab
408. s play in a single picture of the body the complete set of markers that are re quired On the following pages are descriptions of the critical and semi critical marker sets for each portion of the body Also for each marker the complete list of acceptable names is shown Any one of these case in sensitive names in the list can be used to identify the marker in the Cortex capture F 24 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module Lower Body Critical Markers Semi critical Markers The lower body portion of the Mocap Model will be loaded if the critical markers listed below are present in the static trial The thigh shank and feet segments will each be scaled separately based on measurements made from the static trial Each of these segments will be scaled uni formly in the X Y and Z dimensions The pelvis segment will be scaled independently in the X Y and Z dimensions It is not possible to load only one leg of the Mocap Model 1 2 3 10 11 Right ASIS acceptable names R ASIS RASIS RASI Left ASIS acceptable names L ASIS LASIS LASI Posterior pelvis a Sacrum acceptable names V SACRAL V SACRUM SACRAL SACRUM SACR VSAC or b Right PSIS acceptable names R PSIS RPSIS RPSI and Left PSIS acceptable names L PSIS LPSIS LPSI Right lateral knee acceptable names R KNEE R KNEE LAT ERAL R KNEE LAT RKNE Left lateral knee acceptable names L KNEE L KNEE LATERAL L KNEE LAT LKNE
409. s e Save data in a variety of file formats These functions are described in this chapter There are a few preliminary steps that must be taken before starting a suc cessful motion capture session Tracking parameters tuned to your system must be set Names must be assigned to the markers that will be used These names constitute a marker set and building this set is actually done using the Model Edit tools discussed in Chapter 9 Model Edit Tab A template specific to the markers in use must be created A template de scribes the minimum and maximum distances that separate linked mark ers such as the distance between the right elbow and the right wrist Tem plates are created using Motion Capture tools and Post Process tools described in Chapter 8 Post Processing Tab Once these steps are com pleted you are ready to begin a motion capture session 7 1 Chapter 7 Motion Capture Tab Cortex 2 0 Reference Manual Building a Template from the Range of Motion Trial A template is what is used to automatically identify markers in real time and post processing s Template Rectify button In saving the template the software stores the minimum and maximum distances that can exist be tween markers that have linkages It is necessary to allow the software to identify each marker in each frame Template information is saved in the capture cap file Before a template can be created a marker set that will apply to the sub ject being c
410. s for Named markers The characteristics of Template Rectify are as follows e Uses only the Template information to move markers from the Unnamed slots to the Named slots e Uses All Markers or Selected Markers according to the settings e Works only on the highlighted XYZ selected time range starting on the current frame going forward then backward from the current frame e Protects all named markers will not switch them e Works only to move Un named markers into the Named marker slots here all markers are locked e Does not use Linkage Stretch Parameters in Motion Capture gt Tracking Rigid Body Rectify In Post Processing it is used when you have bodies crashing into each other where linkage lengths can get very distorted and Template Rectify can give results which may require some editing Rigid Body Rectify is for very tough trials where you can have the software look for a rigid body with markers on it and it tends not to make mistakes and hence does not require a lot of editing after the fact Work from a frame with known marker IDs to difficult areas A Rigid Body can be any set of 3 or more Selected Markers The software measures the markers with respect to each other and looks for this pattern in the Un named marker to automati cally assign them names It will stop if either of two conditions are met 8 19 Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual 1 It cannot find at least 3 of the marker
411. s in parallel for clocking the multiple USB Devices A single pull up resistor works for all devices A 4 7 KQ pull up resistor is not needed on camera systems where a Raptor camera or a Hawk m camera is set as the Master camera USB 2 0 Cable Lengths The USB 6218 comes with a USB cable It has been tested with longer USB cable lengths up to 16 ft 5 meters and it works well with any mix of cables USB Expansion Ports for Multiple A D Units Internal or External USB Expansion devices also have been tested and work well without problems This allows you use a single USB port on the main capture computer and plug in as many USB devices as needed It is recommended that a powered USB expansion port is used for multiple NI USB devices B 9 Appendix B Analog Input Hardware and Software Cortex 2 1 Reference Manual Table B 2 Analog Input Channel Connections and Master Camera Clocking NI USB 6218 Screw Screw Terminal Cortex Setup Terminal Cortex Setup Channel Name Channel Name 1 PFI O 4 7 KQ Resistor amp A D Sync Cable amp 33 PFI 8 Not Used Jumper Cable 2 PFI 1 Not Used 34 PFI 9 Not Used 3 PFI 2 Not Used 35 PFI 10 Not Used 4 PFI3 Not Used 36 PFI 11 Not Used 5 D GND Not Used 37 D GND Not Used 6 PFI 4 Not Used 38 PFI 12 Not Used 7 PFI5 Not Used 39 PFI 13 Not Used 8 PFI6 Not Used 40 PFI 14 Not Used 9 PFI 7 Not Used 41 PFI 15 Not Used
412. s not visible press F3 on the keyboard or choose Data Views gt 3D View from the Menu Bar 4 With the right mouse button click on the 3D View The 3D View pop up menu and descriptions of the tools are shown in Fig ure 4 50 These options are recorded in your INI file and are reloaded when you launch Cortex Figure 4 50 Post Process 3D View With Pop Up Menu Items Show QuickID Marker ID Template ID Rectify Hide Markers Unhide Markers Make Unnamed Create Template Cut Inside Cut Outside Exchange Smooth Join Cubic Join Linear Join Virtual Undo Search Show options cascading menu Quick ID the markers sequentially Marker ID the selected marker ID marker s based on current template Rectify marker s over the selected frame range Hide selected marker s from view Show selected marker s Make selected marker s unnamed Create a Template Cut data in selected frames from the selected marker s Cut data outside of the selected frames from the selected marker s Exchange data between two markers over the selected frames Smooth selected marker s over the selected frames Join selected marker s over selected frames using cubic splines Join selected marker s over selected frames using linear interpolation Create a temporary virtual marker to fill in missing marker data Undo last data edit action Search data set for spikes and or gaps as defined in the Options panel T
413. s of the Rigid body on a frame so use more than 3 marker if you can 2 The measurements stretch too much It can be re started on a new frame if needed The selected markers must be identified on the Starting Frame The characteristics of Rigid Body Rectify are as follows e Measures all markers in the selected Rigid Body on the Starting Frame e Uses All or Selected Markers mostly used for Selected Markers e Protects all named markers will not switch them e Works only to move Un named markers into the Named marker slots here all the markers are locked e Does not use Linkage Stretch Parameters in Motion Capture gt Tracking Rectify Unnamed Rectify Unnamed sorts the Un named slots into continuous paths based on path continuity similar to the tracking function No templates or link ages are used Path segments separated by 10 or more frames are consid ered to be separate paths and will not necessarily be continuous This is used to clean up the Unnamed path segments and can make the Marker ID function work more smoothly It means you may not need the Rectify Al ways On check box in Marker ID and Quick ID Items First try the Rec tify Unnamed function then try the Marker ID function for the problem areas Template ID Uses the currently defined Template from Create Template to fit the link ages into the current frame s marker cloud If it succeeds it tells you the number of tests on the Status Bar lower left side of
414. s separately Tree View panel and specify the appropriate skeleton engine then save out the MARS file In the Motion Capture gt Objects panel you can select whatever set of MARS file you need for tracking and solving a particular capture All the skeleton information for the capture is saved in the MARS files and refer ences to all the files are kept in the capture file 11 12 Chapter 12 Sky Scripting Interface Overview Installation File Structure The Registry The Script Object Script Examples Updating Old Sky Files Graphical User Interface Sky Compiled Script Reference Overview Sky is the name of the scripting interface for Cortex It s graphical inter face provides the user access to Cortex functionality within a Visual Basic NET language environment Sky is intended as a tool for users to encapsulate elements of repetitive tasks such as file processing data edit ing and parameter setting This tool is intended for users who have some general knowledge of scripting and programming Sky provides added functionality using the NET architecture giving the user access to a con siderably enhanced feature set and the execution speed of a compiled script Installation File Structure Sky is integrated with Cortex and uses the UserFiles folder to store scripts and documentation e UserFiles SkyFiles Contains the list of Global Sky functions This is the root of the Sky folder struc
415. s the cameras does not cycle the power This is used when Cameras changing the camera s IP addresses Note that the camera and software will not recognize the change in IP address until the camera has been re booted If this does not work you can cycle the power of the camera by unplugging it or turning off the camera s power hub Wait for ten seconds before turning the power hub back on Insight Focusing This button starts the Insight Focusing procedure For complete informa tion refer to Insight Focusing for Raptor Series Cameras on page 3 28 Camera Display Codes The digital camera displays indicate which mode the cameras are operat ing Note The smaller Hawk M cameras do not have the display feature Note Displays may vary for each camera type 5 8 Cortex 2 1 Reference Manual Chapter 5 System Tab Table 5 1 Camera Display Codes Code Image Description Master Camera This display code with the active LEDs in the four corners indicates that the camera has been set as a master camera The ringlights are ON which indicates that Connect To Cameras on the Cortex interface is active Yellow Red and Green ON numbering indicates that the camera is in an idle state powered up but not connected Red number displays indicate that the camera is either disabled out of sync or that there is a hardware problem within the camera Standard Camera This display code has no active LEDs other tha
416. sary for the camera systems to function properly A 100 MB Ethernet switch works well for a camera system with up to 15 cameras at a capture frame rate from 60 to 120 Hz For larger numbers of cameras above 16 it is important to use the 1 GB Ethernet NIC net work interface card inside the computer and the 1 GB Ethernet switch that collects and concentrates the camera traffic to the Cortex Host com puter A 3 Appendix A System Hardware Interconnections Cortex 2 1 Reference Manual Ethernet Tutorial and Troubleshooting Guide Troubleshooting There are two types of female Ethernet connections that use the same 8 pin Ethernet connector 1 NIC Type The Ethernet connector that is found on the Network Interface Card on computers and on your cameras 2 Hub Type The standard Ethernet plug that is found on Ethernet switches and hubs There are two types of Ethernet cables 1 Standard Ethernet patch cables 2 Ethernet cross over cables The standard patch cable is used to connect computers to Ethernet switches The Ethernet cross over cable is used for connecting Ethernet switches to other switches unless you use the Uplink port on either switch In this case you can use a standard patch cable The cross over cable would also be necessary if you were to bypass the Ethernet switch and plug the cam era directly into your computer s NIC You can tell if you have a live Ethernet connection if the indicator light
417. see it If you load a TRB or TRC file that has an associated TC file then the Post Processing Dashboard will lock the time code onto the time code display You can step forward or backwards in time or push the play but ton and the time code reads accurately If you switch back to the Motion Capture tab and are connected to the cameras you will see the current time code If you are in the Motion Capture tab and are not connected to the cameras but using Raw Video Files you will see the Time Code asso ciated with the Raw Video File The Digital Video option can be used with the Time Code In our current software the only way to record the time code is with the Time Code Reader card Some cameras have Time Code capability within the cam era but those time codes are not recorded with the DV Digital Video op tion The Time Code must be connected to the Time Code Reader card to have a TC file created and hence be time coded 4 84 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Live Video The Live Video Backdrop allows you to set your streaming live video as the backdrop to your 3D View To activate this function right click in the Backdrop 3D View and select Show Video Figure 4 66 Live Video Backdrop 4 85 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Unload Tracks This button provides a quick method to unload or not save any changes Button to the Tracks files which have b
418. seed and a wand calibra tion A relationship must be established between real world positions ob ject coordinates and the corresponding image coordinates from the cam era view This is called calibrating the system When a target is visible in two or more camera views there is sufficient information available to track the targets in three dimensional space The calibration of a given camera s view is completely dependent on the camera lens focal length and the position and orientation of the camera with respect to an arbitrary reference frame called the object reference frame A change of any sort which alters the relationship between the ob ject coordinates and image coordinates must be followed by a fresh cali bration This includes accidently bumping a camera tripod The calibration process calculates eleven calibration coefficients which implicitly define the configuration of a particular view The calibration coefficients together with the image coordinates of a single target are sufficient to define the path of an optical ray from the target to the camera through the object space If rays from two cameras intersect in space at a specific time they define the 3D position of a target at that time There fore the tracking process is one of intersecting optical rays generated from different views of the same event Cortex employs a best fit track ing algorithm using only good camera views The Calibration In order to calib
419. segment relative to the base position Each section starts with the segment name followed by position data and the scale factor SF for each frame The first segment LowerTorso is unique because it has six values describing its relation to the global coordinate system All subsequent segments have only three rotational degrees of freedom Therefore if you wished to find the global coordinates of any segment in any frame you would follow these steps e Calculate the three rotation values for each segment using the values from the desired frame and the base position for that segment For the root also calculate each of the three translation values Be careful to use the correct rotation order as indicated in the header of the htr file e Using the positions and rotation of the root segment as a starting point calculate the global positions of the origin of the first child s coordinate system in the hierarchy e Using this calculated global position calculate the global position of the origin of the next child s coordinate system e Continue until you have reached the desired segment In the abbreviated example shown in Figure E 3 only the first and last four frames are shown for the first three segments In the actual file all 196 frames for each of the 20 segments would appear After all the seg ments an EndOfFile section terminates the file E 7 Appendix E Import and Export File Formats Cortex 2 1 Reference Manual
420. sferring large raw files is often impractical There are two types of packages that can be created moving the files to a folder and creating a zip file Once the packaging options are set it is possible to select Don t show this again which will prevent the options dialog from displaying when Package Capture is selected Se lected Package Capture gt with options forces the dialog to again be displayed Figure 4 4 Package Capture Interface TT lox m Package Type Compressed Zip File Uncompressed Folder Presets Entire Capture C Exclude Raw and AVI Files C Custom 1 C Custom 2 Options Files to package Setup Setup YE Data SetupWithE vents cal Analog Data VC Data F RawFiles GolfSwing_15GolfSwing_1 vc1 E Analog Data GolfSwing_1 anb E Video Data RawFiles GolfSwing_1 GolfSwing_1 avi Audio Data ker Data Timecode RawFiles GolfSwing_1 GolfSwing_1 te CyberGlove Data MarkerSets Body mars Club mars Trb Marker Data GolfSwing_1 Golfer trb GolfSwing_1 Club trb GolfSwing_1 Unnamed trb Trc Marker Data Htr Skeleton Data GolfSwing_1 Golfer htr GolfSwing_1 Club htr Event Data GolfSwing_1 Golfer evt GolfSwing_1 Club evt Video Data Audio Data ker Data in Data Event Data Q AAAA AAAI I I I m m m D F Don t Show this again Package Cancel Note You may undo the Don t Show this again function by selecting the Wel
421. should also be taken in placing the 4 points on the floor as this determines the global axes and the orientation of the volume dis played in Cortex The points on the 3 point axis must be in a straight line and the spacing of point 2 must be close to 1 3 of the distance between points 1 and 3 6 2 Cortex 2 1 Reference Manual Chapter 6 Calibration Tab Calibrate Panel Figure 6 1 Calibration gt Calibrate Panel Calibrate D 0 Protect Lens Correction Calibration with L Frame C Camera Aiming lename CalSeed Calibrate Calibration with Wand Duration fo Seconds Length foo atWand Calibrate Floor Calibration Marker Center to Floor fi 27 alFloor Calibrate C Refine Camera Positions Property Camera No j1 2470 197 2514 597 2939 508 Elevation 32 12 Azimuth 132 15 Roll 119 02 Principal Pt U 620 8273 Principal Pt V 497 8354 Focal Length 16 81047 Chapter 6 Calibration Tab Cortex 2 1 Reference Manual Protect Lens Correction This locks the lens corrections coefficients for all cameras as saved in your capture file Once you have set your lenses focus and zoom factor the lens distortion maps should not change and they need not be calcu lated with each wand calibration With Protect Lens Correction checked the wand calibration will converge more quickly So if you do not change the lenses it is a good idea to leave this box checked for all yo
422. slots Currently the coordinate system of the prop is displayed in the Motion Capture 3D View When you record a trb or tre file the XYZ coordinates of the prop are also recorded Visually you can see the coordinate system of the Rigid Object defined The coordinate system displayed has the origin at the center of mass of the defining markers and the directions of the XYZ axes are defined par allel to each of the calibration coordinate system axes as defined on frame 1 of the capture Create a global System Objects folder If you want to build a library of props you can create a folder under the launch folder of Cortex next to the Sounds folder and name it SystemObjects note no space between System and Objects Copy any props you want to use into the SystemObjects folder You will need to quit and relaunch Cortex and then you will see a new section at the bottom of the Motion Capture gt Objects panel with the heading System Objects You can select prop files from that list to go into any of the Addi tional Tracking Objects slots Order the objects in the Tracking Objects panel The priority for iden tifying objects is A B C D E and the Main Markerset is identified last You will want to put the props at the beginning of the list into the top slots Done this way it is less likely for the props to be embedded into one of the other human objects 7 8 Cortex 2 0 Reference Manual Chapter 7 Motion Capture Tab Output Pane
423. st desirable type of clothing for the ses sion Remember your goal is to capture the fine details of the movement of the body not the movements of clothing on the body The rule is to apply markers to skin whenever possible The areas on the body that present the greatest potential problems are shoulders the rear neck ster num mid back and the root A tank top shirt may be used to expose the shoulder neck and sternum The root marker should be placed low on the spine in an area below the belt line where there is usually very little cloth ing movement If a mid back marker is used the shirt should be rolled up and taped to expose the back If skin cannot be exposed for all marker placements then tight fitting clothes or a motion capture body suit should be worn Have the subject perform some of the motion capture moves within the capture area If markers have been placed on the subject go ahead and capture some data This would be an ideal opportunity to use a stopwatch to time the duration of each move These trials can give the Cortex user an indication of potential tracking problems and if this data is taken all the way to the animation software it will allow the artist to see how well the data fits their models Finally instruct the subject to speak up during the motion capture if there are any problems with the markers If markers become loose they will need to be reconnected more securely with tape or rubber bands 2 2
424. t problems with different versions of the rom bin software How to tell which cameras have the OLD CPU board and which cameras have the NEW CPU Board is easy e ALL Eagle Eagle4 and Hawk Cameras with the SILVER backplate where the connectors are have the newer CPU boards CE approved and require the newer camera software dated May 9 2005 or later e Cameras with the BLACK backplate have the older CPU card non CE approved can use either the NEWER or the OLDER rom bin software Raptor Camera software is included with the Cortex releases see Figure 5 3 Contact support motionanalysis com if you have any questions about updating the camera software in your MAC digital cameras Allows you to input the IP address for the network interface card NIC of the host computer This is the IP address for the NIC that is connected to the Eagle cameras There must be a dedicated NIC for this purpose Other connections to local area networks LAN must be done on a different NIC to avoid network traffic on the camera network and to keep the Mo tion Analysis camera system working properly 5 7 Chapter 5 System Tab Cortex 2 1 Reference Manual Tell Cameras the This resets all the cameras in the network to the first three digits of the Network camera network IP address Figure 5 5 First Three Digits of Camera IP Network Address New Camera Software Camera Network IP 199 v Tell Cameras the Network Reboot All Reboot
425. t the Ad ditional Tracking Objects list located in the Motion Capture gt Objects panel will be populated with the first ten of the objects in your list and the rest up to the maximum listed in the Title Bar will also be loaded in the order in which they appear in the list Above the buttons on the right is a status message area which will indi cate the status of your last operation If all objects were successfully loaded you will see a massage confirming this An unsuccessful object load function is generally caused by something in the list not being present in the current capture directory If you change capture directories or have deleted a prop or capture file for an object ina group file that can be the cause If you are working from zin files they are remembered in the Recently Used Groups list and can be loaded using the Quick Load button This button will pause the capture session long enough to load the objects if it is currently running and then set it back to run If the Motion Capture was paused it will remain paused after a Quick Load operation 7 6 Cortex 2 0 Reference Manual Chapter 7 Motion Capture Tab Local Objects amp System Objects Figure 7 4 Objects Panel There are two object lists in the Output Panel The Local Objects list and the System Objects list The Local Objects list contains a list of all Mark erSet files mars prop prj which can be loaded from the current work ing
426. ted at the origin Join Virtual and Virtual Marker calculations use the 3D offsets from the problem marker to the coordinate system s Origin Marker and apply that throughout the Join Virtual The results are often astoundingly good and can be used directly to speed up your animation pipelines More study is recommended before applying these results to Biomechanics research and medical applications In short e The Problem Marker is the marker with the gap to be filled e The Origin Marker maintains a fixed distance to the problem marker e The Long Axis Marker defines a line to the origin marker e The Plane Marker defines a plane with the Origin and Long Axis Markers Figure 8 18 TRC File vs TRB File With Join Virtual TRC file no Join Virtual TRB file from same data set with Join Virtual To test the operation of this feature define a Virtual Marker Join for the RHip marker based on 3 others that will remain visible Cover the RHip marker for example and see if it appears in the 3D view This can be done with a live person very easily but if you do not have a setup avail able go to the 2D view of a trial mask out enough regions and cameras so that the RHip is no longer visible It should appear in the 3D view if you turn on the Join Virtual feature 8 26 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Join Virtual Guidelines Note Head Upper Arm or Upper Leg
427. ter If you have an A D system the master camera must be connected to it using the A D sync cable When you see a marker in the 2D display are you simply seeing a digital representation of what the camera sees at the CCD or are any of the tracking parameters incorporated into determining whether the system sees a marker i e marker size centroid parameters etc The black data is the raw edge data affected only by the lighting and the Threshold The red dots lens corrected and or not are the calculated cen troids To calculate a centroid there are two main things 1 Min Lines per Marker usually set to 2 or 3 lines 2 Max lines per Marker usually set to a BIG number like 100 and Shape Analysis None Normal or Weak normally to Normal But sometimes it is set it to None if it is tossing out centroids like during a L Frame seed calibration Can you connect 7 or 8 cameras to an EagleHub We tried connecting 8 cameras to an EagleHub2 and the data transfer to the gigabit switch be came quite unstable Note that this pertains to the older 8 port EagleHubs only not the 12 port EagleHubs There are only 8 useful ports on an older model EagleHub which means 7 cameras can be connected to the EagleHub and one more is used for the uplink to the Network Interface Card NIC An eighth camera can be connected directly to one of the remaining open port son the NIC using a patch cable H 3 Appendix H Questions and Answers f
428. tex 2 1 Reference Manual Included Angles Tab The Included Angles tab allows you to select groups of four markers which define two separate lines in space Between these two lines the angle is calculated for each frame through the tracked data This informa tion proves useful for detecting irregularities in movement such as be tween two parts of a body To delete a row simply click on that row and press Delete You may select and delete several rows at once by pressing shift click on the rows and pressing Delete Figure 8 23 Included Angles Tab B fle uts Gata views Tob Hp CEET 7 2 e O a SEND Parity Teele jemi Template Marker ID Exchange Cubic Vetus Cak Smooth i He 23 2 ip Pe U o MRA MR MLPrky MLWit MAFO MLB 27 M _RoctOrtset j MBRAME 30 iM A Hp tM FRM 2 uruy M M Joinee 35 MRSN 37 M Prieel 38 M Paktioct 3 MRT 40 M LT 4t M Liner 42 MLO AN Exporting Analysis Time Series Information oia Frames 120 FPS zup Unesimen anso e0000 To export an ASCII text viewable file select the Export ts Time Series File button This will write a file with the same file name as the tracked file you are working on It will contain the information from all three Analysis tabs 8 32 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Post Processing Strategies and Tips The steps necessary to c
429. tex filenames and trial numbers The take number is displayed on the slate board and on the Motion Capture Log Every new image recorded on the video tape should have a new take number This should include calibration collection initialization and T pose Init pose stance positions You should never re use or redo a take number If a data collection is aborted for some reason e g a marker fell off then the Cor tex filename and trial number can be overwritten but the take number should change 2 5 Chapter 2 Planning a Motion Capture Session Cortex 2 1 Reference Manual Motion Capture Session Sequence of Events The Day Before The Day of the Motion Capture Subject Preparation Note Note _ Optimize the camera positions and orientation to the capture volume Calibrate the volume of the capture area Determine the correct marker size to use Cortex raw data should show 2 lines or greater per marker Setup the Cortex capture with the correct markers virtual markers linkages segments etc If possible collect and track the markers on a person to verify that the tracking parameters are optimal Verify that there is enough space on the workstation s hard disk If there is not enough space back up the previous files and then erase them from the hard disk Organize the markers tape and props to most efficiently facilitate the session Before the subject arrives N 1 2 3 Load the Cortex c
430. th video data capture To create an anc file from an anb file from the main menu select File gt Export gt Export ANC The data in ANC files is raw analog data in ASCII form and can be read and manipulated by a spreadsheet program Shown in Figure E 4 is the beginning portion of an anc file Figure E 4 Example of an ANC File File Type Analog R C ASCII Generation 1 Board Type National AT MIO 64F 5 Polarity Bipolar Trial Name 1ndbfw Trial 8 Duration Sec 6 000000 Channels 30 Name fix fly flz mix mly miz f2x f2y f2z m2x m2y m2zL tibialis ant Rate 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 Range 10000 10000 10000 10000 10000 10000 10000 10000 10000 10000 10000 10000 2500 0000 0 29 1 2 1 0 13 11 550 0010 1 29 1 2 2 1 13 10 392 0020 1 29 1 3 2 1 13 10 369 0030 1 29 2 3 1 1 13 10 440 0040 29 1 2 2 1 13 342 0050 29 1 2 2 0 13 531 0060 29 1 2 2 1 13 803 0070 28 1 2 2 1 12 738 0080 28 1 2 2 1 13 485 0090 1 2 0 0 453 0100 1 2 1 0 876 0110 0 2 1 1401 0120 1 2 1 1 598 0130 3 3 3 3 141 0140 1 2 2 457 0150 1 2 2 446 0160 1 2 1 569 0170 1 2 1 507 0180 1 2 2 689 0190 2 2 2 501 0200 1 2 2 348 0210 0 2 1 209 H oO N w oO 1 OrRFGOGODOOONTDTOOCOCCO OF oo0o0o0o0000 00 0 0P 00 0OBPRO0OO0OO0OO oooooo0oorroOorOocOCOOrRrGQGCC CO oO 0 0 0 0 0 0 0 0 0 0 0 0 0
431. the Details button and add the setting for English United States This will add the necessary text characters to the computer Alternatively you can install an English language OS on your computer Chapter 1 Introduction Cortex 2 1 Reference Manual Cortex 32 bit and 64 bit Installation Notes Limitations and Recommendations For Different Versions of Microsoft Windows Note The setup file provides the option to install either the 32 bit or 64 bit ver sions or both They can be installed to the same directory if desired since the release folder name is different Dual host computers WinXP and WinXP x64 for example can have both versions installed on the same hard drive The release folder name determines the location of the execut able and associated files On WinXP and Vista 32 bit the default installation folder is C Pro gram Files Motion Analysis Installing on WinXP x64 for Vista 64 bit or Win 7 64 bit the default installation folder is C Program Files x86 Motion Analysis It is recommended to use the default installation folders but Cortex will run on any folder on any drive Win7 64 bit This is a good all around choice for all users Biomechanics Animation and Industrial It supports all peripheral data collection devices such as Analog collection Time Code Reader and Firewire Digital Video cam eras Vista Business 32 bit standard version is a 32 bit version of Windows which is n
432. the best fit of the marker data to the underlying fixed bone length skeleton This tech nology was pioneered by Motion Analysis in 1990 The early version model setup was somewhat cumbersome and required physically measur ing from a person s joint centers to the marker locations before the skele ton could be used Now the skeletons are defined and edited within the Calcium software interface within Cortex This provides a graphical way of either reading in an existing skeleton or creating one from an anima tion package such as Maya or 3DMAX The typical way would be to cre ate the character in the animation package and export the skeleton using an htr file using the MAC File IO plugins The Global Optimization method is an iterative method of seeking the best fitting of the skeleton within the marker cloud of identified markers The results are quite as tounding the animated characters motions derived from this method is very good Final editing of the htr skeleton motion data can be done within the animation package or with a third party tool such as Motion Builder Cortex 2 1 User s Manual Chapter 11 Skeleton Types Which Skeleton Engine Should Use SKB skeletons are good for most biomechanical applications and have been the norm there for many years They are also used for animation cus tomers who want tools for quick pre visualizations of your characters mo tions For the final cut and the big screen presentat
433. the capture and correct the problem 2 7 Chapter 2 Planning a Motion Capture Session Cortex 2 1 Reference Manual Capturing the Moves Note Collecting Calibration Insurance Data Wrapping It Up 2 Prepare the Cortex system by entering a filename If the subject s name is Jane use something like JaneInit For this initialization file use a duration of 2 3 seconds The take number should be set to 3 Click on Collect to arm the event button You can enter a long dura tion e g 20 seconds and then press the hand held event button a sec ond time at the end of the move 3 Update the slate board with the new take number and Cortex file name Make the same entries in the Motion Capture Log 4 When everybody is ready the director can say roll video then slate the video Now the Cortex operator gives the signal for the subject to start and presses the event button to start the data collection The event button must be pressed a second time to stop data collection at the end of the move 5 For initialization use the T pose Init pose In this pose the subject faces forward and raises both arms straight out from their sides with the thumbs oriented up Perform this motion within the duration of the capture time 6 Pause the camcorder 7 Collect two trials of this initialization move 1 Before capturing have the subject practice each move Enter a duration longer than the estimated length of the
434. the screen it took to complete It may also fail or time out in which case you should make sure all of the markers are present on the current frame or perhaps re make your template It only changes data on the current frame if it is suc cessful You can then use Template Rectify to get the correct IDs to other frames 8 20 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Figure 8 14 Template ID Details Summary of When To Use What 10 20 30 1 1 Emu Le TemplatelD 244 tests How good is the Template You can tell how good your template is by how many tests it takes for the Template ID function to work A low num ber means it is working quickly low is say 500 A high number 5 000 or more means the software has to try very hard to ID the current frame It stops trying after about 50 000 tries in Connect Live mode and times out and gives the message Template ID Timed out In Post Pro cessing mode it will not time out until 500 000 tries That means it did not get to try out all possible linkages A large number indicates a poten tial problem It might be because the current frame is stretched beyond the template or in a much different actor position or it might be because the Template is not very good Try to use the Template ID on different frames and see if the number changes a lot If you consistently get large numbers for the Template ID feature try adding more links to your marker setup
435. ticl Unnamed trb V ClevelandClinic mars M Staticl trb Static tr Clear List Select UnSelect All Select Non Raw Files Delete Selected 10 7 Chapter 10 Plugins Tab Cortex 2 1 Reference Manual Capture Inspector This tab contains tools for looking at what is in a capture cap file with out having to load it into Cortex The Inspect Capture button chooses the capture to inspect All files in the capture are listed in the Capture sec tion If a file is listed in the capture but not found on the disk it is pre fixed with not found In addition to inspecting the capture some basic modification options are available If a file in the capture is flagged as not found the Find Miss ing File button will allow you to find the file in the disk The Remove File From Capture button will remove an entry from the capture For ei ther one of these buttons the file must be selected from the Capture sec tion before pressing the button The Add Reference Video File to Cap ture button is used to add additional reference videos to a capture No length checking modification is preformed on this file it is just added to the cap file Once all modifications are made to the Capture the Write Capture Manifest To Disk button will write the new cap file to the disk It can then be loaded into Cortex Figure 10 8 Assistant Panel gt Capture Inspector Interface AssistantPanel x t File Cleanup Capture
436. tion Analysis Cort Network Folder Startup al Autpsave On Auto Run Off Sky form Global Sky Scripts Output Status Bar My Sky Scripts 12 4 Cortex 2 1 Reference Manual Chapter 12 Sky Scripting Interface Toolbar Copy Per Project Copies Sky files from the folder MAC_DIR UserFiles SkyFiles CopyPerProject to the current working capture di rectory This makes it easy to initialize a new capture with your favorite scripts Will not overwrite existing scripts of the same name New Script Clear the Script text editor and start editing a new script Open Script Bring up a file browser to find a sky file not in the same directory Save Script Save the current script Save Script As Save the Script text to a new sky file Run Execute the text in the Script editor Cancel Cancel the currently executing script This works only if the script was written to use the swCancelled Function Refresh Causes Sky to refresh the Local Sky Files Global Sky Files Network Sky Files and clears the Input Text area by re reading the appro priate directory Options e Script Edit Mode Enable editing in the Input Text window To run the script the Run button must be pressed or the menu short cut Control r This is the default mode This mode is the opposite of One Touch Execution mode e One Touch Execution Disable the editing in the Input Text win dow In this mode Sky scripts are loaded and
437. tion Analysis cam era Often it will be locked at its optimum value On most larger SLR style lenses it takes a very deliberate action to change the aperture How ever with c mount zoom lenses often supplied on Hawk cameras almost always 6 15mm it is not lockable and very easy to change accidentally when adjusting other lens parameters If this happens follow the focus card procedure and change the aperture form one extreme to the other When fully open the camera should be able to see most of the markers If there are extra reflections in the view close the aperture until they disap pear Note that a fully closed aperture with bad focus will look similar in the 2D view Trial and error is needed to find suitable lens adjustments For Hawks Eagles and all Raptor cameras this is a software setting It simply controls the amount of light coming from the ring light It is usual to start with this at 100 max Lower the value for small markers or to help combat reflections If the aperture is made smaller the brightness would need to be raised in order for a sensor to receive the same amount of light in any given situation 3 32 Cortex 2 1 Reference Manual Chapter 3 Camera Setup Threshold Setting in Cortex Frame Rate in Cortex Shutter and Strobe setting in Cortex Vignetting Depth of Field Range This sets the value for the pixels on a camera above which data is passed for the software to make circle fitting
438. tion capture trial on a separate computer With this option you will record a time matched Reference Video AVI file with the same trial name in your motion capture folder A separate computer is used in order to not burden your Cortex Host computer which is an issue if your computer is too slow for the number of markers being tracked For single person captures you may connect the DV Cam era directly to the Cortex Host computer In this case the CortexDV soft ware is not needed It is built into the Cortex software You can run Cor texDV on one or more computers and then capture multiple AVI files multiple views They will all have the same AVI file name You may ex perience a small delay in frames from the Cortex software and the Cor texDV software when capturing The Reference Video display has a pop up menu with one item Adjust Frame Offset This allows for time match ing data streams The CortexDV software option is not to be confused with the AVI func tion in the Motion Capture gt Output panel This function creates an AVI file when you collect a trial within Cortex e NTSC 59 94 Hz e PAL 50 Hz 4 70 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Real Time Dashboard Note The Real Time Dashboard is available when Cortex is in Real Time mode as opposed to Post Process mode When you are capturing data in real time this dashboard provides the controls to manage a motion capture session
439. tion is a User Preference and it can be set by launching the Options Form from the Post Process tab 1 Hold the Alt key down 2 Hold both the left mouse and middle mouse buttons down 3 Move the mouse forward and backward In the XYZ Graphs translating is accomplished if you 1 Hold the Alt key down Hold the middle mouse button down 3 Move the mouse in any direction Selecting Markers Virtual Markers Linkages and Segments Note Markers can be selected by the following 1 Clicking on the markers seen on the 3D View Double clicking on the markers seen in the XYZ Graphs 3 Clicking on the markers listed on the Marker Grids which are a part of the Post Process tab the Model Edit gt Markers panel and the Model Edit gt Tree View All of the conventional Shift click and Ctrl click techniques to select multiple items are supported in this software 4 83 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Time Code SMPTE Time Code and Cortex Overview Using the Time Code Reader Option Using the Time Code in Post Processing Time Code and the Digital Video CortexDV Option SMPTE Code reads as HH MM SS FF which is Hours Minutes Sec onds Frame Frame numbers are 0 to 29 in NTSC and 0 to 24 in PAL When you capture at a higher motion capture rate such as 60 or 120 Hz there are multiple motion capture VC frames per Reference Video frame The software takes care of that so
440. to be adequately cov ered by four cameras on each side an additional pair of cameras with wide angle lenses can be placed in the center of each long side of the cap ture volume The first 8 cameras should be 3 meters above the floor Cam eras 9 through 14 should be 5 meters above the floor See Figure 3 7 To use more than 14 cameras effectively it is usually necessary to break the capture volume into two overlapping sections across the long axis Every camera must see at least one of the squares in its entirety All cam eras should be placed at least 3 meters above the floor See Figure 3 8 on page 3 8 For more information and an example refer to Overview of the System Calibrating Process on page 3 18 As capture volumes increase in size more than 16 cameras may be re quired It is best to consider the capture volume as two or more overlap ping regions For large square shaped capture volumes up to 32 cameras can be used with the space broken into four regions See Figure 3 9 Motion Analysis cameras use the same high powered ringlights and have the same limits for marker distances The difference between the cameras is that you can use smaller markers with the Raptor 4 Raptor E Eagle 4 and Eagle cameras about one half the size of the Raptor H and Hawk markers A typical example would be 1 4 inch 6 mm markers for Eagle cameras and 1 2 inch 12 5 mm markers for Hawk cameras 3 3 Chapter 3 Camera Setup Cortex 2 1
441. tonal Equipe siticinanire dsl cuarecindinideaicidnaipadimemnnmenemnasd 2 4 Motion Capture Terminology cccecsseeceesececeeeeseeeeeeeeseeeeeeeeees 2 5 Motion Capture Session Sequence of Events ceeeeeeeeeeeeees 2 6 I Me DAA isiaciteis teicesineioeiesamiarenrneeenae 2 7 Chapter 3 Camera Setup Setting Up a Motion Capture Laboratory ccccceeeseeeeeeeeeneeeeeees 3 1 Deciding On the Optimum Number of Cameras ceeeeeeees 3 2 Seting Up Ie ae sc scree ees 3 10 Raptor 4 Raptor E Eagle 4 and Eagle Series Camera Physical DI ili ei s arene rere tee cr er crer rrr rte er en frente rer errr rere rrr rr ter rerrTr 3 16 Raptor H and Hawk Camera Physical Dimensions 006 3 17 Overview of the System Calibrating Process cceceeeeeeeeeees 3 18 Placing the Calibration Ce IN ss soi cc aaa ctsece a cciccst cr aiei 3 19 Marker Sizes and Maximum Distances for Motion Analysis Cameras 3 21 Troubleshooting Camera Problems cc cccceessceeeeesseeeeeeeseeeees 3 22 Relationship Between Capture Volume and Marker Size 3 27 Insight Focusing for Raptor Series Cameras ccccceeeeeeeeeeees 3 28 Cortex 2 1 Reference Manual Focusing with the Camera Focus Card c cccceceeeeeeeeeeeeeeeeeneeeees 3 31 Chapter 4 The Cortex User Interface Getting Acquainted With the User Interface cccccceeeeeeeenees 4 1 Menu Balroga iain eae 4 3
442. ts 3 19 Coordinate System Calibration 3 18 Copy 8 18 Cortex Segment 9 10 CortexDV Software 1 12 4 70 CP 8 Power Hub Connections A 5 Create Linkages Button 9 3 Create SIMM Calcium Skeleton JNT File 4 12 Create Skeleton from HTR File 4 12 Create Template 7 3 Creating Masks 5 11 Current Camera Information 5 3 Cut 8 16 Cut Inside 8 16 Cut Outside 8 17 Data Viewing 8 2 Data Painting 8 28 Data Views 4 3 4 15 Dedicated Interface 5 7 Degrees of Freedom 9 15 Delete Artificial Data 10 4 Delete Outside Volume 10 2 Delete Short Snippets 10 2 Delete Unnamed 8 19 Devices Panel 5 17 Differential 5 16 Digital Video Option 4 70 Dim unselected MarkerSets 4 32 Disable Sound Effects 4 37 Disconnect Use Raw Files 4 79 Display Codes 5 8 Distance Between Two Markers Tab 8 31 Doc View 4 16 Eagle Camera Dimensions 3 16 Physical Dimensions 3 16 Power Consumption A 3 EagleHub A 6 Editing Tracked Data 8 1 EMG Muscle Name Selection 5 14 Signal Name Conventions B 4 Enable COM Trigger 7 11 Enable External Trigger 7 10 Ethernet Switch Connections A 5 Euler Angle Order 11 11 EVaRT Project File E 3 EVaRT 1ini 4 65 Events 4 72 Events Area 4 51 Exchange 8 17 Cortex 2 1 Reference Manual Exit 4 15 Export 4 11 Export ANC 4 11 Export C3D File 4 11 Export CRC File 4 11 Export File Formats E 1 Export Forces File 4 11 Export HTR File 4 11 Export Kinet
443. ts develop force thus generating moments about the joints SIMM allows you to analyze and test a musculoskeletal model by calculat ing the moment arms and lengths of the muscles and ligaments Given muscle activations the forces and joint moments muscle force multiplied by moment arm that each muscle generates can be computed for any body position By manipulating a model on the computer graphics sys tem you can quickly explore the effects of changing musculoskeletal ge ometry and other model parameters Since the software can be used to study many different musculoskeletal structures it can enhance the productivity of investigators working on di verse problems in biomechanics SIMM provides a framework that orga nizes the parameters of a model and allows people to work together on a modeling project The moving three dimensional images of anatomical structures that you can create are extremely valuable when developing a model and when communicating the results of an analysis SIMM has a wide variety of applications A few examples include the fol lowing e Biomechanics researchers are using SIMM to create models of the human elbow wrist jaw and other anatomical structures These mod els can be altered according to particular surgical procedures to study how the surgical alterations affect muscle function SIMM can also be used to analyze and display the mechanics of injuries e Neuroscientists are using SIMM to study how the c
444. ttings gt Playback interface For more informa tion please reference Tools gt Settings gt Playback Tab on page 4 29 The Run button will start the streaming of live camera data or start the simulation of a motion capture session from existing raw VC files The Run button has the following functions 1 If you are connected to the cameras it starts the data steaming from the cameras You are able to record the Raw Video VC files as set in the motion capture Output panel Check your 2D views to be sure the cameras masks and thresholds are all set properly 4 79 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Time Code Counter Frame Counter Camera Buttons Right Click Camera Buttons 2 If Enable Tracking is checked you will see the marker data appear in the 3D View This requires that the system has been calibrated You are then able to record VC files and TRC or TRB files 3 If Enable Identifying is checked you will see the colored markers and the stick figures in the 3D View This requires that the system is calibrated and a template is defined and operating You are then able to record VC files and TRB or TRC files 4 Tracking from Raw Video files If you are not connected to the cam eras you have the full range of option 2 or option 3 above from your previously collected Raw Video VC file The Time Code Counter displays the frame number in HH MM SS Frame hour minute second
445. tup will be loaded This includes the camera setup analog setup force plate configu ration tracking parameters and most other things that were previously stored in Cortex project or capture files If a Capture is already loaded into Post Processing that Capture will now use the newly loaded Setup File File gt Save Setup Saves the current Setup into the cal file that it was loaded from If a cal file isn t loaded the Save Setup As dialog is opened File gt Save Setup Prompts the user to select a new Setup File cal to save the current Setup As into This file is now the currently loaded Setup File shown in the Cortex 2 title bar If a Capture is already loaded into Post Processing that Cap ture will now use the newly saved Setup File File gt Load System Used to manually load the System Setup which contains all the elements Setup of the Cal file File gt Save System Used to manually save the System Setup which contains all the elements Setup of the Cal file 4 9 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual File gt New MarkerSet Provides a dialog for creating a new MarkerSet A MarkerSet name is re quired as well as the type of MarkerSet Template vs Prop The Marker Set name is not necessarily the same as the file that the MarkerSet will be stored in It is the MarkerSet name that is visible in the Tree View and also which can be edited when modifying a template This Mar
446. ture e UserFiles SkyFiles CopyPerProject This folder contains the Sky files which you are encouraged to add to that will get copied to any current working folder using the CopyPerProject toolbar button e UserFiles SkyFiles SkyDocs Contains the Sky documentation files The root folder contains this document while the sub folder SkyFunctions contains an RTF file for each Sky function 12 1 Chapter 12 Sky Scripting Interface Cortex 2 1 Reference Manual The Registry Sky stores two keys in the Windows Registry under HKEY_LOCAL_MACHINE SOFTWARE Motion Analysis Sky The first key is Network Folder and saves the path for the Network Sky Scripts list box The second key is StartupScript and saves the filename of the Sky script to run when Sky is opened for the first time These scripts apply to the computer and will be the same for all users The Script Object Script Examples The scripting language is Visual Basic Sky loads the script into the VB Compiler which compiles then executes the script code You can create and use variables subroutines and functions in Visual Basic As a com piled assembly the script variables are only defined during execution of the script when you run the script For a more detailed description of how to combine multiple operations into one script run refer to Sky Compiled Script Reference on page 12 8 Sample scripts with data are found under the Cortex installation folder unde
447. ture C Program Files Motion Analysis Cortex Samples Sky Examples Batching with Matt MattRun1 cap 585 Frames 120 FPS V Up Unitsimm _ 11 10 Cortex 2 1 User s Manual Chapter 11 Skeleton Types Exporting the Skeleton Data Into an HTR File The SkB or Solver type skeleton data can be saved to an HTR hierarchi cal translations and rotations file after you calculate it and view it in Cor tex Select the File gt Export HTR file menu item This is for use with animation packages You will then select the default top Euler Angle Order ZYX since that is how the plugins are built to receive the data The following are options on the Export HTR file menu Euler Angle Order Use ZYX which is the default if you are going to import this with a Mo tion Analysis File IO plugin to the animation packages Other Euler Angle orders will be decided by your local mathematicians The numbers in the Cortex software are stored internally in a certain way and exported to the HTR file according to the method above Figure 11 9 HTR Export Options P Htr Export Options bo e Euler Angle Order Base Position Options ZYX No base position for Biomechanics users XYZ S YXZ Current Frame for Animation users YZX Calcium Model Pose Skeleton for Animation users Z Export Base Position Only XZY Export Skeleton htr Base Position Angles in the columns of HTR data are absolute angles according to the Options
448. u see on your screen 4 61 Chapter 4 The Cortex User Interface Cortex 2 1 Reference Manual Figure 4 48 Viewing the Pre Recorded Data Cortex A I Fie Layouts Dataviews Toos Hep eg MotionAnalysis Current Directory C Program Files Motion Analysis Cortex2 Samples BioFeedT rak GolfSwing p Browse System Calibration Motion Capture Post Process Model Edit Plugins Presentation Cameras Analog Devices Markesa Cub Goler 1 2 3 Frame Rate 120 7 Shutter Speed 1000 1 sec K es A 3 Master Syne Internal v e Slave Sync Ethernet x 8 226 29 8 285 34 8 303 37 Using Sunlight Fiter E5 wi u e js a 3 Current Camera Number 2 Mode Unknown a Serial Unknown Version Unknown 8 214 38 8 223 32 8 285 38 Date Unknown 7 8 adi Set As Mester _ Brightness 100 Threshold 500 gt FPGA Date Unknown 0 814 5 0 8 285 11 8 177 42 o TSR Camera Network IP 0 0 0 0 x 379 35 898 43 2474 52 32 99 m Witrecking events Connect To Cameras Disconnect Use Raw Files Settings per a Identifying C Join Virtual O Oin E Run ee tt Base J M C Skeleton i Tenplste GoFSwno1 cap w 00 00 01 024 f 7 2 iL 3 4 fi 6 i g Eea 921 Frames 120 FPS Z Up Unitsimm Analog 600 00 Hz Cortex displays data somewhat differently when in Post Process mode For instance the ana
449. ual Chapter 10 Plugins Tab Assistant Panel File Cleanup This panel is used for inspecting and modifying captures as well as per forming some disk cleanup operations It is divided into two sections each with its own tab File Cleanup and Capture Inspector This tab contains tools for deleting files from the disk The file list is pop ulated by selecting either the Populate List for Delete Capture button or the Populate List for Delete Orphan Files button The Populate List for Delete Capture will add all files that a capture references including the cap file itself to the delete list The Populate List for Delete Orphan Files will scan all directories that are used by any capture in the current direc tory Any file in one of those directories that is not a part of one of the captures is added to the delete list This is useful in cases where Marker Set names have changed and old unmanaged files have been left behind Once the delete list is populated individual files in the list can be se lected unselected check box next to the file in the list Clicking the De lete Selected button will delete all files with check boxes next to them in the list Note that this can not be undone so proceed carefully Figure 10 7 Assistant Panel gt File Cleanup Interface AssistantPanel x File Cleanup Capture Inspector Populate List for Delete Capture Populate List for Delete Orphan Files Static cap Static1 cal V Sta
450. uld be used is provided below as a common use example This is the most com mon use of skins for Animation users If a Collada segment name is con tained within the name of a Cortex segment then that Cortex segment is used to drive the Collada segment The Use Skeleton Translations value of a mapping is set to true if and only if that segment does not have a par ent it is global The rotational offsets are determined by assuming that the first child of a segment is along the bone axis of that segment Then a transformation is calculated which aligns the Collada segment and Cortex segment bone axis Additionally the skin setting for applying the inverse global scale factor is enabled Clear All Segment Mappings This tool clears all of the Collada segment mappings Apply Mapping Offset to All Segments This tool applies the mapping settings in the Mapping for All Segments area to all of the Collada segments When the Skin Represents the Mocap Actor Biomechanics One case for using skins is to represent the person being tracked more ac curately than using markers links segments In this case the Collada seg ments should resize to the segment lengths solved for in Cortex To achieve this affect the segment mappings should all be configured either by manually or using the Auto Detect Segment Mappings button Once the correct segment correspondences and offsets have been configured enable the Use Skeleton Translations option for each
451. uld be a segment touching the floor Graphing Script Note The graphing script may contain event settings which will cause problems in some setups In general it is a good idea to use the graph scripts to set and clear Event Frames with good reason The following issues may help distinguish between their uses 1 Graphs scripts get updated every time the graph is displayed in real time or in post processing This could be a problem if the user goes to edit the event frames in Post Processing When the user goes back to the graph view these edits would be wiped out 2 Event scripts can be turned on and off with the Events check box on the realtime dashboard while graph scripts run ONLY IF the graphs panel is visible 3 Graph scripts get executed first then event scripts If something is calculated in a graphs script the calculated variable s are available in the event script but ONLY IF THE GRAPH is showing See the example below for swGetData_UserGraphs iGraph The below Cortex Sky documentation shows how to get data from a graphs script and use it in the event script This is a good way to develop the event scripts swGetData_UserGraphs iGraph Gets the current data in the specified graph Return Value Double The current value in the graph Input Values NONE See Also swGetData_XXX functions Example Sub FeedbackFromGraph Get the graph value from the second graph Dim Value as Double swGetData_UserGraphs 1
452. um results all cameras should be about 2 5 meters above the floor See Figure 3 3 8 Cameras As a wider range of motion is allowed the probability of markers being occluded increases to the point that eight or more cameras are required This is the minimum recommended configuration for animation applica tions Cameras should be about 3 meters above the floor See Figure 3 4 10 Cameras In an elongated capture space ten cameras may prove beneficial The first 8 cameras should be placed about 3 meters above the floor as in the 8 camera setup The two additional cameras 9 and 10 should be placed 5 meters above the floor at each end of the long dimension of the capture volume and will probably have longer focal length lenses than the other cameras See Figure 3 5 12 Cameras As the capture volume becomes more elongated twelve cameras may be required The first 8 cameras should be placed 3 meters above the floor Cameras 10 and 11 should be placed as 5 meters above the floor on the ends of the capture volume but closer to the center than cameras 9 and 12 3 2 Cortex 2 1 Reference Manual Chapter 3 Camera Setup 14 Cameras 16 Cameras More than 16 Cameras Capture Volumes Between Motion Analysis Cameras same height Therefore one end of the long volume will be covered best by cameras 9 and 11 while the other end will be covered best by cameras 10 and 12 See Figure 3 6 When the sides of the capture volume are too long
453. unction with the timing of the strobe ring light pulse There are 1024 different levels of shutter speed control Cortex 2 1 Reference Manual Chapter 5 System Tab Hardware Sync Using Sunlight Filter Genlocking Master Camera Current Camera Information Set as Master Note Master Sync This sets the type of Frame Rate Synchronization used by the master cam era Slave Sync This sets how each slave camera is synchronized to the master camera An Ethernet connection from camera to camera is the default This is used on the legacy cameras for capturing at frame rates gt 500 fps When activated this feature eliminates large blobs targets and one pixel blobs in the camera hardware caused by typical outside lighting The tracking parameter Max Horizontal Lines per Marker gets set as the max size allowable target in horizontal pixels This is selected when the master camera is synced to an external video source either NTSC or PAL To enable the feature you must have a li cense feature installed in your mac_lic dat license file that looks some thing like the following line Eagle Genlock 9c3856f6 782cb125 Please contact support motionanalysis com if you need this license item To turn it ON check the box called Genlocking Master Camera in the System gt Cameras panel When this is done the Master Camera which can be any of your cameras must have an analog video signal black burst or other s
454. und in li brary you have an older version of a library that is not working or is needed If you do not have the A D option check the C Winnt System32 directory and rename the file nidaq32 dll to be nidaq32 dll old Then close and relaunch Cortex This applies for Windows operating systems If you are using a different operating system you will need to do a search for the file nidaq32 dll Relationship Between Capture Volume and Marker Size Listed in Figure 3 3 are Optimal Highest Accuracy Large Volume and Extended Volume capture areas for the 6 8 and 10 camera systems Larger volumes require more cameras Different shaped capture areas are also possible At the extremes volumes will vary with ceiling heights and can vary with optical conditions including external lighting Table 3 3 Guidelines for Selecting Marker Size Normal Capture Volume Marker Size meters Cameras Highest Raptor Eagle 3 8 inch 9mm 2 5 x 2 5 6 Accuracy Hawk 1 2 inch 12 5mm 2 5 x 3 5 8 Large Raptor Eagle 1 2 inch 12 5mm 3 5 x 3 5 6 Volume Hawk 3 4 inch 19mm 3 5x6 8 Extended Raptor Eagle 3 4 inch 9mm 5x5 6 Volume Hawk 1 inch 12 5mm 5x8 8 1 8 and 1 4 markers are also available for smaller volumes such as face hand or foot capture volumes 3 27 Chapter 3 Camera Setup Cortex 2 1 Reference Manual Insight Focusing for Raptor Series Cameras Setting Up the 1 Cameras for Insight Fo
455. ur calibrations AFTER you have completed a good wand coverage and good wand calibration The results of the successful wand calibration are stored in your capture file and your System Calibration file The System Calibration file can be saved after each wand calibration It is the default calibration that is used when your launch the Cortex software For a very accurate calibration go to the Tools gt Settings gt Calibration gt Other tab and change the Extra wand processing iterations value to 2 before collecting or processing the wand data Figure 6 2 Tools gt Settings gt Calibration gt Other Tab Settings Calibration File Structure Tracking Cameras Playback 3D Display Post Process Tools Misc Id Params Plugins Calibration Frame Lenses Orientation Capture Volume Other Calibration with L Frame Camera Aiming Unconstrained followthrough iterations Extra wand processing iterations v Include wand metric refinement in calibration Origin Offset Applied at L Frame Calibration Time Property X Translation Y Translation Z Translation The above procedure uses the first Wand Calibration to determine the Lens Distortion mappings and uses the second processing of the Wand calibration to refine the calibration Subsequent wand calibrations can be run like steps 3 and 4 if you do not change the lens settings This optional check box has two functions 1 Itis used
456. ure F 4 on page F 21 are the critical and semi critical mark ers for upper body and lower body motion recording If any of the lower body critical markers is missing from the static trial the legs will not be loaded with the Mocap Model Similarly if any of the upper body critical markers is missing from the static trial the torso head and arms will not be loaded Note that the sacral left ASIS and right ASIS markers are crit ical for both upper and lower body motion recording If any of these markers is missing the Motion Module will print an error and not load the Mocap Model The head and hand markers are semi critical If used they allow the Motion Module to track motion at the neck and wrist If not used these joints will remain fixed during animation of motion trials in SIMM F 20 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module Figure F 4 Critical and Semi Critical Markers Top Head Head Top TopHead Front Head HeadTop Head Front FrontHead Rear Head Front Head HeadFront Head Rear j Head Front RearHead FrontHead HeadRear g f o HeadFront 5 I R Shoulder R Shoulder _ L Shoulder R Elbow Medi
457. ure suit However markers can be applied directly the skin If markers must be placed directly on the skin and the subject will be per forming athletic moves in which perspiration might be a problem pre tape liquids like Tuff Skin or New Skin can help make double stick tape adhere better These products must be applied to dry skin and al lowed to set for a minute or two before the marker is attached Rubberbands looped around the marker and limb also work well to stabi lize the markers Rubberbands can be looped together to increase diame ter and prevent restriction of blood flow Rubberbands can be used around the elbows wrists hands knees ankles and toes Spare CD ROMs Zip disks or some other backup medium should be available for backups and data transfers 2 4 Cortex 2 1 Reference Manual Chapter 2 Planning a Motion Capture Session Motion Capture Body Suit Camcorder Tapes Music Player Stop Watch Sample Form A motion capture body suit with Velcro attachments for markers provides a quick way to prepare a subject for motion capture The use of the body suit is especially effective when subjects are involved in rough or contact type motion capture sessions common in animation applications Depending on the length of the capture session spare video tapes should be on hand Either a CD or tape player can provide musical accompaniment Music helps calm and smooth out the subject s performanc
458. us Lateralis 6DOF Transducer L Peroneus Brev Motek VGait vly vv vr rye L Peroneus Long Muscles L Hip Adductor L Glute Max Wireless EMG Clear Channel L Glute Med Clear ALL Channels R Rectus Activate ALL R Hamstring 7 R Lateral Ham j Configuration i p medan jerenced Single Ended defaut v R Gastrocnemius lates R Tibialis Ant lozero Forces R Tibialis Post R Vastus Medialis Sample Rate le of Frame Rate 5 Sample Rate Hz 600 00 R Vastus Intermedius R Vastus Lateralis R Peroneus Brev R Peroneus Long R Hip Adductor R Glute Max pie R Glute Med Units mm Analog 600 00 Hz 5 14 Cortex 2 1 Reference Manual Chapter 5 System Tab Shifting Selected Analog Data Example 9 To save the entries in the Analog panel choose File gt Save Setup from the Menu Bar 10 If you would like to give the file a new name or save it to a different directory choose File gt Save Setup As This series of functions is used to correct the time shift delay in certain telemetered EMG channels These are introduced by Noraxon EMG units model 2400 and later which have a 15ms delay in their signal transmis sion protocols As a result the EMG signals in multi source EMG and force plates analog data collected by the Motion Analysis system become non synchronous with the motion data Cortex allows the user to time shift the EMG data in the analog channels using the following steps
459. ut does import them so that you can create plots of them in the Plot Maker SIMM will only import other data that are identified as such in importVari ables txt This configuration file located in SIMM Re sources mocap misc contains mappings between OrthoTrak and the mocap model of all forces moments and powers for the hip knee and ankle joints You will only need to edit this file if you want to import data other than these In addition to importing tracked marker files SIMM can import motion data that is sent over the network in real time from Cortex SIMM is thus able to animate a musculoskeletal model and plots of joint angles and muscle lengths while the subject s motion is being recorded For this real time connection Cortex solves tracked marker data using the mocap model It then sends generalized coordinate values as well as analog data over the network to the SIMM computer If the same mocap model is loaded into SIMM these generalized coordinates will drive the anima tion of the model in real time with a small delay whose length depends on the network speed and the graphics speed of the SIMM computer Follow these steps to use the real time connection between Cortex and SIMM 1 Find the folder SIMM Cortex on your SIMM computer and look for mocap jnt and solver dll solver dll may be hidden in the folder view because it is a system file Copy both files to the folder on the Cortex machine you ll need to exit C
460. ut from their body with their thumbs facing for ward 5 Remove the medial knee and ankle markers and any others that you do not want to use for capturing motion If you use a marker set with no upper extremity markers the Motion Module will remove the upper extremity from the mocap model and dis play only the pelvis and legs Once you have selected the static pose file to be used for opening the mocap model SIMM displays a dialog box allowing you to set some op tions for importing the static pose In many cases you will want to use the default settings for these options so you can simply click the OK button to import the motion The following list describes each option in the dia log box These fields allow you to specify the starting and ending numbers for the sequence of frames that are averaged together to determine the static pose These fields are initialized to 1 and the number of frames in the file meaning that all frames will be averaged If frames in the chosen se quence are missing some markers locations for markers that are present will still be used in the average This option gives you control over the automatic loading of personal dat When SIMM loads the static marker file it looks for a file called per sonal dat in the same folder This file is identical to the one created and used by OrthoTrak If the file is present SIMM will automatically load it and read model parameters from it such as foot length and hip
461. uto increment after a marker is identified Chapter 8 Post Processing Tab Cortex 2 1 Reference Manual Rectify Re identifies missing markers gaps in a determined frame range For more information on the Rectify functions refer to Rectify Functions way What They Do and When To Use Them on page 8 19 It is also used for cleaning up the Initial Pose for making a template when you have no template to start with Takes ALL markers on the current frame regardless of the All vs Selected radial button measures the link ages on the current frame and uses those measures to automatically sort markers into the correct marker slots Characteristics of Rectify e Uses all markers Named and Un named e Works only on the Highlighted XYZ Selected Time Range e Uses the Named marker linkages and XYZ path continuity e It will switch Named markers Named markers are not automatically locked e Adjusts Linkage lengths dynamically to fit the data including mis takes e Uses the Tools gt Settings gt Identifying Parameters function typi cal Template Create A template for identification can be created which will be used to auto ID markers in Real Time for Template ID and Template Rectify Q For more information refer to Building a Template on page 9 5 Figure 8 12 Create Template Interface Create Template MarkerSet Name Template Prop Definition Golf Person Frames Range Frames Used Current Fram
462. utomatically when the application closes 4 14 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface File gt Exit Layouts Menu Preserve Layouts Data Views Menu Reference Video F1 2 D Display F2 3 D Display F3 Marker XYZ Graphs F4 Analog Display F5 Skeleton Graphs F6 Save Current As A prompt to enter a profile name will be displayed A profile with that name and the current settings will be created and made the current profile Note the current settings are not necessarily the same as the settings for the current profile If any settings changes have been made prior to select ing Save As these will be reflected in the new profile and not the current profile Import Selected This launches the profile import dialog This allows portions of another profile to be loaded for use with the current profile Allows you to exit the Cortex software Make sure you have saved the current capture files The items in this menu are generally self explanatory When checked Cortex remembers the different layouts for each of the mode tabs System Calibration Motion Capture Post Process Model Edit Plugins and Presentation When un checked it keeps the same lay out configuration when you move to the different mode tabs The Cortex interface can accommodate up to four simultaneously open data views and can be resized with the mouse to fit the panes however you desire You can view combinat
463. ve been determined the length of each segment is calculated For most segments the length is simply the distance from one joint center to the next For the foot the Mo tion Module reads the length from personal dat If there are no foot F 13 Appendix F SIMM Motion Module Cortex 2 1 Reference Manual The Marker Set length measurements in personal dat then the foot length is assumed to be 1 4 times the distance from the heel marker to the toe marker the toe marker is actually placed on the top of the foot just posterior to the toes Each body segment in the mocap model contains scaling information that tells the Motion Module how to scale it based on an OrthoTrak skeletal segment The scaling information consists of the name of the OrthoTrak segment and X Y and Z reference numbers that correspond to the un scaled length of the SIMM segment For example the right femur in the mocap model contains the line gait_scale R_THIGH 0 3960 0 3960 0 3960 This tells the Motion Module that the unscaled femur is 0 3960 meters long Once the length of the corresponding OrthoTrak segment is known R_THIGH the femur can be scaled accordingly If the R_THIGH seg ment were 0 35 meters long then the femur would be scaled by a factor of 0 35 0 396 In most cases the three reference values are the same number indicating that the segment should be scaled uniformly in X Y and Z The two exceptions are the TORSO and PELVIS which are scaled
464. vewcty 3 m mm O accer 730 61 Y 1266 76 1910 17 t 555 61 Ows O Simeon Oee EE gt 5T_U_6 Engty et J 53 UJ lt Emotys 53 U_0 lt Ergty pan Bd ER Enns w T roo s ski ey CIES Ce Carte 20 Marker 3O A Frames 120 FPS zup Unisemes Analog 600 00 He I 8 30 Cortex 2 1 Reference Manual Chapier 8 Post Processing Tab Distance The Distance Between Markers tab shows the distance between two se lected markers for each frame throughout the tracked data You may se Between Two lect any two markers in the tracked data to be analyzed by clicking those Markers Tab markers in the 3D View or on the marker list grids To delete a pair of markers from the grid click on the row and press the Delete key You may select and delete several rows at once by pressing shift click on the rows and pressing Delete Figure 8 22 Distance Between Two Markers Tab Cortex 1 0 0 Body _Club_Merged prj Golffemper1 trb Golffempert vc1 E Fle Laot OsteVews Took Hep System Calbration Motion Capture Post Process Model Edt AI OW Quek ID Rectfy Temglate Tenglate Template Marker ID Exchange Create 1D Recttly Posveunce Distances anges Distances Between Markers 600 0 PI eer emea 4 Plo 4 e sea Frames 1206S 2 Up Unesma Janso 600 000 8 31 Chapter 8 Post Processing Tab Cor
465. vis a Sacrum acceptable names V SACRAL V SACRUM SACRAL SACRUM SACR VSAC or Right PSIS acceptable names R PSIS RPSIS RPSI and Left PSIS acceptable names L PSIS LPSIS LPSI Right shoulder acceptable names RSSHOULDER RSHO Left shoulder acceptable names L SHOULDER LSHO Right lateral elbow acceptable names R ELBOW R ELBOW LATERAL R ELBOW LAT RELB Left lateral elbow acceptable names LELBOW L ELBOW LAT ERAL L ELBOW LAT LELB Right wrist a Lateral acceptable names R WRIST R WRIST LATERAL R WRIST LAT RWRI or b Radius acceptable names R RADIUS RWRA Left wrist a Lateral acceptable names L WRIST L WRIST LATERAL L WRIST LAT LWRI or b radius acceptable names L RADIUS LWRA Right medial elbow acceptable names R ELBOW MEDIAL R ELBOW MED Left medial elbow acceptable names L ELBOW MEDIAL L ELBOW MED Right wrist a Medial acceptable names R WRIST MEDIAL R WRIST MED F 26 Cortex 2 1 Reference Manual Appendix F SIMM Motion Module or b ulna acceptable names R ULNA RWRB 4 Left wrist a medial acceptable names L WRIST MEDIAL L WRIST MED or b ulna acceptable names LLULNA LWRB Rig ht Arm To load only the right arm set the MOCAP_MODEL parameter in your SIMM preferences file to rightArm jnt or choose that file using the Op tions Choose Model Model command in the SIMM menu bar Then use the markers listed below Critical Markers Right shoulder acceptable names
466. volume To automatically detect and ignore these frames as the file is read turn on this option it is on by default When the option is on SIMM will start at the first frame and delete it if it is missing one or more markers It will then continue to scan forward through the frames delet ing each one until it encounters a frame containing all of the markers It will then do the same procedure starting at the last frame and working backwards SIMM will not remove frames with missing markers that are in between full frames so there may still be frames in the motion that are missing markers When loading a motion SIMM has the capability of calculating deriva tives of the motion variables When this option is turned on after SIMM has solved the marker data and created a SIMM motion it will calculate first order time derivatives of the generalized coordinate values i e joint velocities during the motion It will also calculate derivatives of any force or EMG data in the analog file if present These derivatives can then be plotted using the Motion Curves command in the Plot Maker see Section 2 5 2 for more details Figure F 2 Tracked Marker Import Dialog Box walk1 c3d Options OK markers 23 frames 477 data rate 120 0 Hz Cancel m Import Options import frames f to 477 increment fi X axis T lquick solve units time sec x I start at0 0 crop ends Analog Data IP calculate derivatives IV auto load an
467. will also be affected by the F stop of the lens A small aperture increases depth of field but if you close it too much you will affect range and cause vignett ing It is recommended to leave the aperture at the factory setting This is the furthest distance that a marker can be adequately tracked to be useful for motion capture It is not possible to give a specific value for a given camera type as it depends on many variables such as ambient con ditions threshold brightness aperture marker size etc 3 33 Chapter 3 Camera Setup Cortex 2 1 Reference Manual 3 34 Chapters The Cortex User Interface Getting Acquainted With the User Interface Menu Bar Setup Files cal Extensions MarkerSet Files mars Extensions Viewing Sample Data Digital Reference Video Option CortexDV Software Real Time Dashboard Join Virtual Post Process Dashboard Post Process Tool Strip Zooming Rotating and Translating in the 3D View Selecting Markers Virtual Markers Linkages and Segments Time Code Getting Acquainted With the User Interface Before using Cortex it is necessary to become familiar with the interface and the names of the tools and controls that will be used throughout this manual The major components are as follows The Graphics Panes in the center of the screen The Menu Bar in the top left side The Directory List below the Menu Bar The Mode Buttons along th
468. will not see that as a candidate since it only looks in the Unnamed markers list Process the data from both ends towards the difficult part assuming there is a crash in the middle and clean data on both ends After doing Rigid Body Rectify from the starting frames to the middle then from the ending frames to the middle use Template Rectify to go it again For difficult data trials this 1 2 3 4 combination will get you a lot of named markers for very little work In the Post Process tab the data is identified or re identified by press ing the Template Identify button This affects the current frame only and it is successful if 1 The template is good and the data fits 2 All markers are present To continue the correct identification to successive frames you need to have the Max Speed and Max Prediction Error settings correctly set for your data This applies to when a marker first appears and is identified with the cur rent template To keep the correct identity into the next frame the soft ware checks to see if it has moved too much to be the same marker It can move in any direction The Max Speed parameter tells how much move ment is allowed It is measured in mm from the first frame hence the units of mm frame If no marker is seen within this search sphere then the target identify is not continued into the next frame If a marker is found within the Max Speed sphere the target identity is continued into the sec
469. worth 3 point moving average or 5 point moving average filter can be applied to the selected markers over the selected frames Filter selection is found in the Tools gt Settings gt Post Process Tools gt Smoothing form For more information refer to Filters on page 8 5 The selected marker s will become unidentified over the selected frames When selected the marker s data will be moved to the first available uni dentified marker slot Makes all unnamed unidentified markers into contiguous paths to follow through the capture sequence For more information on the Rectify func tions refer to Rectify Functions What They Do and When To Use Them on page 8 19 Deletes all unnamed markers over all frames XYZ marker data within the selected frames including endpoints will be cut out and is available for Paste 8 16 Cortex 2 1 Reference Manual Chapter 8 Post Processing Tab Cut Outside Search Q PP Settings Undo HE D Additional Icons Hide Markers Unhide Markers o Cuts the data outside of the selected frames exclusive of the endpoints Finds gaps and or spikes throughout the data set The current frame will be set to the first gap or spike found in either the first selected marker on the marker list or all of the markers See the Tools gt Settings gt Post Pro cess Tools gt Smoothing tab The Acceleration at Spikes function will indicate the frames in which a mark
470. ws you to save a SIMM motion file containing the motion that SIMM calculates from the marker data This file contains exactly the same data that is in the motion that SIMM loads onto the model You can load this motion file into SIMM at a later time rather than re importing the marker file If this box is checked a browse button is enabled that al lows you to specify the name and location of the motion file Analog data files contain force plate and EMG data that was collected in sync with motion data When loading C3D files there are no separate an alog files all of the analog data is contained in the C3D file When load ing TRB TRC files you can load analog files only if they correspond to the chosen TRB TRC files If the analog file has the same base name as the TRB TRC file then the Motion Module will load it automatically when you select the marker file Otherwise you should select the analog file as well in the file browser The same holds for XLS files which are not actually analog files but are treated similarly XLS files can contain other data corresponding to the recorded motion such as kinetic data cal culated by OrthoTrak and stored in a single trial spreadsheet SIMM can recognize three types of analog data ground reaction forces EMG activation levels and other data usually kinetic data from an XLS file These data types and how they are interpreted by SIMM are described below SIMM displays force plate
471. x There are pre defined and fixed values for the diag onal axis values These can be exactly the same for each plate but check the Bertec documentation for the values appropriate to your plate See the sample forcepla cal file Figure C 4 If using other Bertec hardware e g AM6504 or AM6800 please check the out put range and scale factors with the manufacturer C 7 Appendix C Force Plate Configuration Forceplate cal File Setup Cortex 2 1 Reference Manual Figure C 4 Example Forcepla cal File for 2 Force Plates 1 25 51 46 5 2 9350 0 0040 0 0020 2 9930 0 0270 0 0120 0 0000 0 0070 0 0070 0 0020 0 0020 0 0020 0 1000 0 0260 5 6000 25 7000 0 0000 1 0000 1 0000 0 0000 0 0000 0 0000 2 25 51 46 5 2 9340 0 0090 0 0120 2 9750 0 0050 0 0020 0 0040 0 0010 0 0010 0 0020 0 0020 0 0060 0 1000 0 0300 56 5 25 7000 0 0000 1 0000 1 0000 0 0000 0 0000 0 0000 0 0130 0 0470 11 5420 0 0000 0 0000 0 0050 3 8000 4 2000 0 0000 0 0000 1 0000 0 0020 0 0450 11 5480 0 0000 0 0000 0 0000 4 2000 4 2000 0 0000 0 0000 1 0000 0 0480 0 0080 0 0240 1 5390 0 0000 0 0020 C 8 Cortex 2 1 Reference Manual Appendix C Force Plate Configuration Forceplate cal File Setup Figure C 5 The 6x6 Calibration Matrix forces moments a12 a13 a14 a15 al6 a22 a23 a24 a25 a26 The main diagonal represents the basic sensitivities for each channel
472. y what is desired for BioMechanics users Unchecking it means that the skin will be displayed in the scale of the skin probably what is desired for Animation users Segment Mapping The Segment Mapping Tools area provides tools for adjusting all segment Tools mappings at once Auto Detect Segment Mappings for Representing the Subject This buttons attempts to prepare the skin for use in representing the mocap subject More explanation of this scenario and why it would be used is provided below as a common use example This is the most com mon use of skins for Biomechanics users If a Collada segment name is contained within the name of a Cortex segment then that Cortex segment is used to drive the Collada segment The Use Skeleton Translations value of a mapping is set to true if and only if that segment does not have a par ent it is global The rotational offsets are determined by assuming that the first child of a segment is along the bone axis of that segment Then a transformation is calculated which aligns the Collada segment and Cortex 9 10 Cortex 2 1 Reference Manual Chapter 9 Model Edit Tab Two Common Use Examples segment bone axis Additionally the skin setting for applying the inverse global scale factor is enabled Auto Detect Segment Mappings for Representing a Character This buttons attempts to prepare the skin for use in representing a ren dered character More explanation of this scenario and why it wo
473. yses Cotten AS ampir Shy E nampis System _Calbration Monon Capture Post Process Model Edt Plugins Presentation car MON OO a a a a a O a a QehD Retty Cose Temglote Template Morker 1D Exchange Cute Vetus Cok Smooth Make Rectty Doiste Ot Qt Search lad Tengiste D Recity Jon Jon Wes Unnamed Unnamed Unnamed Outside Settings Markeenets New ar j EM ie Cakchum Segments 66 OJ E 7 w a P MBH M_BRHp MFR MJU 5 Landart Lumbar oer Lumbar Sy aP Lunoss Senet j Zw Sone i Y a Se i ve aa ye Pos x y oe 5 Nackt p Y mea neck a Hess LOevicie 2 Lupper zm S Uowsr rm X Wet Lhat ATN rit i LP12 Y s ua GLOBAL 4 48 0 89 1 39 o t 0 0 Lorg oom Cheha nis 4 1 434 4140 2 Kio 1000 2000 3000 4000 5000 5000 7000 B000 en a n 5 f f Cees gre EI Ho Oo 0o E Bt fa fe ee bonua Progam Meeibotin AnDY RACO EZI SkY Exangles od _Twerky TOZ Cap avo Frames enres vu usnm gt Note Solver Interface Si is an older stand alone version of software that is similar in function to Calcium Cortex 2 1 Reference Manual Chapter 1 Introduction Skeleton Builder SkB Figure 1 5 SkB Skeleton A skeleton in animation terms is a hierarchically connected set of bones with translation and rotation data Each bone has a parent and potentially any number of children One special bone has no parent and is usually re fe
474. ystem Calibration and Motion Capture activate Real Time mode and present you the necessary tools to successfully capture motion data Figure 4 45 Mode Tab Buttons Mode Tab Buttons Cortex SetupWithEvents cat GolfSwing_1 cap 4 BG Fie Layp Data Views Tools Help ystem Calibration Motion Capture Post Process Model Edit Plugins Presentation Markersets Golfer Club La The fourth button Post Process activates Post Process mode and trans forms Cortex into a tracked data editing tool The final two buttons Model Edit and Plugins are mode less function buttons that present various tools without switching the program between the Real Time mode and Post Process mode Model Edit is used to define markers to create linkages Panel Tab These buttons give you access to the various tools specific to the different Buttons phases of the motion capture session Figure 4 46 Panel Tab Buttons Panel Tab Buttons aS dk iC eons r s Presentation Cameras Analog Devices ak Frame Rate 120 Shutter Speed 1000 1 sec Using Hardware Syne Using Sunlight Fitter C Genlocking Master Camera 4 58 Cortex 2 1 Reference Manual Chapter 4 The Cortex User Interface Status Bar This feature located in the lower left corner of the user interface provides Messages the status and confirmation of the software in its current processing state Real T

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