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SIMM 7.0 User Guide - MusculoGraphics, Inc.

1. cscceeeseeeees 187 2 20 Function Editor osacaaaasiiniieees ce ees 189 2 20 1 Command Mente ois ences seckeesoacd eeptevedtaraeedaadess 191 2 20 2 Function Editing goccsecic ts cccaislesccosteaneatseets 192 221 Scripting Togolese e Une adanasesay a R dames 195 2 21 1 Top Level Commands sccidsctiscdvadanidesccgcrstess 197 2 21 2 Model Viewer Commands cccceceseeeeeees 200 2 21 3 Plot Maker Commands ccccecssceesseeeeees 203 2 21 4 Motion Reporter Commands ceeeseeeeees 206 2 21 5 Dynamics Tool Commands ceceeeeeeeeees 208 2 21 6 Motion Editor Commands cccccccceeseeeeees 215 2 21 7 Muscle Editor Commands cccscceesseeeees 218 Chapter 3 Input Files sc ccsssessssasecsaantsacsnsssneteassencaseses 221 31 AIL OO UCONN eeose e EEE 221 Fed PB OTE TUR Sal 22 sede haley hd atte a teat Somaya 222 322 SIMM ASCII norane naea a ee ss 224 3 22 Old SIMM ASCI sxsnuceseccasdtnds wcenceeus 225 32 3 SIMM Binary anren a 227 3 2 4 Wavefront OBJ 2 5 6 woes 228 FDS O a E A E ANE A E EREE 229 32 O 0 a ee a ee 230 BD Te IGES wii is 8a Rie a SS 230 DD IOUIL PUES sata xa shad ead poss bx Seg SaaS ede vacua ees aa 231 3 3 1 Body Segments 345 6288 sce on vcadevesaceensen cade seers 238 3 3 2 Fixed SCOMeNE gicinu canescens 242 De IJO Shei e EEE R E 243 3 3 4 Generalized Coordinates cccccecesseeeeseeeenees 245 vil 3 3792 PUNCHONG mene iena a ae aidaa 249
2. These fields let you change the range of the generalized coordinate or motion variable which serves as the X vari able for making new data curves When you choose an X variable the variable s minimum and maximum values are copied into the x min and x max fields respectively When you generate data curves these values serve as the default range for the X variable You can change the range by edit ing these two fields If you change the default range and then choose another X variable the values you entered are erased and the new X variable s default range is copied into the fields If you then re select the original X variable that variable s default range is copied into the fields not the changed values you entered earlier Chapter 2 Tools 49 2 5 Plot Maker 50 Chapter 2 Tools ymin y max scale offset 2 5 8 SUM These fields let you limit the range of the Y coordinates of the data points in the curves that you add to a plot By default y min is a large negative number and y max is a large positive number meaning that all of the data points in the curves should fall within the range and thus not get clipped By changing these values you can clip out data points that do not lie within a desired range Every time a curve is added to a plot each of the data points is compared to y min and y max If the point is less than y min it is set equal to y min If it is greater than y max it is set equal to y m
3. 2 21 Scripting Tool cutes the command printing an error message if there are any problems When you enter a command with a filename that is not an absolute path starting with a drive letter either for opening or saving a file SIMM looks for the file relative to the current folder e g open GaitModel jnt If you do enter an absolute path for a filename the current folder is not used to look for the file e g open C GaitAnaly sis Model GaitModel jnt Top Level Commands These commands are available in the Scripting Tool no mat ter which tool is the current one same as selecting Open from the File menu It displays a file browser so you can choose the file s to open opens the specified file s The rules for opening multiple files at once are the same as if you selected them all in the file browser e g you cannot select more than one muscle file at a time same as selecting Open Mocap Model from the File menu display a file browser so you can choose the static trial to open opens the specified static trial and displays the dialog box with import options closes deletes the specified model SIMM does not prompt you to confirm the action closes deletes the specified plot SIMM does not prompt you to confirm the action saves the specified model to the specified joints file SIMM does not notify you if this action overwrites an existing file Chapter 2 Tools 197 2 21 Scripting Tool save ms
4. 3 3 6 World Objects ssssesssenssesessseeseesreseesseessesressee 254 JIa Material Susain a a 256 Did OS Cameras nane e ia ai arian 257 3 3 9 Wrap Objects ssssesssesssesessseeseesesssesseseessresse 259 3 3 10 Deform Objects eis sates oeeitacsagtieuntreioutece 263 oo LS DeformiteS rini ete a a 267 3 3 12 Constraint Objects 0 0 cee eeceesseeeteeeteeeeees 270 3 3 13 Model Poses sevsateccdgagecesigeseenensfacisiepinndaeeentes 275 3 4 Muscle Files oonooonnonoonnsesenrssrssissessersrerese 277 SA MuSC S anen n E a E a ae 277 3 4 2 Muscle Surfaces a co3q 1s Speseeotoe detsoeeuatntise 284 3 4 3 Ligamento onena nae nii anais 286 SO Moton Files seere a A E E aN 286 3 5 1 Motion File Header isc cist cidscssesics tasadsdaaccor se 289 3 5 2 Gencoords and Muscles ccecceeeseeeeeteeees 293 3 5 3 Motion Objects cesiiceesicota eis eeecees active det 293 es oak Other Datin eani NE E E 296 3 5 5 Standard Deviation Data ceeeeeeeeeees 297 3 5 6 Auxiliary Datars wasietisconeensauainancetes 297 DO PIOC FilES enna cate a E EA 298 3 7 Model Archive Files sje ics ease txatseosensed mteoonene 300 3 0 CIID FUES sen codspsensnansscensete Goa A eines aise 301 39 Movie Files nnan e caine hated hac 303 Chapter 4 NOM sssssssisssssssosssissesisessssssessissssinesssssss 305 Chapter 5 Motion Module scccscssscssssseeeee 311 SI Intr d cti on senin Ree Gate 311 5 2 Opening Tracked Marker Files cc
5. This button lets you toggle the visibility of the normal vec tors for all of the bones in the current segment This toggle button lets you turn on and off the display of the inertia vectors of the current segment Global Parameters These display parameters are applied to all the segments in the model This toggle button lets you turn on and off the display of the mass center locations of all the segments in the model This toggle button lets you turn on and off the display of the inertia vectors of all the segments in the model Chapter 2 Tools 133 2 14 Segment Editor 134 Chapter 2 Tools 2 14 4 Scaling Parameters The scaling parameters allow you to scale the current body segment along its local X Y and Z axes You can type val ues into the X Y and Z fields and then press apply scale to apply the new scale factors to the segment Markers muscle points wrap objects constraint objects joint kinematics for child segments and all other components of a body segment are scaled along with the bones except for the iner tial properties After the scale factors are applied to the seg ment they are reset to 1 0 Model Window Commands Body segments and spring points can be selected and edited using keyboard and mouse commands in the model window To use these commands you must first set the tool mode to the Segment Editor by clicking on the Segment Editor icon in the heads up display HUD on the left side of
6. and the motion of the joints is calculated If the motion of some or all of the joints is prescribed e g to follow motion capture data then the dynamics code calculates and applies the necessary con straint torques in order to ensure that the joints move as pre scribed In a typical forward dynamics simulation muscle and external forces are applied and the motion of the joints is not prescribed In a typical inverse simulation ground reaction forces are applied but not muscle forces and the motion of all of the joints is prescribed In this case the sim ulation will calculate the torques that are required at each joint to create the prescribed motion However because the same numerical method is used to perform both simulations it is possible to mix forward and inverse dynamics For example you can prescribe the motion of all of the joints but also specify the excitations of some of the muscles e g from EMG recordings In this case the simulation will apply the muscle forces to the body segments and then cal culate and apply any additional torques that are required to prescribe the motion This scenario is useful during an inverse dynamics analysis if you want to estimate the forces in the muscles whose EMG data you are collecting Dynamics Pipeline users can create their own DLLs of whatever musculoskeletal models they want and thus can perform dynamic simulations on them in SIMM FIT Mod ule users cannot create the
7. 60 deg genc1 Figure 3 7 Example restraint function Since a restraint function is defined for the entire range of motion of a gencoord it is important to carefully define its values within this range If you want the function to be exactly zero for a portion of the range which is usually the case for dynamic simulations you should define knots coincident control points in the appropriate places For example suppose that a gencoord named genc has a range of motion of 30 degrees to 60 degrees and that if it goes beyond either end of its range you want to apply a torque to drive it back into its range Furthermore suppose that you would like to start applying the restraint torque when the gencoord gets within 5 degrees of its limit to make it less likely that it will go beyond its range In this case your restraint function would look something like the one in Figure 2 1 Note that when the gencoord goes below its range a positive torque will be applied to increase the gencoord value and when it goes above its range a nega tive torque will be applied to decrease its value The func tion definition would look like this Chapter 3 Input Files 253 3 3 Joint Files 254 Chapter 3 Input Files 3 3 6 beginnaturalcubicspline 31 50 0 25 0 40 0 10 0 25 0 0 0 25 0 0 0 55 0 0 0 55 0 0 0 70 0 10 0 80 0 25 0 endfuntion Note the coincident control points at 25 and 55 degrees This
8. B 10 Appendix B SIMM Resources will read personal dat after importing the motion and update the subject information in the Motion Reporter This preference specifies whether or not to use a Bayes filter on EMG data when importing a motion trial The Bayes fil tered data is stored in the output motion in an auxiliary data column that is linked to the EMG column e g semimem_r and semimem r aux and it is used to calculate onset time offset time and average amplitude for the EMG If the Bayes filter is turned off SIMM will use the moving window smoothing algorithm from early versions of the program This preference controls how SIMM scales EMG signals When this preference is on SIMM will calculate the maxi mum value of each EMG channel for the motion trial If the actual maximum is greater than the MVC specified in per sonal dat if any SIMM will use the maximum as the MVC instead of the specified value This preference defines the minimum allowable force when calculating force plate forces Forces below this threshold are set to zero If this preference is not specified a value of 40 0 is used This preference defines the maximum allowable residual when importing XYZ marker data from C3D files Marker coordinates with a residual above this threshold are treated as missing data If this preference is not specified a value of 10 0 is used This preference specifies a vertical offset that is applied to the display of t
9. fixed transformations and are performed in the order in which they are entered on the command line from left to right 5 Motion Module Introduction The Motion Module is an optional component to SIMM that allows you to easily import data recorded by a motion cap ture 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 Corpora tion It can also read analog files in the ANB or ANC format with ground reaction force and EMG data that was recorded in syne 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 Motion Module can connect to a Motion Analysis sys tem and receive and display motion and analog data in real time as it is being recorded Files of tracked marker data contain a sequence of frames each representing 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 coordinate 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 organized 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
10. ord values will be ignored during IK Note IKS files do not support the loading of analog data from ANB or ANC files To include EMG or force plate data in a motion created from an IKS file the processed analog data must be in the IKS file itself A typical use case for IKS files would be the following Start with a TRC TRB C3D file and import it onto a model saving a motion file MOT during the process During the import turn on the show markers box to include the marker coordinates in the MOT file and make sure the analog data is loaded and processed as well The resulting MOT file will contain IK solved gencoord values as well as marker coordinates muscle EMG and force plate forces Modify the file in Excel focusing on the columns of gencoord data Delete any gencoords that you do not want to specify as input For the others modify their values as desired and add auxiliary columns with their weights Save your changes and give the file the IKS suffix You can now import it into SIMM and perform IK using the specified gencoords and markers Using the Mocap Model As described in Section 5 2 SIMM has the ability to read tracked marker data and convert it into a motion 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
11. sphere The radius of the sphere is specified by the keyword radius followed by a single value radius 0 15 cylinder The radius of the cylinder is specified by the keyword radius followed by a single value The height of the cylin der is specified by the keyword height followed by a single value radius 0 10 height 0 25 Chapter 3 Input Files 261 3 3 Joint Files active visible show_wrap_pts 262 Chapter 3 Input Files Note The cylinder s height is used when calculating muscle wrapping If both of the tangent points the points of contact between the muscle and the wrap object are beyond the vis ible portion of the cylinder the muscle is considered to miss the wrap object and is not wrapped ellipsoid The sizes of the ellipsoid in the X Y and Z directions are specified with the keyword radius followed by the X Y and Z sizes respectively radius 0 1 0 2 0 1 torus The inner and outer radii of the torus are specified by the keyword radius followed by the inner and outer radii respectively The outer radius is the distance from the center of the torus to the axis of the curved cylindrical section and the inner radius is the radius of the cylindrical section itself and thus should always be less than the outer radius radius 0 03 0 08 This parameter may be used to disable the wrap object If its value is no or false then the wrap object will have no effect on its associated muscles This
12. the vertices within each polygon are specified clockwise If you use this option norm will reorder every polygon so that they are counter clockwise and will then calculate vertex normals this option is used to specify a reference normal which norm will use as a last resort when calculating vertex normals Norm will attempt to determine the inside and outside of a polyhedron without using a reference normal If the polyhe dron is not a closed object however it may have difficulty finding the outside If norm does have difficulty and you do not know if the polygons are all clockwise or all counter oldascii binary tx num ty num tz num rx num ry num rz num SX num sy num SZ num clockwise you should specify a reference normal This vec tor corresponds to the major direction of the surface normal of the topmost polygon of the polyhedron For opt use one of X X Y Y Z Z The default value of the reference normal is Y write the polyhedron to an old style ASCII file This style of ASCII was the required input format for early versions of norm but has since been replaced with the new ASCII for mat Use this option if you want to output a polyhedron without bounding cube information or vertex normals write the polyhedron to a binary file This option is provided so that you can create polyhedron files in the format which early versions of SIMM required but it is recommended that you create ASCII fil
13. 1 if appropri ate If it is on then after cropping frames or importing only a subset of them SIMM will reset the time values in all frames so that the first frame has time 0 0 If this preference is off Appendix B SIMM Resources B 7 B 1 Preferences MOCAP LOAD ANALOG MOCAP CALIBRATE FORCES MOCAP MARKER NAME SOURCE MOCAP SAVE MOTION FILE B 8 Appendix B SIMM Resources then the imported frames will preserve whatever time values they originally had in the TRB TRC C3D file This prefer ence is used to initialize the appropriate checkbox in the motion import dialog box but you can change it as you load individual motion trials This preference specifies whether or not to load analog data when importing a TRB TRC C3D file When importing a TRB or TRC file SIMM will look for an ANB or ANC file with the same base name When a importing C3D file SIMM will read the analog data directly from the C3D file This preference is used to initialize the appropriate checkbox in the motion import dialog box but you can change it as you load individual motion trials This preference specifies whether or not to calibrate the for ceplate forces when importing a motion trial To calibrate forces SIMM determines the baseline of each forceplate channel and subtracts these values from the data thus zero ing out the force data For more information on force cali bration see Section 5 2 Opening Tracked Marker Files This preference
14. 3 3 Joint Files Joints The body segments can be connected in any arrangement by defining joints A joint specifies the transformations that relate the position and orientation of one body segment to another The body fixed transformations are performed in a user defined order and consist of three orthogonal transla tions and three rotations around user defined axes Body fixed means that the axes are fixed in the child body the body that the joint is to When each joint rotation is per formed the rotation and translation axes are rotated with it Thus the next rotation is performed about the newly rotated axis This is in contrast to space fixed in which all of the rotation and translation axes are fixed in the parent body Each translation and rotation in a joint is either constant i e independent of body position or a function of a gener alized coordinate A generalized coordinate defines a degree of freedom in the musculoskeletal model e g a joint angle The functions that relate the translations and rota tions to the generalized coordinates are called kinematic functions A sample joint definition is shown in Figure 3 4 The translations and rotations that comprise a joint are called dofs The rotation dofs r1 r2 r3 are rotations around axis1 axis2 and axis3 respectively The transla tion dofs tx ty tz are translations along the X Y and Z axes respectively of the first body segment listed after the
15. Bi active x Il positive transform J visible T negative translate rotate a x body fixed rotation translation transform in x 000 0 0000 0 00 0 1486 local frame a 0 00 0 0591 y parent frame ay el clear constraint points points gt name scap_superior segment gt segment scapula_r save points Offset 0 1204 0 0094 0 0359 restore points weight 1 0000 delete point tolerance 0 001000 Figure 2 20 Constraint Editor window Chapter 2 Tools 2 13 Constraint Editor 2 13 3 object name segment radius height plane sphere cylinder ellipsoid 120 active visible Chapter 2 Tools Constraint Object Attributes The panel to the right of the Constraint Editor s command menu can be used to edit the current constraint object s attri butes This field contains the current constraint object s name Click and type in this field to rename the constraint object This field displays the name of the parent segment of the current constraint object To change the current constraint object s parent segment click the segment button to the right of the field These fields let you specify the size of the current constraint object For spherical constraint objects there will be only one field to specify the sphere s radius For cylinders there will be two fields for the cylinder s radius and height For ellipsoids there will be three fields to specify the ellip
16. PO QSOS OO Al S9151 Were 123 AID000 Vs632500 iq221esiL endloop endfacet facet normal 0 016157 0 316683 0 948394 outer loop Werte 123 702500 PI 96A38900 iq S vertex 124 409800 79 707000 1 265451 Were 123 299000 V 6S2500 1 22145 5 1 endloop endfacet e endsolid Figure 3 4 Example bone file in ASCII STL format Chapter 3 Input Files 229 3 2 Bone Files 230 Chapter 3 Input Files 3 2 6 3 2 7 triangles each with a normal vector A complete descrip tion of the STL format can be found on various web sites including http en wikipedia org wiki STL_ file_format Note when a musculoskeletal model is loaded into SIMM all of the model s bones that are specified in the STL format are automatically processed with norm so that the facets polygons can be connected together and vertex normal information is available For bones with many polygons this can add significantly to the time it takes to load a model Thus for large bone files it is recommended that you convert them to the SIMM ASCII format before adding them to your model Collada SIMM also supports bone files in the Collada format dae Collada is an open standard XML format that is supported by many 3D graphics and animation software packages SIMM will read polygonal mesh material and texture map definitions from each Collada file and use them to create one bone for each file If vertex normals are not specified in the file for
17. When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again Command Menu This command lets you select the marker you want to edit When you choose a marker from the pop up menu that marker is added to the set of selected markers it does not unselect any previous selected markers The parameters for the selected marker are displayed in the Marker Editor win dow If more than one marker is selected and they do not have the same parameter values name offset weight those fields in the tool window will be blank To create a new marker choose make new marker from the pop up menu This command saves all of the selected markers in the cur rent model It saves them to a buffer so that you can restore them if you make changes that you later want to undo When you first load a model SIMM saves copies of all the markers so you can restore them back to their original form without having to save them first This command saves all of the markers in the current model It saves them to a buffer so that you can restore them if you make changes that you later want to undo When you first load a model SIMM saves copies of all the markers so you delete selected restore selected restore all unselect all 2 12 3 name 2 12 Marker Editor can restore them back to their original form without having to save them first This comman
18. analyze your musculoskeletal models The tools are Model Viewer Plot Maker Muscle Editor Joint Editor Gencoord Editor Segment Editor Bone Editor Constraint Editor Wrap Editor Deform Editor Motion Editor Marker Editor Function Editor Skin Editor and Motion Reporter Also if you have the Dynamics Pipeline Mod ule or FIT Module options to SIMM there is a Dynamics Tool for interfacing SIMM to dynamic simulations There is also a Scripting Tool that enables you to automate some of the functions in SIMM This chapter gives a detailed description of each tool The tools use menus forms sliders and toggle buttons to give you access to a variety of information Menus are used to make selections e g choosing a muscle Forms are used to enter information e g entering a title Sliders let you change the value of something e g a generalized coordinate smoothly Toggle buttons are used to control the state yes no or on off of a parameter Definitions A menu is a vertical list of options or commands each enclosed in a box You can select a menu option by click ing the left mouse button in its box The command is per Chapter 2 Tools 7 2 1 Introduction 8 Chapter 2 Tools muscle menu formed as soon as you press the mouse button not when you release it Some menu items display pop up submenus when they are selected Menu items that do this can be dif ferentiated from other menu items by an angle bracket gr
19. defined 63 specifying in file 282 active toggle button 51 analog data files opening 321 animations see movies animations see snapshots AVI files see movies B body segment groups changing drawmode 24 defining in joint file 239 body segments 238 241 changing display parameters 133 restoring 128 saving to buffer 128 setting inertial parameters 129 Bone Editor 137 149 boolean operations 138 command menu 138 deleting polygons 140 deleting vertices 140 flipping normals 140 information header region 138 model window commands 145 running norm on bone 138 splitting polygons 138 unselecting polygons 140 bone files 222 230 Collada format 230 IGES format 230 opening 12 saving 19 SIMM ASCII format 224 SIMM binary format 227 SIMM old ASCII format 225 STL format 229 Wavefront OBJ format 228 bones deleting 140 editing 146 exporting 140 moving to different body segment 140 reading from files 142 selecting 145 specifying in body segments 238 writing to files 140 C C3D files see tracked marker files cameras restoring position of 22 saving position of 22 specifying in joints file 257 capturing images see snapshots color factor using to display muscles 60 colors setting in simmcolors file 16 Constraint Editor 116 126 information header region 116 model window commands 121 objects command menu 117 points command menu 124 Index 1 constraint objects creating 117 defined 116 del
20. filename r_shoe asc contact object gt new spring contact NURBS object NURBS object gt pame right_heel filename shoe_heel igs info filename shoe_heel nurbs NURBS pring total mass of model 75 000204 y xy yy zy 0 015600 0 0000000000 0 0023140000 0 0000000000 zi 0 000000 xZ 0 0000000000 yz 0 0000000000 Zz 0 0026830000 Bec display parameters J visible Ij show mass center browse J show inertia show segment axes show normals global parameters show mass center show inertia l apply scale 2c 1 00000000 ve 1 00000000 ZA 1 00000000 l active Jj visible browse browse Figure 2 21 Segment Editor window Chapter 2 Tools 127 2 14 Segment Editor 128 2 14 2 segment gt save segment restore segment drawmode material Chapter 2 Tools Command Menu This command lets you select the body segment you want to edit When a segment is selected the tool window is updated to show that segment s parameters This command saves the current state of the current seg ment in the model It can be used in combination with the restore segment button to help you undo changes made while editing segments This command restores the most recently saved copy of the model s current segment It can be used in combination with the save segment button to help you undo changes made while editing segments This command lets you ch
21. is restraint function currently active tolerance in degrees is gencoord clamped to range of motion is gencoord locked at current value is gencoord slider visible in Model Viewer stiffness for PD controller during dynamics Figure 3 5 Example generalized coordinate Chapter 3 Input Files 3 3 Joint Files tion 2 4 Model Viewer To define a default value for a gen eralized coordinate use the keyword default_value followed by some number in the range of motion This will be the starting value of the generalized coordinate and the value it will be reset to when you select reset ge values in the Model Viewer The keyword clamped is an optional parameter that lets you specify whether or not the gencoord is constrained to remain within its specified range By default gencoords are clamped and cannot assume values outside their range The keyword locked is an optional parameter that lets you spec ify whether or not the gencoord is locked By default gen coords are unlocked If a gencoord is locked its value cannot change Restraint functions can be specified for each gencoord These are used by Dynamics Pipeline simulations to apply restraint torques to prevent the gencoords from moving beyond their ranges of motion They are also used by the inverse kinematics solver to assign weights to the gencoords when finding model configurations to satisfy the loop con straints A restraint function i
22. lates the proper foot print information from the heel strike and toe off events so you normally do not need to specify these values yourself This optional parameter followed by a filename specifies the movie to load when the motion is loaded The movie is assumed to already be synchronized with the motion See 3 5 2 3 5 3 3 5 Motion Files Section 3 9 Movie Files for a list of supported movie for mats and information on how to view the movie in the model window Gencoords and Muscles The most common types of data found in motion files are generalized coordinate values and muscle activation levels You can also specify velocities of one or more generalized coordinates in a motion file These velocities can be used to estimate fiber velocities when calculating muscle forces during the motion To specify the velocity of a gencoord the column name must be the name of the gencoord appended by vel Note it is usually preferable to have SIMM calculate gencoord derivatives by specifying the calc derivatives parameter in the motion file header rather than defining them explicitly in the motion file Since the thickness and color of the muscles in the model window depend on their activation levels specifying mus cle activations in a motion file can create more informative animations As the body segments are animated through the motion sequence the muscles will change their appearance to reflect their relative levels of
23. segments keyword The second body segment listed is the one on the other side of the joint the reference frame you end up after doing the ordered transformations To make any of the dofs a constant put the keyword constant after the name of the dof then enter a value This value should be in degrees for the rotations For translations you can use any units you like but they must match the units used in the bone and muscle files meters are used in the sample leg Chapter 3 Input Files 243 3 3 Joint Files model To make a dof a function of some generalized coor dinate put the keyword function after the name of the dof then enter a function name followed by the name of a gen eralized coordinate in parentheses The function name must start with the letter followed by a number In the example in Figure 3 4 the femoral tibial joint defini tion part of the knee joint specifies the transformations from the femur segment to the tibia segment The order of the transformations indicates that to move from the femur reference frame to the tibia reference frame a translation is performed first followed by rotations around axisi axis2 and axis3 respectively The translation is divided into three orthogonal components tx ty tz where the X Y and Z directions are defined by the axes of the femur ref erence frame The rotation axes are also defined relative to the femur reference frame and their orientations can be FEMO
24. selected point helping to show you how far the points have moved To move the selected spring points in the X Y and Z direc tions relative to their respective body segments you can use the x y z and Shift keys Pressing x translates the points in the negative X direction while pressing Shift and x translates them in the positive X direction Note if multiple spring points are selected and they are attached to different body segments then the x y and z keys will move all of the points along the axes of the current segment in the Seg ment Editor the one containing the contact polyhedron RIGHT CLICKING SPRING POINTS You can right click on a spring point to display a pop up menu with several editing options The options allow you to select unselect the point for editing hide the display of the spring object pair deactivate the spring object pair and delete the point Note you can right click on any spring point without holding down any keyboard keys and without first clicking on the Segment Editor icon in the HUD Bone Editor The Bone Editor allows you to transform bones translate rotate and scale and move individual vertices of a bone as well as perform simple boolean operations between bones addition subtraction intersection This tool is especially useful when you are creating a new model and need to move or scale bones within their reference frames It provides a graphical interface to all the functionality o
25. surface definition should be the same as the first so that the surface is a complete cylinder Figure 3 23 beginmusclesurface beginpoints 0 0337 0 0326 0 0434 0 0103 0 0594 0 3291 0 0121 0 0439 endpoints beginpoints 0 0364 0 0335 0 0392 0 0108 0 0523 0 3298 0 0064 0 0433 endpoints beginpoints 0 0364 0 0335 0 0392 0 0108 0 0523 0 3298 0 0064 0 0433 endpoints beginpoints 0 0309 0 0320 0 0477 0 0104 0 0664 0 3291 0 0177 0 0439 endpoints beginpoints 0 0337 0 0326 0 0434 0 0103 0 0594 0 3291 0 0121 0 0439 endpoints endmusclesurface 0 0 ooo o ooo o oooo o 0 0 0 0 0877 0059 0930 0139 0060 0016 0930 0139 0060 0016 0931 0139 0060 0016 3 4 Muscle Files To make the muscle surfaces change color with activation you can specify their activation levels in a motion file As with muscles use the name of the muscle surface as a col umn label and enter activations from 0 0 to 1 0 The materi als muscle_mat0 through muscle_mat20 specified in the joint file are used to color the muscle surfaces For exam ple muscle mat0 is used when the activation is 0 0 rf surface segment segment segment segment 0072 0090 segment segment segment segment segment segment segment segment segment segment segment segment 0877 0059 0072 0090 segment segment segment segment pelvis femur femur patella pelvis femur femur
26. unselecting markers 111 Vv velocities of muscle fibers 52 279 specifying in motion file 293 vertices moving 149 selecting 148 W wireframe defined 239 world objects 254 256 Wrap Editor 82 93 command menu 83 information header region 83 model window commands 89 tips amp techniques 92 wrap objects creating 83 defined 82 specifying in joint file 259 transforming 88 wrapping methods see ellipsoid wrapping methods Index 9
27. v torus axial constrain to quadrant x J positive To negative hd Zz translation 0 0019 0 2890 0 0140 7 37 7 88 1 76 x Zz reset Figure 2 10 Wrap Editor window Chapter 2 Tools 85 2 10 Wrap Editor 2 10 3 object name segment radius height sphere cylinder ellipsoid torus 86 Chapter 2 Tools Wrap Object Attributes The panel to the right of the Wrap Editor s command menu can be used to edit the current wrap object s attributes The previous section describes how to assign muscles to wrap objects and wrap objects to body segments The controls described in this section allow you to edit the other parame ters of the current wrap object This field contains the current wrap object s name Click and type in this field to rename the wrap object This field displays the name of the parent segment of the current wrap object To change the current wrap object s parent segment click the segment button to the right of the field These fields let you specify the size of the current wrap object For spherical wrap objects there is only one field to specify the sphere s radius For cylinders there are two fields for the cylinder s radius and height For ellipsoids there are three fields to specify the ellipsoid s X Y and Z radii For torus objects there are two fields for the inner and outer radii These radiobuttons let you choose the current wrap object s shape
28. when you move the cursor to the oppo site side of the window the gencoord will move in the other direction If you specified that a gencoord can wrap around its range of motion then you will not reach these stopping points With wrapping when a gencoord reaches the end of its range it will wrap around to the other end of its range and continue to move RIGHT CLICKING MODEL WINDOW BACKGROUND If you right click on the background in the model window i e away from any object SIMM displays a pop up menu with three options Set all tools to this model sets all of the editing tools to that model Edit model preferences displays a dialog box that lets you modify some of the model prefer ences Look at segment ground sets the ground segment to be the fixed one for display purposes as described in Sec tion 2 4 2 in the description of the look at button Hot Keys The following hot keys work in the model window regard less of which tool the heads up display is set to Equivalent to the left mouse button Equivalent to the middle mouse button Equivalent to the right mouse button Starts stops the current hotkey motion Equivalent to pressing the start stop button in the Model Viewer Toggles the display of each of the muscles in the model If they are all on they will be turned off and vice versa If some of the muscle are displayed those will be turned off and the hidden ones will be turned on Chapter 2 Tools 35 2 4
29. 0 278098 0 868048 0 500083 0 005 0 0 0 0 109 167633 movie gait cycle wmv endheader time hip flexion knee angle ankle angle semimem 0 008 17 3492 21 7508 4 2261 0 10 0 016 13 8255 21 2797 3 8606 0 10 0 024 12 3931 20 5520 1 6857 0 12 0 032 10 8606 19 2399 0 2093 0 12 Figure 3 24 Example motion file Chapter 3 Input Files 3 5 1 name datacolumns datarows x_column 3 5 Motion Files When you load a motion file into SIMM using the File Open command in the menubar the new motion is linked only to the current model so you should make the model window the topmost one in SIMM before loading a motion file to link to it Alternatively you can drag and drop a motion file onto a model window to link the motion to that model Note Case is significant when entering text into motion files All SIMM keywords e g datacolumns datarows must be in lower case letters You are free however to use upper as well as lower case letters for labeling the columns of data and SIMM will display these names exactly as you type them into the motion file Spaces are not allowed within the names of the data columns Motion File Header A header in each motion file names the motion specifies any events forceplates and foot prints associated with the motion and specifies some parameters that control how the motion data is displayed when the model is animated Here is a description of each header parameter The name of the
30. CA We would like to thank Frans C T van der Helm Ph D of the Delft University of Technology for his contribution of muscle wrapping algorithms We also thank Stephen J Piazza Ph D and Ryan Landon M S of Pennsylvania State University for their contribution of the NURBS based contact detec tion algorithm Table Of Contents Chapter 1 Introduction sscsscssaesscsvensevasseiasecesssdacsetsedeccaad 1 L1 SIMM Wh t itis uein cess Sings Genk eee a mara t natant l 1 2 Applications clei is shbhhigeashede Hedoi petit deta teed aa twkas 2 LI Design Godls gomas A AE ER 3 1 4 The SIMM Environment 5 0ccce Hass ode ane Goren soi 4 1 5 About the Manual ee cceelsagGont can elie Rana 5 TGS SIMM Tutorials acest ita ccteasiarsueu ee asennad Riba E ESE 6 Chapter 2 LOOMS s sssssssssssssosssssrsssssssssssossssssossssssisss ssesssss 7 2 Jntroducti n socane irena e A E A e e T DA Le Definitions serae are a a 7 22 Opening Files nararima a o Oa A EA A 11 22 1 Drag and Diop isens easi iE 15 DIS DAVIN FUES iru a a E R 17 24 Model Viewer mareiro o e codes A 20 Dh Ae SEIS OTOP Menu sissioni aa 20 2 4 2 Command Menu 12 1 c5s2rscitleesnenaency teeta eieuss 22 ZA SEP OWNS oana Gia nedecia case i o aai 28 2AA SWOT Saha eosin susan skh salen seats Warnell oc acta an 30 2 4 5 Toggle BUtt S sasoira aiai 31 2 4 6 Model Window Viewing Commands 31 2 3 Plot Maker caves isis aia e R iN 37 2 5 ASSL CHOE MENU cass iadaeassati
31. Each function is defined by a series of XY control points in parentheses e g 5 7 12 6 A comma separates the two components and you can put spaces between the values commas and parentheses The control points are interpolated using one of four methods step function piecewise linear function natural cubic spline and GCV spline A step function also called piecewise constant or zero order hold has a slope of zero at all points and is represented by a series of intervals at the specified Y values For X values less than the first XY control point X Y the function evaluates to Y The definition of a step function must have at least two control points and looks like this beginstepfunction 20 0 0 5 0 4 4 3 10 8 9 7 endstepfunction A piecewise linear function is a first order interpolation of the control points i e they are connected by straight lines For X values beyond the range of the XY control points the slope of the function at the nearest endpoint is used for extrapolation The definition of a linear function must have at least two control points and looks like this beginlinearfunction 22 0 0 5 Chapter 3 Input Files 249 3 3 Joint Files 250 Chapter 3 Input Files 0 7 4 5 10 0 9 7 35 4 5 8 endlinearfunction A natural cubic spline is a third order piecewise polynomial interpolation of the control points It has a continuous sec ond order derivative and thus is a
32. Editor T 4 New 5 ae 2 n f Ca a gt 4 i Figure 2 19 Sample Constraint The constraint object is an ellipsoid fixed to the ribcage There are two constraint points both fixed to the posterior edge of the scapula model has no constraint objects in it then the Constraint Editor window will be blank except for the constraint object button which will let you add new constraint objects to the model Clicking on the help button opens a window containing helpful text about the Constraint Editor When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again Objects Command Menu Select this command to create a new constraint object or to select an existing constraint object for editing When you select this item a pop up menu of existing constraint objects is displayed The first item in the pop up menu new con Chapter 2 Tools 117 2 13 Constraint Editor 118 segment gt save all restore all delete Chapter 2 Tools straint object creates a new constraint object adds it to the current model and makes it the current constraint object for editing object for editing When a constraint object is cre ated a default point is created as well The remaining items in the pop up menu allow you select existing constraint objects for editing Select this command to change the body segment to which the current
33. IK solver is on SIMM will try to find a set of gencoord values that keeps all of the loops of body segments closed while still satisfying the joint constraints When solving SIMM tries to keep clamped gencoords within their ranges applies restraint functions if specified to unclamped gencoords to keep them within limits and keeps locked gencoords at their locked values When a model is loaded SIMM uses the solver to assemble the system and close all the loops using the default values If the solver is on when joint definitions are changed changing dof types editing functions and when motions are applied to a model the solver tries to close all loops given the current configuration If individual gencoords are changed by entering values moving the slider or using the gencoord keys in the model window loops are solved keeping that gencoord value fixed to the value you just set it to Whenever the solver cannot find a solution with the exact gencoord value it will try to find the solution with the closest gencoord value In cases where no solution can be found an error message will pop up and the model will be displayed with loops broken If the restraint functions are poorly defined the solver may be unable to find a solution because the errors are too large An error message will be displayed alerting you of this If there are no loops in your model this button has no effect If your model has closed loops and constraints obj
34. If dynamic simulations are required it also verifies that each stance phase of a stride occurs on a force plate so that correct inverse dynamics moments can be calculated If a part of stance occurs off of a force plate that stride is not included in the report Generating a Report When you generate a motion report SIMM performs the following steps 1 2 3 4 2 18 Motion Reporter Examine each selected motion to see if it already contains the kinetic variables e g moments powers chosen for output to the report If it is missing any of them the motion is flagged as requiring a dynamic simulation If any dynamic simulations are required set up the simulation module using the current settings in the Dynamics Tool The output variables should be set so that they include all of the variables needed for the report and the set of muscles to include in the simulation should be set appropriately For example if you want only muscle lengths in the motion report then you do not need to include muscles in the simulation However if you want optimized muscle activations in the report then you need to select the optimized muscle activations output variable and choose the appropriate set of muscles Run a dynamic simulation on each motion that requires it If the gait option is not selected the simulation is performed on the entire motion In this case you are responsible for making sure that the motion is cropped
35. Muscle Editor Current Path panel When a muscle wraps over a wrap object two attachment points are introduced to the list One is the tangent point at which the path first comes into contact with the wrap object and the other is the tangent point at which the path leaves the wrap object The Type column also shows the name of the wrap object that is making contact Selected Attachments Panel This panel lists all of the attachment points that are selected in the current model The first column shows the name of the muscle followed by the index of the point the same index as in the Attachments panel The second column shows the type of point and the third column shows the body segment to which the point is attached If there is only one attachment point selected and a polygon on that point s body segment is selected then a fourth column is displayed in the panel showing the name of the bone and the index of the polygon The attachment point can be moved toward the vertices of the polygon as described in the next section Chapter 2 Tools 67 2 7 Muscle Editor 68 Chapter 2 Tools 2 7 8 Selected Attachments The list of selected muscle points in Full Body Model Foint Type Segment deltoid2_r 4 fixed scapula_r deltoid1_r 3 via scapula_r deltoid1_r 4 fixed clavicle_r teres_minor_r 2 fixed scapula_r long_thor_r 1 via torso Figure 2 7 Muscle Editor Selected Attachments panel The selected attachment points show
36. Rt Tibialis would be considered the same as rt tibialis The second column in a variable definition specifies the type of the variable It must be one of the following key words force plate muscles marker Or other data These keywords must be lowercase Following each key word is information describing the variable This keyword specifies a ground reaction force variable It must be followed by three values 1 The forceplate number 1 2 3 etc then 2 The keywords force or moment then 3 muscles 5 4 Analog Configuration Files The channel component x y or z for AMTI or Bertec forceplates or x12 x34 y14 y23 z1 z2 z3 z4 for Kistler forceplates For example a 6 channel AMTI or Bertec forceplate map ping for forceplate 1 would look like this F1X force_plate 1 force x F1Y force_plate 1 force y F1Z force plate 1 force z M1X force plate 1 moment x M1Y force plate 1 moment y 1 M1Z force_plate moment z An 8 channel Kistler forceplate mapping for forceplate 2 might look like this F1X1 2 force_plate 2 force x12 F1X3 4 force_plate 2 force x34 F1Y1 4 force plate 2 force yl4 F1Y2 3 force plate 2 force y23 F1Z1 force plate 2 force z1 F1Z2 force plate 2 force 22 F123 force_plate 2 force z3 F1Z4 force plate 2 force 24 This keyword specifies an EMG variable It must be fol lowed by one or more SIMM muscle names The keyword mvc may optionally appear after the last muscle name If mvc a
37. SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Joint Editor When you are done read ing it close the window using its close box You will be able to re open it at a later time by selecting help again Command Menu This command lets you select the joint you want to edit When a joint is selected the six degrees of freedom dofs that comprise the joint are displayed in the dof form in the lower left corner of the Joint Editor window Chapter 2 Tools 53 2 6 Joint Editor 54 restore current Chapter 2 Tools ra Joint Editor Model Dynamic Mocap Model model gt joint gt name knee_flexion_r ar CUTA Parent segment femur r Child segment tibia_r restore current transform order CEINT V X Si Z D 0 000000 1 00000 0 00000 0 00000 0 000000 0 00000 1 00000 0 00000 F f knee_flex_r 0 00000 0 00000 1 00000 f knee_flex_r f knee_flex_r 0 000000 Figure 2 3 Joint Editor window make changes that you later want to undo When you first load a model SIMM saves copies of all the joints so you can restore them back to their original form without having to save them first This command restores a previously saved joint description Selecting it restores the current joint from a buffer that was saved last time you used the save command When you first This command saves the current joint of the current mo
38. Section 3 3 7 Materials for information on defining a material If no drawmode is defined the default is gouraud_shading There are six drawmodes available wireframe solid fill flat_shading gouraud_shading outlined and none Wireframe means draw just the outlines of the polygons in the bone Solid_fill means draw the bone as a collection of filled polygons For both of these drawmodes the color used to draw the bone is the ambient color specified in the bone s material see Section 3 3 7 Materials Flat shading means use the light sources in the model window to shade the bone polygons but fill the polygons using only one color each This drawmode will accentuate the individual faces on the bone surface Gouraud_shading means to smooth shade each polygon This is often the slowest draw mode because it uses the light sources to calculate the color of each pixel on the bone surface so that it is rendered smoothly hiding the polygon edges outlined means to draw the polygons in the bone s normal material and high light the edges in a darker color None means to not display the body segment at all You can also interactively change the drawmode of any bone or world object using the draw mode command in the Model Viewer or by right clicking on the bone or world object in the model window If you interactively change the material or drawmode the new val ues will be written to the joint file when you save the model The begingroup
39. The coordinates are expressed in the body segment s reference frame These fields let you specify the inertia matrix of the current segment These values are expressed in the reference frame of the body segment and are relative to the mass center of the segment You can specify inertia in whatever units you want but they should match the units you use to specify mass muscle forces and external forces and torques The inertia units in the models that come with SIMM are kilo grams meters meters Force Matte Force mattes are used only by dynamic simulations They transform external forces expressed in the ground reference frame into the reference frame of the body segment to which the force matte is attached Their primary use is to apply forces measured by forceplates to the feet during a simulation To learn more about how force mattes work consult the Dynamics Pipeline manual Chapter 2 Tools 129 2 14 Segment Editor 130 Chapter 2 Tools A body segment in SIMM can contain only one force matte To create a force matte for the current segment click on the new force matte button The name field specifies the name of the force matte The filename field specifies the name of the SIMM bone file which contains the polygon descrip tion s that comprise the force matte Type a name into this field or click on the browse button to browse for a file The visible checkbox controls whether or not the force matte is displayed in
40. The last item in each muscle menu is labeled lt lt done gt gt Selecting lt lt done gt gt with the left mouse button puts away the menu so that it is no lon ger displayed If any of the muscles in the menu are selected when you put away the menu they remain selected even form 2 1 Introduction though you can no longer see the menu When you are fin ished selecting muscles from a particular muscle menu you do not have to put the menu away by selecting lt lt done gt gt Doing so is merely a convenience so that you can display other muscle menus without taking up too much space in the tool window A form consists of a group of fields that can be edited A field is a boxed region that contains a number or other text You can position the cursor anywhere in a field by clicking the left mouse button at the desired position A text cursor appears at this location to indicate that any text you type in will be inserted at this location You can use the left and right arrow keys to move the text cursor one character at a time You can highlight a section of the text field that you want to delete or change by sweeping the cursor over the region To do this press the left mouse button at one end of the region move the cursor to the other end then release the left mouse button You can adjust the size of this highlighted region by holding down the shift key while pressing the left and right arrow keys to move one character a
41. They are described in Section 3 4 2 Ligaments are modeled as mus cles with zero length fibers and are described in Section 3 4 3 Muscles Each muscle tendon actuator is defined by specifying its geometry and force generating properties The geometry is defined by a series of attachment points connected by line segments A minimum of two points is required to define the muscle path There are three types of muscle attachment points described below An example muscle illustrating all three types of points is shown in Figure 3 22 The most common type of attachment point is called a fixed point A fixed point is rigidly attached to one of the body Chapter 3 Input Files 277 3 4 Muscle Files 278 Chapter 3 Input Files segments with its location specified by XYZ coordinates that are constants The second type of attachment point is called a via point Like a fixed point a via point is rigidly attached to a body segment but it is active included in the path only when the specified generalized coordinate is within a certain range Via points can be used to implement simple wrapping of a muscle path over a bone or other constraint that obstructs the path only in some body positions In order to ensure that the muscle length and moment arm changes smoothly when a via point turns on or off it is important to carefully specify its position along the existing muscle path The third type of attachment point is called a moving
42. a material the default material def_bone will be used The drawmode parameter gives you additional control over the shading of the object s surface As with body segments flat shading gou raud_shading wireframe outlined solid fill and none are supported The default drawmode is solid fill You can also define a texture to be used when displaying the object The texture map must be an image file in the TIFF format and you must also create a texture coordinates file which specifies the UV texture coordinates of each ver tex in the bone file The texture coordinates for a simple world object such as a rectangular floor would look like this OrFRO o000 rPROoOO o000 This means that the first vertex of the floor object is mapped to the upper left corner of the texture image 0 0 0 0 the second vertex is mapped to the upper right corner of the tex ture 1 0 0 0 the third vertex is mapped to the bottom right name of this world object bone file describing floor surface XYZ vector from world frame to origin of object scale floor asc to half size XYZ Euler rotation of object in degrees use this material defined in joint file override default and use flat shading TIFF images to be used as texture map texture coords file floor tex file with UV coordinates for each vertex endworldobject Figure 3 8 Example world object Chapter 3 Input Files 255 3 3 Joint
43. a yellow wireframe sphere and the marker name will be shown in a tool tip box If you then left click on the marker it will be added to the group of selected markers If you click on an already selected marker it will be unselected You can also box select markers by pressing and holding down the left mouse button and dragging the cursor to form a rectangle around the markers you want to select or unselect Box select selects all markers inside the box whose visibility is turned on even if the marker is hidden behind a bone or another marker This makes it possible to select a group of coincident markers such as those at a key anatomical land mark with different names As you select and deselect markers the Marker Editor win dow updates to show the number of currently selected markers and their offsets and weights which can be helpful for making sure only the appropriate ones are selected owe 2 12 Marker Editor EDITING MARKERS To move the set of selected markers press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Moving markers net move seg X Y Z where X Y and Z are the distances that the markers have moved relative to the body segment seg If all of the selected markers are attached to the same body segment then seg is that segment Other wise seg is the ground frame To translate the selected markers in the plane of the screen press and
44. a yellow frame and the title bar of the Bone Editor will be highlighted in yellow When the Bone Editor is the active tool in the model win dow three buttons are displayed to the right of the Bone Editor icon in the HUD These buttons are labeled b p and v When you click on the b button the Bone Editor activates bone mode meaning that you can select and edit bones as described below When you click on the p button the Bone Editor activates polygon patch mode meaning that you can select and edit polygons if the current bone is a polyhe dron or patches if the current bone is a NURBS surface as described below When you click on the v button the Bone Editor activates vertex mode meaning that you can select and edit vertices if the current bone is a polyhedron as described below SELECTING BONES To select a bone first make sure the b button next to the Bone Editor icon in the HUD is highlighted then press and hold the S key While this key is pressed the HUD text box in the lower left corner of the model window displays Selecting bonel As you move the cursor around the model window if it hovers over a bone the name of the bone will be shown in a tool tip box If you then left click on the bone it will be selected as bone J and the Bone Edi Chapter 2 Tools 145 2 15 Bone Editor 146 G Chapter 2 Tools tor will update accordingly You cannot select more than one bone at a time EDITING BONES To ed
45. and the wrap object Include the wrapobject keyword in the muscle definition followed by the name of the wrap object to be wrapped over See Section 3 3 9 Wrap Objects for more information about defining wrap objects in your joint file If the muscle is assigned to wrap over an ellipsoid then the name of the wrap method to be used may follow the wrap object name The valid wrap method names are hybrid midpoint and axial If no wrap method is defined then the hybrid method is used by default For more information on wrapping methods see Section 2 9 5 Ellipsoid Wrapping Methods You may also specify the section of the muscle path that is allowed to wrap over the wrap object To do this put the keyword range after the wrap object name or after the ellipsoid wrapping method if specified followed by the indices of the starting and ending muscle points Only mus cle path segments that are between these start and end points will be checked for intersection with the wrap object A value of 1 for the start point means to start at the first muscle point and a value of 1 for the end point corre Chapter 3 Input Files 283 3 4 Muscle Files 284 Chapter 3 Input Files 3 4 2 sponds to the last point in the muscle Note that these mus cle point numbers refer to the points as they are listed in the definition of the muscle in the muscle file If there are via points that are currently inactive when muscle wrapping is computed they a
46. and world objects to achieve this effect you should position the shadow a small distance away from the world object so that you can see it For example if you position the floor with a Y coordinate of 0 9 you should position the shadows at about 0 895 along the Y axis If you put them at exactly 0 9 they would be coincident with the floor and you may or may not see them depending on the viewing angle Appendix A Tips on Using SIMM A 5 A 6 Appendix A Tips on Using SIMM When a body segment or world object is displayed in wireframe mode the color that is used to draw the object is taken from the ambient color component of the material assigned to that object For the def_bone material this color is not white but rather a light gray If you want pure white wireframe objects you should define a new material with an ambient color of 1 0 1 0 1 0 and assign it to the object you want to display in wireframe mode If you press a key or select a menu item and nothing seems to happen you may have lost the input focus to that window This means that your key presses are either going to another window or getting lost entirely This can happen when you press a lot of keys while moving the cursor into several different windows To fix it just release all the keys and mouse buttons click the left mouse button on a different window and then click it again over the window you were originally working in Whenever SIMM pops up
47. appropriately i e that there are no time frames involving unrecorded external forces If gait is on SIMM divides each motion into left and right strides based on heel strike and toe off events The original motion is then replaced by the individual stride motions It then checks each stride to see if the entire stance portion occurs on a force plate If it does not the stride is excluded from the dynamic simulation If it does the simulation is performed and the output variables are added to the motion If gait is on calculate stride and step information for each motion e g stride length step width as well as foot progression angle Chapter 2 Tools 175 2 18 Motion Reporter 176 2 18 2 model gt help 2 18 3 gencoord values Chapter 2 Tools 5 Normalize each motion so that it contains 101 time frames Each column of data in the motion is interpolated with a cubic spline and sampled at 101 evenly spaced time steps It also adds a new column called percent to the motion with values from 0 0 to 100 0 6 Check each motion to see if it contains all of the selected muscle output variables activations lengths forces Calculate the missing ones using SIMM s isometric muscle model and add the results to the motion 7 Calculate the mean and standard deviation if requested of each selected output variable Write this information to a binary Excel file organized with sheets for eac
48. 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 This checkbox turns on the calculation of gait events Heel strike and toe off events are calculated using a combination of force plate forces and trajectories of the sacral heel and toe markers Essentially the type of event right vs left heel strike vs toe off is determined by the marker trajecto ries and the timing of the event is determined by the force Chapter 5 Motion Module 317 5 2 Opening Tracked Marker Files 318 load movie live model update load personal dat output model markers read marker names from Chapter 5 Motion Module plate forces If no forces are available for the event the tim ing is calculated from the marker trajectories This checkbox controls the import of a movie file associated with the motion trial When a motion trial is selected for import SIMM checks to see if there is a movie file in the same folder with the same base name If there is this check box is enabled and checked To see the movie in the model window synchronized to the motion there must be an object called moviescreen obj in the model See Section 3 11 Movie Files for more information about importing and displaying movies When this option is turned on the model window will up
49. are transformed accordingly It is usually easier to create new deform objects using the SIMM Deform Editor rather than editing a joint file directly See Section 2 10 Deform Editor for information on how to do this However it can be useful in certain situa tions to create or modify deform objects manually by edit ing the model s joint file Deform objects are defined within a segment definition in the model s joint file within a begindeform enddeform pair All deform object fields have reasonable default val ues so it is possible to specify a simple deform with just two lines as shown in Figure 3 13 Chapter 3 Input Files 263 3 3 Joint Files Figure 3 13 Minimal deform object specification located within a segment definition In most cases however you will also define the dimensions of the deform object s inner and outer boxes the transforma tion necessary to position the deform within the reference frame of its associated body segment and the starting and ending transformations of the inner box that creates the object s deformation see Figure 3 14 Figure 3 14 Example deform object If the deform object is an auto reset deform then it is not necessary to specify the starting and ending transformations since they will be computed automatically Also remember 264 Chapter 3 Input Files innermin outermin innermax outermax 3 3 Joint Files that auto reset deform objects should be the last d
50. arms of the selected muscles for every generalized coordinate the moment that each muscle applies to the gencoords The right click dialog allows you to select which muscles you want to output The simulation will output the moments of the selected muscles for every generalized coordinate the total net moment applied to the gencoords by all of the muscles The right click dialog allows you to select which gencoords you want to output The simulation will output the total muscle moment of all muscles for each selected gencoord the dynamic activations of the muscles as calculated by a static optimization algorithm This algorithm estimates the muscle activations required to generate the input motion At each time step in the simulation the inverse dynamics gen coord moments are first calculated Then a least squares solver is used to determine the activations that will result in the muscles exerting the calculated moments The optimiza tion is static in the sense that it is performed independently at each time step without regard to activation dynamics but it does take into account the velocities of the muscle fibers See Section 5 5 of the Dynamics Pipeline manual for a detailed description of the algorithm The right click dialog allows you to select which gencoords and muscles you want to include in the optimization The simulation will optimize the activations of all of the specified muscles in order to generate the inverse dynami
51. be written to the output motion adds or removes the specified gencoord to the list whose accelerations will be written to the output motion if output of gencoord accelerations is turned on Name can also be the name of a gencoord group or the word all turns on off the output of gencoord accelerations If output is on only the selected gencoord accelerations will be writ ten to the output motion adds or removes the specified muscle to the list whose activations will be written to the output motion if output of muscle activations is turned on Name can also be the name of a muscle group turns on off the output of muscle activations If output is on only the selected muscle activations will be written to the output motion adds or removes the specified muscle to the list whose lengths will be written to the output motion if output of muscle_lengths lt on off gt muscle forces lt name gt lt on off gt muscle_forces lt on off gt muscle_velocities lt name gt lt on off gt muscle_velocities lt on off gt fiber_lengths lt name gt lt onl off gt fiber_lengths lt on off gt fiber_velocities lt name gt lt on off gt 2 21 Scripting Tool muscle lengths is turned on Name can also be the name of a muscle group turns on off the output of muscle lengths If output is on only the selected muscle lengths will be written to the out put motion adds or removes the specified muscle to the list
52. bone from a file It displays a file browser allowing you to select the file and it adds the bone to the body segment specified in the add to segment field Norm Options Norm is used to process a bone when you select the norm bone 1 button and it is also used to postprocess the bone that is output from a boolean operation The options to norm are used for both types of calls unless otherwise specified convexify polygons triangulate 2 15 Bone Editor When norm performs the specified transformations on a bone it does them in the following order First it applies the rotations in a body fixed manner X then Y then Z Then it applies the X Y Z scale factors and translations relative to the X Y and Z axes of the body segment s reference frame not the rotated frame After the transformations have been applied the translation and rotation fields are reset to 0 0 and the scale fields are reset to 1 0 If you are unsure what the result will be of a series of different transformations it is best to apply them one at a time processing the bone with norm after each one When rotating translating or scaling a bone using either the keyboard commands described in the next section or typ ing values into the fields described below remember to pro cess the bone with norm using the norm bone 1 button in order to apply the transformations to the bone vertices Until you do this the transformations are stored in a temporary
53. both images repre sents a deform object that twists the femur about its long axis We call this deform object Anteversion The smaller magenta box represents a deform object that bends neck of the femur up and down We call this deform object Neck Shaft Angle In this example Anteversion is the first deform in the list followed by Neck Shaft Angle Notice in the pic ture on the right how the smaller Neck Shaft Angle box has followed the twisting rotation of the larger Anteversion box The reference frame of each deform box is itself deformed by any deform objects that precede it in the segments list of deforms This allows each deform box to stick to the region of bone that it was originally assigned to as deforms are applied to the segment This also implies that the order in which deforms are applied contributes to the overall deformation of the body segment Auto Reset Deform Objects A special type of deform object called an auto reset deform is available to simplify the task of maintaining the spatial 2 11 Deform Editor characteristics of a deformed segment s proximal joint Auto reset deforms were designed specifically to keep the ball and socket joint at the hip intact as the femur undergoes deformation However auto reset deforms are not limited to the femur they may be used to preserve the proximal joint of any deformed segment In general terms an auto reset deform ignores its deform start and deform end transformati
54. bottom of the window then selecting it again will hide it Selecting individual muscles from these group menus will cause the muscles to wrap over the current wrap object The muscles will continue to wrap even if you turn off the display of these muscle menus This command saves the current state of all wrap objects in the model to a buffer It can be used in combination with the restore button to help you undo changes made while editing wrap objects This command restores the most recently saved copy of all of the current model s wrap objects It can be used in combi nation with the save button to help you undo changes made while editing wrap objects This command deletes the current wrap object from the model 2 10 Wrap Editor EM Wrap Editor Model Full Body Model model gt wrap object gt muscles gt save current restore current save all restore all delete transform translate rotate segment humerus_r radius x 0 0150 y 0 0150 Z 0 1000 er visible show pts X z transform in y clear local frame y parent frame _ anconeus_r Ji biceps_longhead_r J biceps_shorthead_r _ brachialis_r J brachioradialis_r _ pronator_teres_r _ triceps_lateralis_r _ triceps_longhead_r _ triceps_medialis_r lt lt done gt gt Object name elbow _bic_br body fixed rotation help dr method hybrid midpoint V sphere vz cylinder ellipsoid
55. change the view of a model without having to open the Model Viewer window These model window viewing commands are described in Section 2 4 6 Selector Menu The model selector lets you select which model you will change with the Model Viewer The menus and forms in the Model Viewer window always correspond to the current hi 2 4 Model Viewer Model Viewer Model Gait Model model gt restore camera gt save camera gt restore pose gt save pose gt muscles gt start gt look at gt draw mode gt gencoords gt snapshot gt movie gt name Gait Model Motionspeed 100 0 Wf trackball muscle points hip_add_r hip_rot_r hip_flex_r knee_flex_r ankle_flex_r subt_angle_r toe_angle_r walk_01 walk 02 J gracilis_r J semimem_r l semiten_r J bi_fem_lh_r J bi_fem_sh_r WW sartorius_r J rectus_fem_r _ vas_med_r _ vas_int_r _ vas_lat_r _ patlig_r gas_med_r EEES lt lt done gt gt gas_med_r EEES J soleus_r _ tib_post_r _ tib_ant_r BM ext_dig r J ext_hal_r flex_dig_r flex_hal_r _ per_brev_r _ per_long_r _ per_tert_r lt lt done gt gt w 400 gt shadows Figure 2 1 Model Viewer window Chapter 2 Tools help hy 400 crosshairs 21 2 4 Model Viewer 22 help 2 4 2 restore camera gt Save camera gt restore pose gt Chapter 2 Tools model setting the current model does not aff
56. clicking on the Wrap Editor icon in the heads up display HUD on the left side of the model window To indicate that all keyboard and mouse commands are being directed to the Wrap Editor the icon will be highlighted with a yel low frame and the title bar of the Wrap Editor will be high lighted in yellow SELECTING WRAP OBJECTS To select a wrap object press and hold the S key While this key is pressed the HUD text box in the lower left corner of the model window displays Selecting wrap objects As you move the cursor around the model window if it hovers over a wrap object the object will be highlighted and its name will be shown in a tool tip box if the wrap object is already the current object in the Wrap Editor it will be unhighlighted when you hover over it If you then left click on the wrap object it will be selected and the Wrap Editor will update to show it as the current object You cannot select more than one wrap object at a time EDITING WRAP OBJECTS To edit the current wrap object press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Editing current wrap object Also a GUI box will be displayed around the wrap object This box lets you move rotate and scale the wrap object by left clicking on the box handles As you hover the cursor over a handle a tool tip describes the handle s func tion To move the wrap object click on any edge of
57. creates a SIMM bone file containing the cur rent skin in its current pose All of the skin vertices are transformed into the ground frame and then exported as a bone file When you select this command SIMM displays a file browser that lets you choose the name and type of the out file 2 19 3 segment weight 2 19 Skin Editor Skin Attachments When one or more skin vertices are selected for editing the Skin Editor displays GUI items for modifying the weights and XYZ locations of the attachments for those vertices These combo boxes and number fields are located to the right of the command menu Each row contains the proper ties of one attachment If you select more than one skin ver tex the combo boxes and number fields will be blank if the vertex attachments do not have the same values However you can still enter a value to change a property for an attach ment in all selected vertices This combo box shows the name of the body segment for the attachment You can change the segment by clicking on the name and choosing a different body segment from the pop up menu If more than one skin vertex is selected and those vertices have attachments on different body segments than the other selected vertices then the combo box will show Choose Segment instead of a segment name If you click on the combo box and choose a segment that attach ment for all of the selected skin vertices will be changed to the chosen segment The we
58. current plot If the current plot is new then this field contains the title that will be used when a new plot window is created The title of an existing plot can be changed by first making the plot the current one using the plot selector and then editing the plot title field When the current plot is new the default plot title generator can be used to title the plot If you have not yet edited the title of a new plot the title defaults to a string containing the current Y variable and the current X variable When you change the X and Y variables the title changes to indicate the new variables If you do not want to use the default title you can edit the field Once you enter your own title into the field the default plot title generator is de activated so the title does not change when you choose different X and Y variables If you want to turn the default plot title generator back on edit the title field and enter a title of zero length simply delete the current title The title will then change to a default one consisting of the X and Y variable names and it will then change as you select new X and Y variables as described above Note that the default plot title generator functions only when the current plot is new Once a plot has Chapter 2 Tools 47 2 5 Plot Maker 48 Chapter 2 Tools curve name been created you cannot use the default plot title generator to automatically re title it As described above however y
59. curves 50 script files 301 opening 14 saving 19 Scripting Tool 195 219 Segment Editor 126 137 command menu 128 information header region 126 model window commands 134 setting inertial parameters 129 segments editing 135 selecting 135 selector menu 10 shadows defining 239 displaying 31 specifying color of 240 Skin Editor 181 189 attachments panel 185 command menu 183 group weighting 186 information header region 182 model window commands 187 unselecting skin points 184 skin vertices changing attachment weights 185 186 group weighting 186 skins editing attachments 185 exporting as bones 184 making 184 restoring 183 saving to buffer 183 saving to files 184 unselecting points 184 slider defined 10 snapshots 25 27 auto snapshot mode 26 choosing snapshot file 26 including an alpha channel 26 motion snapshots 27 taking 26 solid_ fill defined 239 spring floors adding to body segments 131 spring points adding to body segments 131 moving 136 selecting 135 standard deviations in motion files 297 standard deviations toggle button 180 static pose see Motion Module step function defined 249 sum toggle button 50 surface normals 305 systemInfo txt file 17 T tendon slack length defined 63 tendon strain defined 44 45 TIFF images see snapshots toggle button defined 10 tracked marker files cropping ends 316 opening 312 TRB TRC files see tracked marker files U units specifying in input files 222
60. data files have the same base name as your TRB TRC file e g subject14 trc subjectl4 anb and subject14 xls then it is not necessary to drag and drop ana log files or select them in the file browser SIMM will auto matically 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 Tracked Marker Options Dialog Once you have selected one or more tracked marker files using the process 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 the OK button to import the motion The following list describes each option in the dialog box use these options for all trials 5 2 Opening Tracked Marker Files name PL model Gait Model OK markers 43 frames 557 1 to 557 data rate 120 0 Hz camera rate 120 0 Hz Cancel i Import Motion Trial Options import frames ji to 557 increment f x axis M quick solve p units time sec v D startat 0 0 crop ends R Analog Dat calculate derivatives pe a IV auto load analog files v show markers al fz V calibrate forces v calculate gait events V ada
61. ending transformation auto reset active visible 2 11 4 2 11 Deform Editor The slider to the right of the deform end radiobutton allows you to smoothly move the inner deform box between its starting and ending positions This toggle button allows you to override the current deform object s standard behavior by making it automati cally restore the current segment s origin to its original undeformed position For more information on auto reset deforms see Section 2 11 5 Combining Multiple Deform Objects This toggle button lets you turn the current deform object on and off When a deform object is deactivated it has no effect on bones joints muscle points or wrap objects within it This button lets you toggle the visibility of the current deform object in the model window When the Deform Edi tor is in position mode both the inner and outer boxes are displayed for all visible deforms in the current segment When the Deform Editor is in deform start or deform end modes only the inner box is displayed for all visible deforms in the current segment Typically once you are done editing a deform object you will make it invisible so that it does not obscure the other features of your model Model Window Commands Deform objects can be selected and edited using keyboard and mouse commands in the model window To use these commands you must first set the tool mode to the Deform Editor by clicking on the Deform Editor icon i
62. fiber velocity is used to scale the mus cle force according to the muscle s force velocity curve See Section 3 4 Muscle Files for details on how fiber velocities are estimated and used to scale isometric muscle force Note fiber velocities affect only force and moment calcula tions and only when plotting against motion variables which contain gencoord velocity information For all other plotting scenarios this toggle button has no effect 2 6 2 6 1 model gt help i 2 6 2 joint gt 2 6 Joint Editor Joint Editor The Joint Editor enables you to graphically manipulate the kinematics of the joints Once you select a joint the three rotations and three translations the DOFs that comprise the joint are displayed If the rotations and translations are constants you can change them by clicking in their fields and typing in new values If they are functions of the gener alized coordinates they can be changed by moving adding and deleting the control points of the splines that define the kinematic functions Figure 2 3 To display the kinematic function for a DOF click on the field for that DOF You can also change whether a given translation or rotation is a func tion or constant thereby interactively increasing or decreas ing the complexity of the joint model Selector Menu The model selector lets you select the current model If you never have more than one model at a time loaded into
63. files is that you can use them to specify gencoord values as inverse kinematics targets in addition to marker locations That is for each frame of input data the IK algorithm will optimize the gencoords of a model to best fit the marker coordinates and the gencoord values specified in the IKS file If the IKS file contains a column of gencoord values and a corresponding column of gencoord weights using the auxil iary data feature as described for motion files in Section 3 5 6 e g knee flexion r and knee flexion r aux the specified gencoord values will be used as targets during inverse kinematics The least squares algorithm will attempt to keep the gencoord close to its specified value using a penalty determined by the gencoord weight If the weight of a gencoord for a given time frame is greater than 1000 0 the IK algorithm will lock the gencoord at the specified value instead of solving for it Because the auxiliary column con tains a weight value for each time frame you can vary the gencoord weight from frame to frame You can also use this auxiliary mechanism to specify frame specific weights for the marker coordinates in the IKS file If you do not specify weights for a column of marker coordinates the marker s Chapter 5 Motion Module 327 5 3 Using the Mocap Model 328 5 3 Chapter 5 Motion Module weight in the model will be used However if you do not specify weights for a column of gencoord values the genco
64. fixed weight 1 fixed in place gait scale R_ SHANK 0 39 0 39 0 39 used for scaling generic model endsegment Chapter 3 Input Files Figure 3 3 Example body segment shown in Figure 3 3 the shadow of the femur would be dis played at a Y value of 0 9 meters from the origin of the world reference frame and would look as if the light casting the shadow were positioned on the Y axis The shadow color parameter can be used to specify the red green and blue components respectively of the shadow s color Each of the components can range in value from 0 to 1 0 and the default color is 0 08 0 08 0 08 To display a body seg ment s shadow in the model window use the shadows tog gle button in the Model Viewer see Section 2 4 5 Toggle Buttons When you turn shadows on only those body seg ments for which you have specified shadow properties will cast a shadow 3 3 Joint Files The axes parameter is used to display the coordinate system of the body segment in the model window The number after the keyword axes is the length of each vector forming the reference frame To use the model with the Motion Module or the C3D Mod ule for importing tracked marker data you must also specify markers on some of the body segments A marker is speci fied with the keyword marker followed by its name Marker names can contain spaces so the name must be followed by a tab and then the XYZ location of the marker in the body segme
65. 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 GaitModel jnt contains several macros that are used to properly define 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 GaitModel jnt with the new file Instead copy the relevant portions of the new file into GaitModel jnt using a text edi tor thus preserving the macros and comments The Static Pose 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 Helen Hayes Lower Body Helen Hayes Full Body and Helen Hayes Full Body with Head It is also strongly recommended that you include the medial knee and Chapter 5 Motion Module 331 5 3 Using the Mocap Model 332 Chapter 5 Motion Module ankle markers in the static
66. function for the force property It creates a simple two point function that can then be edited in the Function Editor after choosing right clicking again and choosing edit function Force Parameters Form On the left side of the Force Parameters panel is a form con taining the five fiber and tendon parameters used by the SIMM mucle model A detailed description of how these parameters are used to compute isometric muscle tendon force is beyond the scope of this manual For more details consult the documents listed at the end of Section 1 6 SIMM Tutorials To change the value of one of these param eters click on its field and type in a new value If the field is grayed out it means that this parameter is inherited from the default muscle and cannot be edited If you want to modify the parameter for this muscle only then you must first right click in the field and choose make unique from the pop up menu This will give the muscle its own copy of the param eter from the default muscle which you can now edit by left clicking on the field To remove the muscle s own copy of the parameter and instead have it inherit it from the default muscle choose inherit from default from the pop up menu If you want to edit the default muscle s copy of the parameter you must first select the default muscle using the muscle button Below is a description of the five parame ters Its Fmo Imo pen act 2 7 Muscle Editor tendon s
67. g percent of gait cycle were a gencoord Just press the key s that you specified in the motion file and move the cursor horizon tally to move the model forwards or backwards through the motion sequence The keys associated with each motion are also shown in the Motion Editor window You can also animate a motion frame by frame using the left and right arrow keys Press the left arrow key to move back a frame in the current hotkey motion and the right arrow key to advance a frame Pressing the up and down arrow keys cycles through the motions linked to the model setting each one in turn to be the current hotkey motion When you right click on a bone or world object in the model window a pop up menu is shown with various dis play options You can change the object s drawmode and material as well as turn on and off the display of the seg ment axes and object s normal vectors You can also set the camera to look at that segment as if you had used the look at command described in Section 2 4 2 You can also right click on many other model components to show a pop up menu with display and editing commands These commands are described in the editing tools specific to those model components Chapter 2 Tools 33 2 4 Model Viewer 34 F fF amp 2 moving the joints Chapter 2 Tools The following commands work on the model only when the Model Viewer icon in the HUD is selected When it is se
68. gencoords in order to restrain them from going outside their ranges of motion However restraint functions are also used by SIMM s inverse kine matics IK solver when you have one or more closed loops of body segments In this case the restraint functions define error values that restrain the gencoords from going outside their ranges of motion while the IK solver is satisfying loop constraints see Section 2 8 5 Inverse Kinematics for more details on the IK solver If there are no loops of body segments in your model the IK solver will be inactive and the gencoords restraint func tions will not be used in SIMM If your model does have loops you may want to define restraint functions to better control the IK solver If you do define restraint functions for use with IK you should define them so that they also have appropriate dynamic behavior and thus can be used with the Dynamics Pipeline as well KINEMATIC FUNCTION tx of the femoral tibial joint beginnaturalcubicspline f1 defines x translation from femur to tibia knee angle degrees tx meters 120 100 80 60 40 20 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 003 001 004 004 002 001 003 0 0 endnaturalcubicspline 005 252 Chapter 3 Input Files Figure 3 6 Example kinematic function 50 25 40 10 3 3 Joint Files 25 Nm 70 10 80 25
69. good candidate for kine matic and restraint functions For X values beyond the range of the XY control points linear extrapolation is used using the slope of the function at the nearest endpoint The defini tion of a natural cubic spline must have at least two control points and looks like this beginnaturalcubicspline 20 0 0 5 0 0 4 2 12 05 IET 35 55 5 8 endnaturalcubicspline Note In earlier versions of SIMM natural cubic was the only type of function supported Thus if an old style func tion definition is used beginfunction endfunction a natural cubic spline is assumed Also although a natural cubic spline is a third order function and thus requires at least four control points earlier versions of SIMM allowed definitions with as few as two points If three points were specified then quadratic interpolation was used and if two points were specified then linear interpolation was used The current version of SIMM maintains backwards compa bility by allowing the same function specifications A GCV spline is a third order function that uses the general ized cross validation and mean squared prediction error cri teria developed by Craven and Wahba and implemented by Woltring It has a continuous second order derivative and thus is a good candidate for kinematic and restraint func 3 3 Joint Files tions It also has support for smoothing a feature used by the Dynamics Pipeline to smooth data input to i
70. gt mean 2 21 Scripting Tool sets the name in the curve name field to the specified name This name will be given to the next curve created by the Plot Maker Enter a name of null to make the field empty so that SIMM will generate a default name when a curve is created sets the step size field to the specified number sets the activation field to the specified number which must be greater than or equal to zero Setting the activation also turns on the act override checkbox sets the x min field to the specified number sets the x max field to the specified number sets the y min field to the specified number sets the y max field to the specified number sets the scale field to the specified number sets the offset field to the specified number turns on off the sum checkbox turns on off the rectify checkbox turns on off the active checkbox turns on off the passive checkbox turns on off the act override checkbox turns on off the isometric checkbox calculates the mean and standard deviation of all curves in the current plot This information is then added to the plot as a data curve Chapter 2 Tools 205 2 21 Scripting Tool 2 21 4 set model lt model gt gencoords lt name gt lt on off gt moments lt name gt lt on off gt powers lt name gt lt on off gt joint_forces lt name gt lt on off gt external_forces lt name gt lt on off gt muscle_activations lt name gt lt
71. gt lt on off gt output_file lt filename gt name lt name gt examiner lt name gt study lt name gt height lt number gt weight lt number gt age lt age in _years gt id lt value gt test_date lt day month vear gt gait lt on off gt standard_deviations lt on off gt output_strides lt on off gt 2 21 Scripting Tool turns on off output to the motion report of the force of the specified muscle Name can also be the name of a muscle group or the word all turns on off output to the motion report of the velocity of the specified muscle Name can also be the name of a muscle group or the word all turns on off the specified motion for inclusion in the motion report sets the output file field to the specified name sets the name field to the specified name sets the examiner field to the specified name sets the study field to the specified name sets the height field to the specified number For most mod els the height should be entered in meters sets the weight field to the specified number For most mod els the weight should be entered in kilograms sets the age field to the specified number sets the id field to the specified value which can be any string of characters sets the test date field to the specified date The date should be entered as three numbers with forward slashes between them Day month year is preferred but month day year is acceptable turns on o
72. i e gencoord values so you can output them without including the muscles in the dynamic simulation of the motion trial This command lets you select which muscle forces you want to include in the report The output force for each mus cle is the average of its force for each motion trial The force for a particular motion trial depends on whether the muscle is included in the dynamic simulation of that trial If it is included then the force is the dynamic force calculated by the simulation If it is not included then its force is the iso metric force that SIMM calculates based on its length and activation See the description of the muscle activations command for information about how the activation of a muscle is calculated This command lets you select which muscle velocities you want to include in the report Muscle velocities are calcu lated from the kinematic data i e gencoord values so you can output them without including the muscles in the dynamic simulation of the motion trial This command generates the motion report using the cur rently selected motions and output variables See Section 2 18 1 Generating a Motion Report for information on how the report is generated 2 18 4 output file name examiner study height weight age id test date 2 18 Motion Reporter Forms Output File Form The name of the report file to generate The generated file will be a binary Excel file with the data
73. illumination which hits all sides of an object Diffuse illumination is brightest where the light source strikes the object perpendic ular to the surface Specular lighting accounts for high lights or glare when the light reflects off the surface directly towards the viewer Emission is the property of giving off light which happens equally at all locations on the object s 3 3 Joint Files MATERIAL default bone beginmaterial def bone ambient 0 7 diffuse 0 6 specular 0 7 emission 0 0 shininess 10 endmaterial ooooo o vil 0 7 45 0 4 55 0 4 0 0 0 3 3 8 def bone is the name of this material red green and blue components red green and blue components red green and blue components red green and blue components not very shiny 10 out of 128 Figure 3 9 Example material surface Finally the shininess value which ranges from 0 0 to 128 0 specifies the shininess of the object s surface and controls the size and brightness of the specular high light Note When an object body segment or world object is displayed in wireframe or solid_ fill modes the color used to draw it is the ambient color specified in the material assigned to that object SIMM has eight materials stored internally that it uses to draw various elements of a model You can override these defaults by re defining the materials in your joint file These eight materials with the
74. is then displayed in the Function Editor window allowing you to move add and delete control points You can also change the type of a function the supported types are natural cubic GCV Chapter 2 Tools 189 2 20 Function Editor f Function Editor Model Gait Model l model gt Active Force Length Curve default muscle A j g 0 0 0 2 0 4 0 6 0 8 1 0 ly 14 1 6 1 8 PAO normalized length v v amp s E E S z save restore cutoff frequency control points Figure 2 28 Function Editor window spline linear and step If a particular function in your model is being used by several model components e g the same restraint function might be used by multiple genco ords when you modify it in the Function Editor it will modify the behavior of all model components that use it If you want to modify a function only for the model compo nent you selected it from use the clone command described below in the Right Click Menu section The Func 190 Chapter 2 Tools 2 20 1 save restore cutoff frequency control points 2 20 Function Editor tion Editor also allows you to switch the selected model component to use a different function or to create and use a new function These commands are also described in the Right Click Menu section Command Menu This command saves a copy of the function being edited It can be used in combination with the restore button to he
75. is used to initialize the appropriate checkbox in the motion import dialog box but you can change it as you load individual motion trials For C3D import only This preference specifies whether the marker names for the motion trial should be read from the POINT LABELS field or the POINT DESCRIPTIONS field in the C3D file This preference is used to initialize the appro priate field in the motion import dialog box but you can change it as you load individual motion trials This preference specifies whether or not to save a motion file when importing a TRB TRC C3D file This file contains exactly the same data that is in the motion that SIMM loads onto the model when importing This preference is used to initialize the appropriate checkbox in the motion import dia MOCAP MOTION FILE MOCAP SAVE _HTR_FILE MOCAP_HTR_ FILE MOCAP LIVE MODEL UPDATE MOCAP LOAD PERSONAL DAT B 1 Preferences log box but you can change it as you load individual motion trials This preference specifies the name of the motion file to create when importing a TRB TRC C3D file For most applications you do not want to explicitly set this preference because every time you import a motion trial the saved motion file will have the same name unless you browse for a different name Instead do not define this preference and let SIMM determine an appropriate motion file name for each motion trial that you import This preference is useful primarily when
76. joint or muscle file not to overwrite an existing file Instead save the data to a new file and then use a text editor to copy the modified model elements into the original joint or muscle file Use model archives A model archive is a compressed file containing all of the files associated with a model including joint file muscle file bones files and any motion files currently linked to the model It contains everything needed to load the model back into SIMM at a later time Because everything is in one file it is a good way to share models with other users or to backup your models before modifying bone files or other components that are typically shared among models Live plot curves are very helpful when creating or modifying models see Section 2 9 2 Live Plot Curves for details on how to create them For example if you make a plot curve of a muscle moment arm as a function of a generalized coordinate and make the curve live it will be automatically updated as you move muscle attachment points move wrap objects modify joint parameters or make any other change that affects the muscle s moment arm Live plot curves are particularly helpful when positioning wrap objects because they enable you to see the wrap object s affect over the entire range of motion not just in the model s current pose When using live curves it is often helpful to create the same muscle curve twice and make one of them live so you can ea
77. lets you choose the boolean operation to per form on bone J and bone 2 The available operations are add intersect and subtract The result of the operation will be one or more polygonal surfaces depending on the input If the separate bones checkbox is turned off then all of these surfaces will be combined into a single output bone If the checkbox is off each surface will be output to a separate Chapter 2 Tools 141 2 15 Bone Editor bone 2 gt 2 15 3 change segment gt new bone name load bone 142 Chapter 2 Tools 2 15 4 bone The boolean operation is performed when you press the do boolean button This button lets you choose bone 2 which is used only in boolean operations as shown in the boolean equation below this button Boolean and Read Write Options Performing a boolean operation is similar to reading a bone file into SIMM in the sense that they both create a new bone Thus the options to specify the name of the new bone and to which body segment it is added are located in the boolean and read write options region This command changes the body segment to which the new bone will be added when a boolean operation is performed or when a bone file is read It does not move the currently selected bone 1 to that segment This field specifies the name of the bone that will be cre ated either from the result of a boolean operation or from reading in a bone file This command loads a
78. locations of the joint centers for all of the joints in the OrthoTrak model The pel vis 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 values are percentages of the dis tance between the left and right ASIS 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 Right Hip Posterior Displacement 22 00 Right Hip Lateral Displacement 32 00 Right Hip Inferior Displacement 34 00 Left Hip Posterior Displacement 22 00 Left Hip Lateral Displacement 32 00 Left Hip Inferior Displacement 34 00 To change these values edit the file personal dat as described in Appendix D of the OrthoTrak manual The knee and ankle centers are found using the medial and lateral markers It is strongly recommended that you use medial markers for a more accurate calculation of joint cen Chapter 5 Motion Module 335 5 3 Using the Mocap Model 336 5 3 4 Chapter 5 Motion Module ters 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 default method for determining shoulder elbow and wrist joint
79. lt name gt lt time gt show markers lt on off gt show markers lt on off gt lt name gt show marker _trail_ lines lt on off gt show marker_trail_lines lt on off gt lt name gt show marker_trail_points lt on off gt show marker_trail_points lt on off gt lt name gt show force_plates lt on show external_forces lt on show body_forces lt on show joint_forces lt on show joint_torques lt on off gt off gt off gt off gt off gt 2 21 Scripting Tool deletes all motions in the current model SIMM does not prompt you to confirm the action deletes all events in the current motion SIMM does not prompt you to confirm the action adds an event with the specified name and time to the cur rent motion turns on off the display of markers in the current motion turns on off the display of the specified marker in the cur rent motion Name can also be all turns on off the display of marker trail lines in the current motion turns on off the display of marker trail lines for the specified marker in the current motion Name can also be all turns on off the display of marker trail lines in the current motion turns on off the display of marker trail lines for the specified marker in the current motion Name can also be all turns on off the display of force plates in the current motion turns on off the display of all external forces in the current motion
80. mouse button and typing in a new value You can change it to a function by right clicking on the field and selecting function and then a generalized coordinate from the pop up menu If the coordinate is a function you can right click on the field and choose from the pop up menu to change it to a constant change the generalized coordinate used in the function or send the function to the Function Editor for editing 2 7 Muscle Editor If the Via box is checked for the attachment the point is a via point meaning that it is active only when a generalized coordinate is in a certain range For via points you can change the generalized coordinate that controls them by clicking on the name and choosing a different one from the pop up menu You can also change the coordinate range for which the point is active by clicking in the Min and Max fields and typing in a new value Attachment Points Sel Segment X we Z Via Gencoord Min Max 1 femurr V 0 0127 0 3929 EEI 2 femurr V 0 0239 0 4022 0 0258 i Knee p y 20 0000 44 1200 Sm ubar Wi f43 knee_flex_r f99 knee_flex_r 0 0295 4 footr f 0 0034 0 0320 0 0063 Figure 2 5 Muscle Editor Attachments Panel Muscle Wrapping Form If the muscle has one or more wrap objects associated with it SIMM will display the wrapping parameters in a region labeled wrapping At the top of this region is a button labeled object Clicking on it will display a pop up menu of
81. muscle semiten 1 0 350749 on muscle bi fem 1h 1 0 000000 on muscle bi fem sh 1 0 000000 off muscle rectus fem 1 0 021301 on endpose Figure 3 19 Example model pose This pose represents the position of the body during the stance phase of the right foot during gait due to limited space only some of the gencoords and muscles are shown Each gencoord line specifies the name value velocity clamped state and locked state Each muscle line specifies the name activation and visibility state 276 Chapter 3 Input Files 3 4 3 4 1 3 4 Muscle Files Muscle Files Muscle files contain descriptions of muscle tendon actua tors Each musculoskeletal model you load into SIMM must have all of its muscle tendon actuators defined in one mus cle file If you do not have any muscle tendon actuators in your model then you do not need to create a muscle file When you load a model SIMM will first check the joint file to see if you specified the name of the muscle file to load with it using the muscle file keyword If no name is specified SIMM will read the muscle file that you selected with the file browser if any Within muscle files you can define two types of objects muscles and muscle surfaces Muscles are biomechanical elements that have lines of action and that can generate forces and moments They are described in Section 3 4 1 Muscle surfaces are display primitives designed to make musculoskeletal models look more realistic
82. on This parameter specifies the background color of the model window The RGB components are in the range 0 0 to 1 0 The default color is 0 2 0 2 0 2 background_color 0 2 0 2 0 2 rotation_axes_color segment axe s_ color vertex _label_ color crosshairs color length_units force units 3 3 Joint Files This parameter specifies the color of the vectors used to rep resent the joint rotation axes in the model window The RGB components are in the range 0 0 to 1 0 The default color is 1 0 1 0 0 0 background_color 1 0 1 0 0 0 This parameter specifies the color of the reference frames of the body segments in the model window The RGB compo nents are in the range 0 0 to 1 0 The default color is 1 0 1 0 1 0 background_color 1 0 1 0 1 0 This parameter specifies the color of the polygon outline and the vertex numbers used by the Muscle Editor in the model window The RGB components are in the range 0 0 to 1 0 The default color is 1 0 0 0 0 0 background_color 1 0 0 0 0 0 This parameter specifies the color of the crosshairs shown in the model window when the crosshairs checkbox is selected in the Model Viewer The RGB components are in the range 0 0 to 1 0 The default color is 1 0 1 0 1 0 background_color 1 0 1 0 1 0 These parameters specify the length and force units of the model which are used for two purposes First the Motion Module uses them to convert 3D marker coordinates and forceplate data in TR
83. parameter may be used to disable the display of the wrap object s shape in the model window If this parame ter s value is no or false then the wrap object will not be visible in the model window but its associated muscles will still wrap over it This parameter may be used to display the XYZ coordinates of muscle tangent points for each muscle that wraps over the wrap object If this parameter s value is yes or true then the tangent point coordinates will be displayed in the quadrant wrapmethod 3 3 10 3 3 Joint Files model window The display of these points can be helpful when creating the wrap object or adjusting muscle attach ment points to improve the wrapping behavior This parameter may be used to limit wrapping to one half of the wrap object The valid quadrants are x x y y Z or z for spherical and ellipsoidal wrap objects and x x y or y for cylindrical wrap objects This parameter may be used to specify the algorithm to be used to compute muscle wrapping paths around ellipsoidal wrap objects The valid wrap methods are hybrid mid point and axial For more information see Section 2 9 5 Ellipsoid Wrapping Methods Deform Objects Deform objects allow you to twist bend and warp portions of a body segment that would normally be considered rigid When a segment is deformed all bone vertices distal joint centers muscle attachment points and muscle wrapping objects in the deformed region
84. patella pelvis femur femur patella pelvis femur femur patella pelvis femur femur patella Surface desc of Rectus Femoris line 1 defines the anterior contour of the muscle surface proximal to distal X sai line 2 defines the medial contour of the muscle surface proximal to distal line 3 defines the posterior contour of the muscle surface proximal to distal oy 7 i o h line 4 defines the lateral contour of the muscle surface proximal to distal ay line 5 same as line 1 needed to close the muscle surface Figure 3 23 Example muscle surface Chapter 3 Input Files 285 3 5 Motion Files 286 Chapter 3 Input Files 3 4 3 muscle matl0 is used for activations of 0 5 and muscle_mat20 is used for activations of 1 0 You cannot interactively edit the points that define a muscle surface so as you create them you should make each line an ordinary muscle so you can move the points using the Mus cle Editor Then write the muscles to a file and copy the attachment points to a muscle surface definition Ligaments Ligaments are modeled in SIMM as muscles that have fibers of zero length The muscle tendon unit is thus only a tendon with no active force properties To define a liga ment create a muscle definition and specify an optimal fiber
85. press this key to make the model walk x column 1 first column is used as X axis in plots units sec the units of the X column are seconds wrap when animating continuously loop motion enforce loops no enforce loops when animating enforce constraints no enforce constraints when animating show markers yes show markers when animating show marker trails yes show marker trails when animating show forces yes show forces when animating show force trails yes show force trails when animating show force plates yes show force plates when animating show foot prints yes show foot prints when animating cursor 1 00 1 00 0 00 color of cursor in motion plots event 0 111111 rhs a heel strike event for the right foot event 0 388333 lto a toe off event for the left foot event 0 697917 lhs a heel strike event for the left foot event 0 821667 rto a toe off event for the right foot event color 1 000000 0 000000 1 000000 color of events in motion plots calc derivatives no calculate derivatives of all columns force plates are specified by size location and orientation forceplate 0 46 0 51 0 041 0 642230 0 251 0 039 180 0 0 0 90 0 forceplate 0 46 0 51 0 041 0 125860 0 252 0 040 180 0 0 0 90 0 foot prints are specified by size location and orientation rightFootPrint 0 208933 1 215807 0 120825 0 005 0 0 0 0 77 857691 leftFootPrint
86. recorded motion no additional moments will be needed to produce the prescribed motion and the gencoord moments will be zero In a simulation that has no prescribed motion e g forward dynamics the gen coord moments will be zero the moments required to generate the input motion as cal culated by a PD controller Instead of prescribing the inverse dynamics motion using constraints as the gencoord moments option does the PD controller tracks the input motion by using the errors between the current and desired kinematics to apply corrective moments to the gencoords This method depends on the specification of appropriate PD stiffness values for each gencoord See Section 5 3 of the Dynamics Pipeline manual for a complete description of the PD controller method the powers of the generalized coordinates Power is defined as the moment multiplied by the velocity the forces applied by the spring floor objects Each force is expressed in the reference frame of the corresponding spring point s body segment There is no right click option for this output since the number of spring forces output is specified in the simulation code the moment arms of the muscles in the simulation The right click dialog allows you to select which muscles you Chapter 2 Tools 161 2 16 Dynamics Tool muscle moments total muscle moments optimized muscle activations 162 Chapter 2 Tools want to output The simulation will output the moment
87. region Likewise if the tool does not operate on specific plots e g Model Viewer the plot selector is not displayed Also in this region of every tool is a help button at the far right Click the left mouse button on it to open a window with some helpful text In general the interface for each of the tools is confined to the tool window That is the tool window must be the active window for you to perform any of that tool s commands However three of the tools Model Viewer Muscle Editor and Plot Viewer can recognize key and mouse button presses when they occur in the model or plot windows For example to select muscle points in the Muscle Editor you press the Space Bar and click the left mouse button in the model window This feature allows you to operate on the models and plots without having to open the tool window In some cases the same command can be performed in the tool window as well in other cases the command can only be performed in the model or plot window See the relevant tool section in this chapter for more details Opening Files To load files into SIMM you can use either the File menu in the menu bar or drag and drop them from a Windows File Explorer window to the SIMM window To use the File menu select File gt Open and use the Windows file browser to locate the files By default the file browser dis plays all files with SIMM file name extensions You can use the Files of type popup menu at the bo
88. rotation DEFORM START translation _DEFORM_ START xyz body rotation _DEFORM END 266 translation_DEFORM_END Chapter 3 Input Files active This field specifies the deform object s rotation relative to its associated body segment This keyword must be fol lowed by three numbers that specify body fixed rotations that are applied in X then Y then Z order The default val ues are 0 0 0 0 0 0 This field specifies the deform object s translation relative to its associated body segment This keyword must be fol lowed by three numbers that specify the XYZ translation from the segment s origin The default values are 0 0 0 0 0 0 This field specifies a rotation of the deform object s inner box relative to the deform object s reference frame This rotation specifies the deform object s starting deformation The default values are 0 0 0 0 0 0 This field specifies a translation of the deform object s inner box relative to the deform object s reference frame This translation specifies the deform object s starting deforma tion The default values are 0 0 0 0 0 0 This field specifies a rotation of the deform object s inner box relative to the deform object s reference frame This rotation specifies the deform object s ending deformation The default values are 0 0 0 0 0 0 This field specifies a translation of the deform object s inner box relative to the deform object s reference frame This translation specifies
89. sacral marker and the MARKER_TOE_OFF_OFFSET MARKER EVENT TOLERANCE EMG SMOOTHING WINDOW B 1 Preferences heel marker in the forward direction For some subjects and marker placements it may be desirable to use a fixed offset from the local maximum rather than the maximum itself The offset is specified in seconds and affects the cal culation of all marker based heel strike events for all motion trials This preference specifies the offset from the local minimum of the marker trajectory to the time of the toe off event A toe off event is defined as a transition from negative to posi tive in the distance between the sacral marker and the toe marker in the forward direction For some subjects and marker placements it may be desirable to use a fixed offset from the local minimum rather than the minimum itself The offset is specified in seconds and affects the calculation of all marker based heel strike events for all motion trials This preference specifies the tolerance when determining if a marker based event occurs at the same time as a force based event To calculate heel strike and toe off events for a motion trial SIMM uses two methods ground reaction force vectors and marker trajectories The force based method is consid ered more accurate but the marker based method can differ entiate between left and right foot events When a marker based event is within the specified tolerance of a force based event the events a
90. taken into account Biologists interested in animal movement can create models to quantify limb function Investigating movement strate gies in other species can provide insights needed to design machines that move Computer scientists who develop models of the human body for virtual environments can use SIMM to create the models and compare them with biomechanical data for veri fication Animators can use SIMM to develop realistic representa tions of human and animal movements World objects can be added to provide a context for the animation Design Goals We established four goals in designing and implementing the software Specifically it should i be general enough so that a wide variety of musculoskeletal structures can be modeled ii provide realistic models of muscle and tendon and allow accurate specification of joint kinematics iii provide an interactive graphics based environment so the model can be visualized altered analyzed and tested efficiently and iv be extensible so that new features such as a more complex muscle tendon model can easily be added to the software Chapter 1 Introduction 3 1 4 The SIMM Environment 4 1 4 The SIMM Environment SIMM allows you to load one or more musculoskeletal models by reading sets of input files Once loaded a model can be acted upon by a number of editing and analysis tools Figure 1 1 Each tool is contained within its own window and has a di
91. tas iaveoao Ae 110 2 12 3 Marker Parameters an ss cakstits lane neti Ate des 111 2 12 4 Global Parameters 2 3801 assed nesses ees 113 2 12 5 Model Window Commands ccccceeeseeees 113 Constraint Editor mesonen halos ihe 2a thas E Gate vata ts 116 2 13 1 Selector Menu 25a y Nocnsas ee Rost Gea a leet tetas 116 2 13 2 Objects Command Menu ecceeceeeceeeteeeees 117 2 13 3 Constraint Object Attributes 200 0 120 2 13 4 Model Window Commands csccecsseeees 121 2 13 5 Transforming Constraint Objects 0 0 eee 123 2 13 6 Points Command Menu ccccceeseeeeseeeeees 124 2 13 7 Constraint Point Attributes ce eeeeeeeees 125 Segment Editor sniiotucngindsyoatcunvciain ema 126 2 14 1 Selector Men acviaskcsen ean aie 126 2 14 2 Command Menu 35 5 seacdis adinnceyieeewiceiatss 128 vi 2 15 2 16 2 17 2 18 2 19 2 14 3 Segment Parameters s es 129 2 14 4 Model Window Commands c00 134 ONE ATIOP raisa n n a imi es 137 2 15 1 Selector Menu ssesossseessessssseessessrsseessesseese 138 2 15 2 Command Menu ssisyhiesatissveins kines 138 2 15 3 Boolean and Read Write Options 142 2 15 4 Norm Options sssessesesssssssessessrsssessessrssresseese 142 2 15 5 Model Window Commands 0008 145 Dynamics Tool A ctisic ian dtasicd eis adtoestdeatianaicae 149 2 16 1 Selector Menu 3 osccs saaicodscdetaveeieteidd 153 2 16 2 Input an
92. the slider The value can only be changed if the gencoord is restored using the restore gencoord command in the Gen coord Editor or the model s gencoord values are restored using the restore gc values command in the Model Viewer 2 4 5 trackball muscle points shadows crosshairs 2 4 6 2 4 Model Viewer Toggle Buttons This button toggles the trackball method of interactively translating and rotating the 3D model window view See Section 2 4 6 Model Window Viewing Commands for a description of trackball and non trackball view navigation This button toggles the display of larger muscle attachment points on the current model When this option is off the spheres representing the muscle points are displayed with the same radius and in the same color as the cylinders repre senting the muscle lines of action When this option is on the muscle points are displayed in blue and with larger spheres making them easier to see and select for editing This button toggles the display of the body segment shad ows Initially shadows of the bones are not displayed in the model window When you turn shadows on they are drawn only for the body segments for which you defined a shadow direction and distance in the segment definition See Section 3 3 1 Body Segments for more details on specifying the shadow parameters for a body segment This button toggles the display of cross hairs in the model window Cross hairs are useful f
93. the JNT file is set appropriately the default is mocap jnt and the static pose is set to the proper static tracks file Then click Create Launch SIMM Open the Mocap Model by dragging the static trial marker file from a Windows file explorer and dropping it onto the SIMM background window You can also open it using File Open Mocap Model in the menu bar and browsing for the marker file Set the options as desired in the dialog box and click OK Open the Model Viewer window Chapter 5 Motion Module 325 5 2 Opening Tracked Marker Files Inthe Model Viewer window choose start gt realtime con nection to lt hostname gt SIMM will display a dialog box allowing you to set some options for the connection The motion buffer size options control 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 con tinue to increase as new data is received Se SIMM will now wait to receive data from the Cortex com puter Once the connection is established SIMM will dis play 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 ca
94. the body segments and measure and record the offsets of all of the markers the Motion Module has the ability to automatically scale a pre made model the mocap model to fit the subject 5 3 1 5 3 Using the Mocap Model To use the mocap model drag and drop the static pose marker file onto the SIMM background window or use File Open Mocap Model in the menu bar and browse for the marker file This static pose described in more detail in Section 5 3 2 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 recreates 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 Cleve land 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 seg ment 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
95. the deform object s ending deforma tion The default values are 0 0 0 0 0 0 This field specifies whether the deform object is enabled or not When disabled deform objects have no affect on their associated body segment This keyword must be followed by the word yes no true or false The default value is yes visible autoreset translationonly 3 3 11 range 3 3 Joint Files This field specifies whether the deform object is visible in the 3D model window or not This keyword must be fol lowed by the word yes no true or false The default value is yes This field specifies whether the deform object is an auto reset deform or not If this keyword is followed by the word yes or true then the deform is an auto reset deform and will behave as such See Section 2 10 5 Combining Multi ple Deform Objects for more information about auto reset deforms The default value is no This field specifies whether an auto reset deform should limit its deformation to translation only instead of both translation and rotation If this keyword is followed by the word yes or true and the deform is an auto reset deform then the auto reset deform will translate the segment s ori gin back to its original undeformed position but it will not apply a rotation to realign the segment s reference frame with its original axes The default value is no Deformities Deformity sliders are specified in the model s joint file after all of
96. the floor All other polygons in the file will be ignored Once a spring contact is defined you can define one or more spring points on other body segments Note that Chapter 2 Tools 131 2 14 Segment Editor 132 Chapter 2 Tools although these points are defined on segments other than the currently selected segment they are only accessible in the Segment Editor when the current segment is the one to which their corresponding contact polyhedron is attached The spring point button lets you select from the existing points or create a new one The segment button lets you change the segment to which a point is attached The X Y and Z fields specify the coordinates of the point in its asso ciated segment s reference frame The parameters friction a b c d e and f control the calculation of the spring force Consult the Dynamics Pipeline manual for details on how these parameters are used NURBS Object NURBS objects are used only by dynamic simulations and they are used in conjunction with NURBS spring objects to model contact between a NURBS surface and a mesh of springs A NURBS object consists of an IGES file that con tains the NURBS patches representing the surface of the object and an information file with suffix nurbs that con tains scale position and surface normal information about the patches You can make a NURBS object using the make NURBS obj button in the Bone Editor To learn more about how NURBS based c
97. the motion objects built into SIMM are force ball contact joint force joint torque and spring force You can override the properties of these six motion objects or add additional motion objects in the joint file See Section 3 3 13 Motion Objects for more informa tion about defining motion objects The bone file used to display the built in force motion object is named arrow asc This shape is an arrow of unit length with the tail of the arrow at the origin and the head of the arrow pointing up the Y axis This produces force vec tors that are displayed with their tail positioned at the point of application and their arrow head pointing away from the point of application If you prefer to have force vectors dis beginmotionobject force scale 1 0 0 002 1 0 endmotionobject 3 5 Motion Files played with the arrow head pointing toward the point of application you can use norm to translate the shape defined in arrow asc from the positive Y axis to the negative Y axis with the following command norm arrow asc arrow asc ty max Lastly the built in force motion object includes XYZ scal ing factors designed to produce force vectors of a reason able size when forces are specified in newtons and your model length units are meters You can override the default scaling factors by adding a motion object definition to your joint file like this Figure 3 25 Overriding built in motion object parameters The scale factors shown h
98. the segment definitions There is no way to create or modify deformity sliders within SIMM so they must be added to the model s joint file manually Each deformity defined in the model s joint file appears as a slider at the bottom of the SIMM Deform Editor window Deformity Fields This field specifies the minimum and maximum allowable values of the deformity slider The default values for range are 0 0 to 100 0 Chapter 3 Input Files 267 3 3 Joint Files begindeformity anteversion range 20 0 60 0 value 0 0 deform anteversion twist deform neck angle deform auto reset enddeformity Figure 3 16 Example deformity value This field specifies the default value of the deformity slider The default value is 0 0 deform This field specifies the name of a deform object that has been specified earlier in the same joint file A deformity slider may contain one or more deform fields Each deform object associated with the deformity will be controlled by the deformity s slider in the Deform Editor window 3 3 12 Motion Objects Motion objects are shapes that are added to the display of the model while a motion is being played back They are useful for displaying ground reaction forces joint contact forces contact points and other values calculated by exter nal software packages The basic shape of the motion object is specified in a SIMM bone file For each frame of data in a motion file you can specify the position orientatio
99. them when animating the motion in order to determine how well the model is tracking the markers The value is used to initialize the appropriate checkbox in the motion import dia log box but you can change it as you load individual motion trials This preference specifies whether or not to crop incomplete frames from the beginning and end of a motion trial when importing a TRB TRC C3D file When this preference is yes frames at the ends of the motion that are missing one or more markers are removed from the output The value is used to initialize the appropriate checkbox in the motion import dia log box but you can change it as you load individual motion trials This preference specifies whether or not to calculate heel strike and toe off events when importing a TRB TRC C3D file The value is used to initialize the appropriate checkbox in the motion import dialog box but you can change it as you load individual motion trials For information about how the events are calculated see Section 5 2 Opening Tracked Marker Files MOCAP QUICK SOLVE MOCAP CALC DERIVATIVES MOCAP X AXIS MOCAP_ START AT ZERO B 1 Preferences This preference specifies whether or not to use the Gauss Newton solver when importing a TRB TRC C3D file The Gauss Newton method is usually faster than the default method Levenberg Marquardt but can be less robust when some of the markers are missing The value is used to initial ize the appropriate checkbo
100. these data but 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 import Variables txt This configuration file located in SIMM Resources mocap misc contains mappings between Chapter 5 Motion Module 323 5 2 Opening Tracked Marker Files 5 2 4 324 Chapter 5 Motion Module 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 Real time Import 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 musculoskele tal 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 com puter If the same mocap model is loaded into SIMM these generalized coordinates will drive the animation 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 First time setup only Find the folder SIMM Cortex on your SIMM computer and look for GaitM
101. those of the markers placed on the subject the Motion Module can adjust the model s gencoord values Chapter 5 Motion Module 311 5 2 Opening Tracked Marker Files 5 2 312 Chapter 5 Motion Module 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 corresponding marker in the marker cloud It then uses this best fit as the starting posi tion 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 The Motion Module has two primary components The first component reads files containing tracked marker data in the TRC TRB or C3D format and creates SIMM motions from them as described above For more information on how this process works and the various options for import ing marker data see Section 5 2 Opening Tracked Marker Files 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 algorithms that are used to scale the model are the same as those used in OrthoTrak a full body gait analysis package available from Motion Analysis For more information on the mocap model and how it is cre
102. value is calculated using the length of the diagonal of the object s bounding box Colors You can change any of the colors in SIMM by editing the color file called simmcolors txt SIMM reads this file when the program is launched and you can also reload it while SIMM is running by choosing Options Reload Color File from the SIMM menu bar When SIMM reads the file it first looks for it in your user application data folder e g C Users Peter AppData Local MusculoGraphics SIMM 7 0 simmcol ors txt If it is not found there it looks in the resources folder where SIMM was installed e g C Program Files x86 Mus culoGraphics SIMM70 Resources simmcolors txt To change a color in SIMM open the file in a text editor and find the name of the item whose color you want to change After the name are listed the red green and blue components respec tively of the color The numbers can range from 0 0 to 1 0 Change the color components as desired and then reload the color file Note model specific colors and materials are specified in the joint file for that model not in simmcolors txt See Section 3 3 Joint Files and Section 3 3 7 Materials for more infor mation on changing model specific colors and materials Password txt The first time you run SIMM on your computer you will be prompted to enter your SIMM password At that point SIMM B 4 B 5 B 4 SystemInfo txt will automatically store your password in a file na
103. whose forces will be written to the output motion if output of mus cle forces is turned on Name can also be the name of a mus cle group turns on off the output of muscle forces If output is on only the selected muscle forces will be written to the output motion adds or removes the specified muscle to the list whose velocities will be written to the output motion if output of muscle velocities is turned on Name can also be the name of a muscle group turns on off the output of muscle forces If output is on only the selected muscle forces will be written to the output motion adds or removes the specified muscle to the list whose fiber lengths will be written to the output motion if output of muscle fiber lengths is turned on Name can also be the name of a muscle group turns on off the output of muscle fiber lengths If output is on only the selected muscle fiber lengths will be written to the output motion adds or removes the specified muscle to the list whose fiber velocities will be written to the output motion if output of muscle fiber velocities is turned on Name can also be the name of a muscle group Chapter 2 Tools 211 2 21 Scripting Tool fiber_velocities lt on off gt contact_forces lt on off gt mass_center_positions lt name gt lt on off gt mass_center_positions lt on off gt mass_center_velocities lt name gt lt onl off gt mass_center_velocities lt on off gt system_energ
104. window gives you access to the three rotation axes in the current joint To display a rotation axis in the model window click on the checkbox to the left of the axis defintion To change the axis orientation click on its X Y or Z field and type ina new value Note When modifying a rotation axis you do not need to enter the XYZ coordinates of a unit vector SIMM will nor malize the vector automatically when it calculates the joint transform It will also normalize the vector and update the display of the coordinates in the Joint Editor when you choose a joint for editing For example you can enter values of 2 0 2 0 0 0 for a rotation axis and the Joint Editor will 2 7 2 7 1 model gt help 2 7 Muscle Editor show these values When you switch the Joint Editor to a different joint and then back to the original one the axis dis play will be updated to show 0 70711 0 70711 0 0 Also these normalized values will be output when you save the model to a file Muscle Editor The Muscle Editor gives you access to all of the parameters that describe the muscles The paths of the muscles can be altered by selecting and moving the attachment points in the model window see Sections 2 7 3 and 2 7 4 The Muscle Editor has several features to help you edit the muscle paths such as an algorithm that moves a muscle point toward a specific vertex on a bone surface The muscle tendon parameters can also be changed with this t
105. with its outer box Note If you hold down the Alt or Ctr1 key while clicking the reset button each of the deformity sliders at the bottom of the Deform Editor window will be reset to their default values Combining Multiple Deform Objects To simulate complex bone deformities you will typically need to apply more than one deform object to a body seg ment Using multiple deform objects allows you to apply different types of deformation to different regions of the same segment When working with multiple deform objects it is important to keep in mind that the overall deformation applied to a body segment is the result of each of the individual deformations applied in sequence starting with the first deform object in the segment s list The order in which deform objects appear in their parent segment s list is significant Rearranging a segment s list of deforms will change the aggregate deformation applied to the segment Furthermore the only way to rearrange a segment s list of deform objects is to edit the model s joint file then reload the model For these reasons it is helpful to have an under standing of how multiple deforms behave Chapter 2 Tools 103 2 11 Deform Editor Figure 2 16 The left image shows the femur and deform boxes before any deformation has taken place The right image shows the result of the first deform represented by the larger box 104 Chapter 2 Tools In Figure 2 14 above the larger box in
106. with motion trial load with motion file drag and drop 3 9 Movie Files same folder as the archive it will not be read when the model is loaded Movie Files Movie files can be loaded into SIMM and displayed in the model window in conjunction with motions There are sev eral ways to load a movie into a SIMM model but in all cases the movie is linked with one or more specific motions in that model The movie file formats that SIMM supports are WMV AVI MPG MOV and Mp4 Here are the three ways of loading a movie file into SIMM When you load a TRB TRC C3D IKS file motion trial SIMM checks to see if there is a movie file in the same folder with the same base name If there is the Joad movie checkbox in the dialog box is enabled and checked If this checkbox is checked when the motion trial is loaded SIMM will automatically load the movie and link it to the motion In the header of a motion file you can specify the name of a movie file to load with the motion movie lt name of movie file gt When the motion file is read the specified movie file will be loaded and linked to the motion When you drag and drop a movie file onto a model window SIMM does one of the following If no motions are in the model SIMM will display an error message Chapter 3 Input Files 303 3 9 Movie Files 304 Chapter 3 Input Files If one motion is in the model SIMM will link the movie to that motion replacing the previo
107. with the time of the last frame of data and you will not be allowed to change the value you must crop the motion to change the end time step 2 16 4 motion gt 2 16 Dynamics Tool This specifies the step size or reporting interval for the dynamic simulation As the simulation proceeds it will write data to the output file and return the same data to SIMM every step seconds When you choose a motion for inverse dynamics the step size will automatically be filled in with the step size of the data in the motion and you will not be allowed to change it Motion for Inverse Dynamics This button lets you choose a motion to use for the dynamic simulation primarily for inverse dynamics When you press this button a pop up menu is displayed with an option called no motion followed by the list of motions currently loaded for this model For forward dynamics you will usu ally want to choose the no motion option However if you would like to prescribe the motion of some of the gencoords during a forward simulation then choose the appropriate partial motion For inverse dynamics choose a motion with data for all of the gencoords When you choose a motion SIMM will automatically fill in the input file field with the name of a motion file that SIMM will generate This file will contain the same data as the chosen motion but will also include the smoothing parameters you have chosen see Section 2 16 5 Smoothing Low Pas
108. 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 For more infor mation on the markers built into the mocap model and how to add your own read the Guide to Mocap Model Markers document The mocap model and the algorithms used to scale it are described in the following sections The Mocap Model SIMM comes with several musculoskeletal models that can serve as the mocap model in the Motion Module The Chapter 5 Motion Module 329 5 3 Using the Mocap Model 330 Chapter 5 Motion Module default model is a full body model that has been customized for gait analysis but can be used to import and display any type of full body motion The model has 41 body segments 41 joints 40 degrees of freedom and 88 lower extremity muscles It represents an adult male approximately 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 represent normal joint motion as closely as possible This model also includes mass and inte ria properties for all of the body segments so it can be used by the FIT Module or Dynamics Pipeline for inverse and forward dynamic simulations The joint file for this model is SIMM Models GaitModel GaitModel jnt There are other legacy mocap models located in SIMM Resources mo
109. wrist jaw and other anatomical structures These models can be altered according to partic ular surgical procedures to study how the surgical altera tions affect muscle function SIMM can also be used to analyze and display the mechanics of injuries Neuroscientists are using SIMM to study how the central nervous system controls movement For example muscle activation patterns determined from electromyographic recordings can be used to estimate muscle forces and joint moments generated during a task The computed joint moments can then be compared to experimentally recorded moments Medical students and residents use models created with SIMM to study musculoskeletal anatomy and function In addition to visualizing anatomical structures students gain an appreciation for the interplay of muscle architecture and joint geometry Kinesiologists who record and analyze the motion of per sons with movement disabilities are using SIMM to create three dimensional animations of a person s movement Movements such as walking can be quantitatively com pared to normal movement to gain insight into the causes of movement deformities Motion can also be analyzed in the context of optimizing athletic performance Human factors engineers who need to account for muscle strengths when designing products or work stations can use 1 3 1 3 Design Goals SIMM to study how posture effects muscle strength Limits on joint ranges of motion can also be
110. 0 which means no merging will occur This preference specifies the frame rate of movies generated using auto movie mode in the Model Viewer Once auto movie mode is turned off and the movie file is saved SIMM will modify the frame rate in the file to this value If this pref erence is not specified a value of 10 0 frames second is used This preference is used when exporting skins as Collada files that will be imported into Maya Due to an incompatibility between some versions of Maya and the open source Collada parser the units specified in the file need to be modified in order for the skin to load properly If this preference is off the following line will be written to the Collada file lt unit name meter meter 0 001 gt If this preference is on this line will be written instead lt unit name meter meter 1 0 gt DISPLAY FORCES AS ARROWS DISPLAY FORCES SPHERE SIZE MOTION SMOOTHING FREQUENCY HIDE DIALOGS NURBS SPRING SEPARATION B 1 Preferences If you are creating the Collada skin file to import back into SIMM this preference should be off the default If you intend to import the file into Maya this preference should be on This preference specifies whether or not to display body forces joint forces and gencoord moments in the model win dow as arrows or as spheres When this preference is on each force and moment is displayed as a single arrow When this preference is off the X Y and Z compo
111. 1 pref MOCAP MODEL D GaitAnalysis Model GaitModel jnt open mocap static trb open walkl trb walk2 trb tool pm yvar norm musculotendon_ length xvar walkl muscles semimem_r on muscles semiten r on muscles semimem 1 on muscles semiten 1 on make xvar walk2 make open D GaitAnalysis NormalData NormalHamstrings plt rename norm musculotendon length vs walk1i MyHamstringsPlot save plt hamstrings plt MyHamstringsPlot close Gait Model close MyHamstringsPlot Figure 3 27 Example script file In this example the mocap model Gait Model is loaded using static trb as a static trial Then two walking motions are loaded walk1 trb and walk2 trb A plot of hamstrings lengths is created plotting left and right semimem and semiten as a function of each walk ing motion An external plot file is then loaded and its data is added to the plot The plot is then renamed and saved to a file Lastly the model and plot are closed Chapter 3 Input Files 301 3 8 Script Files 302 Chapter 3 Input Files SIMM uses a script file to save and restore settings each time the program is launched or closed If the WRITE STARTUP SCRIPT preference is on SIMM will write a script each time the program is closed The file is named SIMM ssc and is written to your user application data folder e Q C Users Peter AppData Local MusculoGraph ics SIMM 6 0 SIMM ssc If the READ_STARTUP_SCRIPT prefer ence is on this file will be read by SIMM the ne
112. 1 3 set model lt model gt set plot lt plot gt y lt Y variable gt 2 21 Scripting Tool sets the motion speed of the current model to the specified value which is interpreted as percent of real time The value must be between 1000 0 and 1000 0 turns on or off trackball mode for the current model See Section 2 4 6 Model Window Viewing Commands for a description of trackball mode turns on or off the highlighted display of muscle points in the current model turns on or off the display of shadows in the current model turns on or off the display of crosshairs on the current model window Plot Maker Commands The following commands are available in the Scripting Tool when the Plot Maker is the current tool enter the command tool pm to make the Plot Maker the current tool sets the Plot Maker to the specified model sets the Plot Maker to the specified plot sets the Y variable which must be one of the following musculotendon_length norm_musculotendon_length musculotendon_velocity fiber_length norm_fiber_length force tendon_length tendon_strain total_positive_moment total_negative_moment Chapter 2 Tools 203 2 21 Scripting Tool y lt Y variable gt lt gencoord gt x lt gencoord gt x lt motion gt make delete delete lt plot gt lt muscles gt lt name gt lt on off gt lt muscle_menu gt lt group gt lt on off gt motion_curve lt motion gt lt curve gt segment l
113. 2 5 2 This allows you to select one or more data columns and plot them versus the X column of the motion usually time You can also plot a column of motion data versus any other column of data in any motion Here are the steps Chapter 2 Tools 41 2 5 Plot Maker 42 2 5 5 moment musculotendon length norm musculotendon length Chapter 2 Tools 1 Click on y variable From the pop up menu choose motion curves then from the submenu choose the motion and then the data column that you want to plot on the Y axis 2 Click on x variable From the pop up menu choose motion curves then from the submenu choose the motion and then the data column that you want to plot on the X axis 3 Click on make curves The Y data column will be plotted versus the X data column and the curve will be added to the current plot Y variables The moment of the selected muscles with respect to the cho sen generalized coordinate Moment is defined as force multiplied by the moment arm with respect to a generalized coordinate The generalized coordinate is chosen from the submenu that appears when you move the cursor off the right side of the moment selection You cannot compute the moment of a muscle with respect to a motion variable so the moment submenu lists only true generalized coordi nates When selecting moment as the Y variable you must choose a generalized coordinate from the submenu The origin to insertion length of th
114. 24 In addition to joint angles and muscle activation levels you can also specify animation data for arbitrary objects to be added to the scene when the motion is played back These are referred to as motion objects SIMM provides several built in motion objects for displaying forceplates forceplate forces markers foot prints contact forces contact points and joint forces You can also add your own custom motion objects and animate their position scale orientation and color See Section 3 5 3 Motion Objects for more informa tion about adding motion objects to an animation Columns of data in a motion file can correspond to a gener alized coordinate possibly with a suffix a muscle possi bly with a suffix a motion object component or other data Other data can be any motion data that you want It is not used to animate the model when you play the motion but can be plotted in the Plot Maker If you always want to load a certain motion file or files with a musculoskeletal model you can put the name of the motion file inside the joint file preceded by the keyword motion file You can specify up to 100 motion files in this way See the beginning of Section 3 3 Joint Files for more details Chapter 3 Input Files 287 3 5 Motion Files 288 Walking motion name gait cycle name of this motion datacolumns 6 6 columns of data datarows 64 64 rows of data 1 for each time step keys w_key
115. 5 Appendix A Tips on Using SIMM The following is a list of tips on using SIMM It is strongly recommended that you read through the entire list before using SIMM for any of your work Drag and drop is a very handy method of loading files into SIMM Every type of file that SIMM can read can be dropped onto the SIMM window to load it Read Section 2 2 1 Drag and Drop for a description of the rules that SIMM follows when a file is dropped onto one of its windows Drag and drop is particularly useful for loading models simply drop a JNT or SMM file onto SIMM and loading motion capture files drop a TRB TRC C3D file onto the SIMM background to load it as a static trial and onto a model window to load it as a motion trial Use the SIMM hot keys Ten of the function keys work as hot keys in SIMM as described in Section 2 4 6 Model Window Viewing Commands They can be very handy for turning on or off muscle and marker displays or for stepping through a motion frame by frame Annotation mode F11 can be particularly useful when you want to identify an object in the model display Appendix A Tips on Using SIMM A 1 A 2 Appendix A Tips on Using SIMM Saving joint and muscle files Many joint and muscle files including all of the models that come with SIMM contain comments and macros that are not preserved when the model is loaded into SIMM and then saved back to a file For this reason you should be careful when saving a
116. 6 3 Start end SIMM will create this file with all the appropriate data col umns and smoothing parameters when you initialize the simulation This field specifies the output file created by the dynamic simulation As the simulation proceeds it will write each time frame of output data to this file When you select a motion for inverse dynamics see Section 2 16 4 Motion for Inverse Dynamics SIMM will automatically fill in the out put file field with the name of a file based on the name of the input motion Simulation Time The fields in this region control the time of the dynamic simulation and how often the results are written to the out put motion For most inverse dynamics applications you do not need to set these parameters they will be set automati cally when you choose a motion see Section 2 16 4 Motion for Inverse Dynamics This specifies the starting time for the dynamic simulation For forward dynamics set this field to the desired starting time usually 0 0 When you choose a motion for inverse dynamics the starting time will automatically be filled in with the time of the first frame of data and you will not be allowed to change the value you must crop the motion to change the start time This specifies the ending time for the dynamic simulation For forward dynamics set this field to the desired ending time When you choose a motion for inverse dynamics the ending time will automatically be filled in
117. B C ANB C and C3D files into SIMM model coordinates Second the units are used for display purposes when creating plots In this case SIMM does not use the units to convert any data values it merely adds the unit labels to the plot labels Length_units speci fies the units of all lengths and translations in your model Force units specifies the units of muscle force These parameters can be changed within SIMM by right clicking Chapter 3 Input Files 235 3 3 Joint Files 236 window _position window_size gravity solver accuracy solver max _ iterations solver_method Chapter 3 Input Files on the background in the model window and choosing edit model preferences from the pop up menu length_units m force units N This parameter specifies the position of the model window when the model is first loaded into SIMM The X and Y coordinates are relative to the top left corner of the main SIMM window with X going to the right and Y going down window position 800 20 This parameter specifies the size of the model window when the model is first loaded into SIMM The numbers fol lowing the keyword are the width and height respectively window _size 400 600 This parameter specifies the direction of the gravity vector which is used only during dynamic simmulations The default gravity vector is Y Available options are X X Y Y Z Z gravity Z There are three parameters you can specify to control t
118. EMG is the column of motion data and the step function is the auxiliary data See Section 3 5 6 Auxiliary Data for more details on specifying auxiliary data This command lets you add a text label to the plot with the lower left corner of the text located at the cursor position when you right clicked Labels that are added to the data region of the plot will move with the data e g when the plot is zoomed or scaled and labels that are added to the margins of the data box will remain fixed in the margins This command lets you save the plot to a file and functions the same as the Save Plot File option in the File menu When you select this command and then a model from the submenu SIMM will copy the image of the plot window and display it on an object called plotscreen obj in the model you must add this object to the model before send ing the plot to it The plot in the model window will then update automatically as the regular plot changes Similar to the moviescreen obj object for displaying movies plotscreen obj can be dragged and dropped onto the model window and then moved and scaled however as desired A file named plotscreen obj is available in the folder SIMM Resources bones Plot Window Commands These keys allow you to zoom and pan within the plot win dows just like you can in the model windows The i and o keys move the plot curves in and out the u and d keys move the curves up and down and the 1 and r keys mov
119. ENT POINTS To select muscle attachment points press and hold the S key While this key is pressed the HUD text box in the lower left corner of the model window displays Selecting muscles points N selected where N is the number of attachment points currently selected As you move the cur sor around the model window if it hovers over an attach ment point the point will be highlighted with a yellow wireframe sphere and the muscle name and point index will be shown in a tool tip box If you then left click on the point it will be added to the group of selected points If you click on an already selected point it will be unselected You can also box select attachment points by pressing and hold ing down the left mouse button and dragging the cursor to form a rectangle around the points you want to select or unselect Box select selects all muscle attachment points inside the box on all muscles currently being displayed even if the muscle or point is hidden behind a bone or another muscle This makes it possible to select a group of coincident points such as those at the insertion of the Achil les tendon on the calcaneous As you select and deselect points the list of currently selected points is updated in the Selected Attachments panel if the Muscle Editor is set to the same model Chapter 2 Tools 69 2 7 Muscle Editor 70 Chapter 2 Tools owe EDITING ATTACHMENT POINTS To move the set of selected muscle attachm
120. Files 256 Chapter 3 Input Files 3 3 7 corner and the fourth vertex is mapped to the lower left cor ner For more complicated world objects you may need to use a third party software package to generate UV coordi nates for each vertex The Wikipedia page on UV map ping has some additional information Note you can create a scene or room to surround your musculoskeletal model using a set of flat panels with a tex ture map on each one An example is provided in the Mod els Texture folder in your SIMM installation The model has a floor and three walls Each object is a 4 vertex bone file with a different TIFF image for the texture map Materials Materials define the color and surface reflectivity of objects Once you have defined a material you can assign it to any number of body segments world objects muscles and motion objects If you do not assign a material to a bone or world object the default bone material def bone is assigned to it See Figure 3 10 for a complete list of the default materials and how they are used A sample material definition is shown in Figure 3 9 You should consult the OpenGL Programming Guide for a complete description of material properties but a brief summary follows The key words ambient diffuse specular and emission should each be followed by the red green and blue color compo nents of that material property These values range from 0 0 to 1 0 Ambient refers to the background
121. Marker Files 320 calibrate forces adaptive MVCs for EMGs use Bayes filter for EMGs EMG smoothing passes EMG moving window size Chapter 5 Motion Module 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 calibration of the forceplate data When this box is checked SIMM determines the baseline of each forceplate channel and automatically subtracts these base line values from the data thus zero ing out the force data Note SIMM calibrates forces by finding the frame with the smallest vertical force and assuming that this force should be zero The analog channel values for this frame are then subtracted from every frame in the motion If you load a motion during which one or more forceplates has weight on it for the entire motion then there is no frame which should have zero force and SIMM will not calibrate correctly To load such a motion turn on this checkbox so that SIMM will not perform any calibration of the force channels When this option is on SIMM will calculate the maximum value of each EMG channel for the motion trial If the actual maximum is greater than the MVC specified in personal dat if any SIMM will use the maximum as the MVC instead of the specified value When this option is on SIMM will apply a Bayes filter to each EMG channel and then calculate onset time offset time and average amplitude from th
122. Model Viewer 36 Chapter 2 Tools F7 F10 PLT F12 Toggles the display of the markers in the model If all of the markers are on pressing F7 will turn them all off If some or none are on they will all be turned on This only affects the display of the pink markers defined in the body seg ments not experimental markers in motion data Toggles the display of the selected polygons on bonel as specified in the Bone Editor When you press and hold down the F11 key in the model window a small box with a yellow border is shown in the bottom left of the window containing information about the object currently under the tip of the cursor Some of the objects will be highlighted as you mouse over them while others will not But every object will be annotated in the text box including motion objects such as force plates markers and foot prints Saves an image of the model window to a TIFF file Equiv alent to pressing the snapshot button in the Model Viewer and choosing take snapshot Pressing the right arrow key advances the current hotkey motion by one frame and pressing the left arrow key moves it backward one frame The hotkey motion can be selected using the up and down arrow keys as described below Pressing the up and down arrow keys cycles through the motions linked to the model setting each one in turn to be the current hotkey motion A message is then printed to the SIMM Messages window indicating whi
123. OLDER MOTION MOVIE SPEED B 1 Preferences will change to the ones used in the plot you are choosing Thus you can add additional curves of the same type to the plot without resetting these variables This preference specifies which body pose to use when nor malizing musculotendon lengths In the Plot Maker there is a Y variable called norm musculotendon length that calculates the length of a muscle and then divides it by the length in the anatomical position all gencoords 0 0 If this preference is set to yes then instead of the anatomical position SIMM will use the default pose the pose that is applied when you select restore gc values in the Model Viewer This option specifies the base file name to use when creat ing snapshot files of models in the Model Viewer See the description of the snapshot command in Section 2 4 2 Command Menu for more details By default this option is set to snapshot To use a different file name delete the default and type in a new name This preference specifies the current folder within the Script ing Tool This is the folder that is used when opening and sav ing files within the tool and can be changed within the tool using the cd command This preference affects how SIMM creates movies of motions using the movie button in the Model Viewer When MOTION MOVIE_SPEED is defined as a positive number SIMM will create one movie frame for each frame of data in the motion regardless of th
124. RAL TIBIAL JOINT beginjoint femoral tibial name of this joint segments femur tibia joint from FEMUR frame to TIBIA frame order t rl r2 r3 translate then rotate about axisl axis2 and axis3 axisl 0 0 0 0 1 0 axis2 1 0 0 0 0 0 rotation axis definitions axis3 0 0 1 0 0 0 loopjoint ie show axisl 0 2 display rotation axisl length 0 2 tx function f1 knee angle The kinematic functions f1 and 2 ty function 2 knee angle specify the relations between the tz constant 0 0 generalized coordinate knee angle rl function 3 knee angle and tx and ty the translations in r2 constant 0 0 the x and y directions respectively r3 constant 0 0 3 specifies the relation between endjoint knee angle and the rotation around axisl Figure 3 4 Example joint definition 244 Chapter 3 Input Files 3 3 4 3 3 Joint Files changed by adjusting the axis definitions Since all of the translations and rotations in this joint are either constants or functions of a single generalized coordinate knee_angle the joint has only one degree of freedom It is not a simple revolute however because two of the translations tx ty are functions of knee angle If you want to display any of the axes of rotation in the model window put the keyword show in the joint definition followed by the name of the axis i e axisi axis2 or axis3 and the desired length of the ax
125. Software for Interactive Musculoskeletal Modeling User Guide SIMM 7 0 for Windows User Guide September 2013 Part SPC 70001 Important Notice The information in this manual is subject to change without notice and should not be construed as a com mitment by MusculoGraphics Inc The software described in this manual is furnished under a license agreement and may be used or copied only in accordance with the terms of such agreement Copyright 1992 2013 Motion Analysis Corp All rights reserved This manual may not be repro duced in whole or in part without the expressed per mission of Motion Analysis Corp MusculoGraphics a division of Motion Analysis Corp 3617 Westwind Blvd Santa Rosa CA 95403 Phone 1 707 579 6500 Fax 1 707 578 8473 E mail support musculographics com http www musculographics com Trademarks Adobe Postscript is a registered trademark of Adobe Systems Incorporated Windows is a registered trade mark of Microsoft Corp QuickTime is a registered trademark of Apple Computer Inc ii Credits Program Creation amp Documentation Peter Loan Krystyne Blaikie Scott Delp Kenny Smith Cover Illustration Idd Delp Technical Support 1 707 579 6500 x3 support musculographics com Acknowledgements Development of the initial version of SIMM was funded by the Rehabilitation Research amp Develop ment Center Veterans Affairs Medical Center Palo Alto
126. To move a control point press and hold the left mouse button while the cursor is on the point Drag the cursor to move the point to the desired location and then release the left mouse button To select multiple points for moving you can Shift click on a point to add it to the set of selected ones and Ctrl click to toggle its selection You can also box select control points by pressing the left mouse button away from a point and dragging the cursor to form a box around the desired points When you start to box select all currently selected control points will be deselected so that only the ones in the box will be selected You can Shift box select to add the points in the box to the set of selected ones and Ctrl box select to toggle the selection of points in the box Once you have selected the desired set of control points click on any one of them and drag them to a new location To help you edit a function you can press the i 0 1 r u and d keys to move the view of the function in out left right up and down respectively You can also use the x and y keys to zoom in and out along just the X or Y axes press the Shift key along with x or y to zoom out Depending on the function being edited there may be enhancements to the display of the graph area to help with editing For example with gencoord restraint functions Figure 2 29 the red regions mark the limits of the genco ord s range of motion red lines if the gencoord i
127. Typically you will choose the shape that best resem bles the surface you intend to wrap muscles over Spheres and cylinders are simpler to define and more straightfor ward for calculating wrapping Ellipsoids are more compli cated and there are three techniques available for wrapping muscles over them see Section 2 10 5 for a description of these methods Torii are very useful as pulleys but they work best if the muscle path remains roughly perpendicular to the plane of the torus hybrid midpoint axial active visible show pts constrain to quadrant 2 10 Wrap Editor These radiobuttons let you choose which method is used to compute the wrapping path around ellipsoidal wrap objects If the current wrap object is not an ellipsoid then these radio buttons will not be visible in the Wrap Editor window See Section 2 10 5 for more information about the hybrid midpoint and axial wrapping methods This toggle button lets you turn the current wrapping object on and off When a wrap object is not active it is drawn in red and it has no effect on muscles that intersect it This button lets you toggle the visibility of the current wrap object in the model window Once you are done editing a wrap object you will typically make it invisible so that it does not obscure the display of other features of your model A wrap object can be invisible but still active This button toggles the visibility of muscle tangent points for mu
128. _vy _vz components in the motion file The motion object will also be scaled along this axis The default value for this field is y Constraint Objects Constraint objects provide a way of constraining points on one body segment to remain on the surface of a geometric primitive the constraint object on a second segment This mechanism is useful for creating joint kinematics that are too complex to be modeled with a traditional SIMM joint For example in the shoulder two or more points on the scapula can be constrained to remain in contact with the rib cage which is represented as an ellipsoid Once this con straint is activated when you change the value of one of the generalized coordinates in the shoulder SIMM will adjust 3 3 Joint Files the values of the other generalized coordinates in order to satisy the constraints It is usually easier to create new constraint objects using the Constraint Editor rather than editing a joint file directly See Section 2 13 Constraint Editor for information on how to do this However it can be useful in certain situations to create or modify constraint objects manually by editing the model s joint file Example constraint object beginconstraintobject r_ scapula con constrainttype ellipsoid segment ribcage xyz _ body rotation 9 12 16 21 10 42 translation 0 0399 0 1799 0 0743 radius 0 0800 0 1800 0 0800 active yes visible no quadrant x beginpoints name x Y Z w
129. a confirm window you can use keyboard keys as well as the right mouse button to confirm the action Pressing y will select the yes box and pressing n or c will select the cancel box You can copy and paste text from the Windows clipboard into text and number fields in SIMM as well as into the Scripting window Appendix B SIMM Resources B 1 The SIMM installation procedure creates a directory named Resources within the directory where SIMM is installed For SIMM to execute properly the SIMM Resources directory must not be moved or renamed SIMM needs to access sev eral files within the Resources directory while it runs Some of these files can be used to modify the way SIMM works The following sections describe these files Preferences The file preferences txt contains a set of parameters that you can define to change the behavior of various features in SIMM The file is read by SIMM when the program is launched and it can also be reloaded while SIMM is running by selecting Options Reload Preferences File from the SIMM menu bar When SIMM reads the preferences file it first looks for it in your user application data folder e g C Users Peter AppData Local MusculoGraphics SIMM 7 0 pref erences txt If it is not found there it looks in the resources folder where SIMM was installed e g C Program Files x86 MusculoGraphics SIMM70 Resources preferences txt To edit the preferences while SIMM is running select Opt
130. activity Muscle activation levels must be in the range 0 0 to 1 0 To specify a muscle s activation in a motion file the column name must be the name of the muscle Motion Objects SIMM allows you to visualize phenomena such as ground reaction forces and joint contact points by animating arbi trary shapes when a motion is played back By default SIMM provides an arrow for visualizing vectors and a sphere for visualizing points Chapter 3 Input Files 293 3 5 Motion Files 294 Chapter 3 Input Files Animation data for motion objects are labeled in the motion file by combining the name of the body segment to which the object should be attached with the name of the motion object and the name of the component to be animated The components that may be animated are e position px py pz e scale sx sy sz e vector vx vy vz e color cr cg cb For example you can display force vectors attached to any body segment e g ground by specifying their point of application and size in a motion file For each vector enter six columns of data in the file three for the X Y and Z coordinates of the point of application and three for the X Y and Z coordinates of the vector itself The column labels should be the name of the body segment to which the vector is attached appended by _force px _force py and _force pz for the point of application and _force_ vx _force_vy and force _vz for the force vector The names of
131. al axis that is most parallel to the muscle line This method produces a good result unless the most parallel axis happens to change during the range of motion of the muscle In this sit uation a discontinuity in wrapping path will occur when the choice of axis switches from one principal axis to another The hybrid method described above automatically detects when an axis switch is about to take place and shifts its weighted average to favor the midpoint method to conceal the effect of the axis switch If you are able to orient your wrap object such that muscles that wrap over it remain mostly parallel to the same axis throughout their range of motion then the axial method will produce well behaved wrapping paths Wrapping Tips amp Techniques Use the constrain to quadrant controls to specify which side of a wrap object muscles will wrap over If you do not con strain wrapping to one side of a wrap object then muscles will automatically wrap over the side that permits the short est muscle path Thus the muscle may switch from one side 2 11 2 11 Deform Editor of a wrap object to the other depending on the positions of the body segments By constraining the wrap object you can force muscles to wrap over the desired side of the object even if it is not the shortest path around the object How ever when calculating a muscle path other than the true shortest path SIMM may occasionally calculate an undesir able muscle
132. ames 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 X axis 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 mark ers see the crop ends option above 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 Analog Data When this box is checked SIMM will look for and automat ically 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 Chapter 5 Motion Module 319 5 2 Opening Tracked
133. an object file do not have to be closed surfaces they can have holes in them However norm may have difficulty computing surface nor mals for such polyhedra If norm reports that it was unable to compute normals for one or more polyhedra it will still create an output file but some of the surface normals will be incorrect These polyhedra will not be shaded properly in SIMM but you can still use them as object files in your model Also if there are concave polygons in the object file norm may have difficulty computing surface normals for the object However norm has an option described below to subdivide polygons as it processes the file To process an object file open a DOS window change directories to where norm is installed it is in the same directory as the SIMM executable and type norm followed by one or more file names and the desired options if any Norm can read any of the three file formats described in Section 4 2 Bone Files and by default writes out bones in the newer ASCII format File names may appear anywhere on the command line In other words you can intersperse options and file names in any order Norm identifies file names by their lack of an initial dash Here are some examples of how you can specify file names and the rules that norm follows when processing them norm file Norm will process file and save the output object in file It will prompt you to confirm that the contents of file will be over
134. ange is made to the model that affects the values in the plot curve the curve is updated instantly and automati cally On slower computers you may notice that the graphi cal interface will appear more sluggish if you make many plot curves live It is recommended that you make plot curves live only when modifying muscle properties that will affect them To stop a plot curve from being updated live right click on the name in the plot key and choose Jive Chapter 2 Tools 81 2 10 Wrap Editor 82 Chapter 2 Tools 2 10 Wrap Editor The Wrap Editor allows you to create and edit muscle wrap ping primitives wrap objects Wrap objects provide auto matic muscle wrapping without the need to explicitly specify intermediate muscle points a k a via points Mus cle via points are described in Section 3 4 1 Muscles Each wrap object is associated with fixed to a specific body segment in the model and its position is specified rel ative to the reference frame of that segment A wrap object may have one or more muscles assigned to it When muscles assigned to a wrap object make contact with the wrap object s surface the muscle is automatically deflected to prevent it from penetrating the wrap object A muscle may have more than one wrap object assigned to it Each time a wrap object is assigned to a muscle the object is added to the end of the muscle s list of wrap objects When SIMM wraps a muscle over its assigned objects
135. ange the drawing mode for all of the bones in the current segment The six available modes are gouraud shaded filled polygons smooth shading flat shaded filled polygons flat shading solid fill filled poly gons no shading outlined white polygons with high lighted edges wireframe hollow polygons and none no display To change the drawing mode of individual bones in a body segment right click on the bone in the model win dow This command lets you change the material that is used to display the bones in the current segment The pop up menu shows the materials that you defined in the joint file plus a set of default materials that are defined within SIMM To change the material of individual bones in a body segment right click on the bone in the model window 2 14 3 Mass mass center inertia 2 14 Segment Editor Segment Parameters Inertial Parameters This panel can be used to modify the mass and inertia prop erties of the current segment These properties are used only in dynamic simulations The individual fields are described below This field lets you specify the mass of the current segment You can specify the mass in whatever units you want but they should match the units you use to specify inertias mus cle forces and external forces and torques The mass units in the models that come with SIMM are kilograms These fields let you specify the location of the mass center of the current segment
136. ated and used see Section 5 3 Using the Mocap Model Opening 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 Cortex manual contain X Y and Z coordinates for each identified marker for each time frame You can also import analog data files containing forceplate and EMG 5 2 Opening Tracked Marker Files 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 a trial When you open a tracked marker file along with any asso ciated analog files SIMM attempts to map the data onto the current musculoskeletal model thus creating a SIMM motion that is linked to the model Therefore 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 loca
137. ax If the sum option is being used to sum curves from more than one selected muscle the individual curves are compared to this clipping range not the final summed curve The scale field allows you to specify a scaling factor when generating plot curves using the make curves command Whenever you generate a curve each data point is multi plied by this scale factor before adding the curve to the plot window This scaling is performed before the offset is applied The offset field allows you to specify an offset factor when generating plot curves using the make curves command Whenever you generate a curve this offset value is added to each data point before adding the curve to the plot window This offset is performed after the scale is applied Toggle Buttons This toggle button lets you choose whether or not you want to sum the curves of the selected muscles to generate a sin gle curve If sum is off then each selected muscle creates a curve that is added to the plot If sum is on then the individ ual curves are summed and only one curve is added to the plot The current setting of sum has no effect if you are plot rectify active passive act override 2 5 Plot Maker ting data from plot data files or columns of data from motion files This toggle button controls the sign of the data points in the curves as they are added to a plot If rectify is on then all of the data points are made positive in effect plotting t
138. ayed as its own sphere with red for X green for Y and blue for Z Each sphere is centered on the joint center and drawn partially transparent to help see overlapping spheres This option toggles the display of contact forces in the motion data if there are none this option is grayed out Contact forces are the forces calculated by the rigid body contact algorithm and by the NURBS based contact algo rithm in the Dynamics Pipeline You can right click on the checkbox to display a dialog box showing all of the contact forces in the motion which you can use to turn on or off the display of individual forces This option toggles the display of spring forces in the motion data if there are none this option is grayed out Spring forces are the forces calculated by the spring based contact algorithm in the Dynamics Pipeline You can right click on the checkbox to display a dialog box showing all of the spring forces in the motion which you can use to turn on or off the display of individual forces show moments show other objects loop motion enforce constraints enforce loops 2 17 Motion Editor This option toggles the display of moments that are applied to the generalized coordinates These moments are usually the results of inverse dynamics calculations but you can also display moments that you apply to the generalized coordinates during a forward simulation The dialog also contains a checkbox called Display as arrows T
139. bjects con straint objects and materials Each model you load into SIMM must have one joint file defining all of the segments joints generalized coordinates and kinematic functions that comprise the model You may list these components in the file in any order but the order in which you enter segment names can affect the display of the model by influencing the choice of the fixed segment see Section 3 3 2 Fixed Seg ment for more information The joint file also contains a number of parameters that specify various properties of the model such as its name some of the colors used in the display and the units of length and force in which the model is specified All of these parameters are optional and have reasonable default values if they are not specified in the joint file These Chapter 3 Input Files 231 3 3 Joint Files name muscle file motion file 232 Chapter 3 Input Files parameters generally go at the top of the file although they can be placed anywhere The rest of this section describes these optional parameters Note Case is significant when entering text into joint files All SIMM keywords e g name beginsegment must be in lower case letters You are free however to use upper as well as lower case letters for naming your model compo nents e g names of joints and segments and SIMM will display these names exactly as you type them into the joint file To give your model a name use the key
140. buffer and the bone itself is unchanged though you can see the effects of the transformation in the model window When editing polygons and vertices of a bone you should also run norm on it occasionally to recompute the surface normals and update its shading Lastly you should fre quently save the bone to a file as you make modifications because there is no way to undo changes or restore the bone to a previously saved copy If you make changes that you want to undo you will need to delete the bone and read it back in from a previously saved file When selected norm will attempt to make every polygon in the bone convex by splitting concave polygons into convex pieces When selected norm will triangulate every polygon in the bone by splitting polygons without adding vertices Chapter 2 Tools 143 2 15 Bone Editor separate bones fill holes preserve normals vertex tolerance 144 Chapter 2 Tools tx ty tz rx VY YZ SX SY SZ When selected norm will output a separate bone for each distinct polyhedral surface in the original object This option is used only when postprocessing a bone created by a boolean operation When selected norm will attempt to fill in holes in the bone surface by adding triangles If the bone contains large holes norm may be unable to fill them When selected norm will not recalculate polygon and ver tex normals for the bone This option is useful if you are working on a polyhe
141. cap SIMM keeps track of which mocap model to use by storing a pointer to the appropriate joint file When SIMM is first launched it initializes this pointer by reading the MOCAP MODEL variable in the preferences file SIMM Resources preferences txt The default setting for this variable is SIMM Models GaitModel GaitModel jnt If you want to change the mocap model while SIMM is run ning click on Options in the menu bar and select Choose Mocap Model You can then browse for the joint file of the desired model You may change any of the mocap models however you wish For example you can add or remove muscles from the model or change the tendon and fiber parameters of exist ing muscles You can also add degrees of freedom to the model in order to more accurately represent a particular motion 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 5 3 2 5 3 Using the Mocap Model First the model has been set up to correspond to the skeletal model that OrthoTrak uses when processing gait data The lower extremity body segments and orientations of the ref erence 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 segment These relations are specified in the mocap model by defining scale segments and scale factors
142. ccccccccccccseetseesees 312 5 2 1 Selecting Tracked Marker Files 0 0 314 viii 5 2 2 Tracked Marker Options Dialog eee 314 5 2 3 Analog Dafa cssstein et nese eeaea eh ata s 321 5 2 4 Real time Import mcsaedcsacnfecesteroutetnrtonatecentenes 324 52N AKS FileSend aie aias 327 5 3 Using the Mocap Model fasiciccsiesnsweas obsidian 328 5 3 1 The Mocap Model ick sca ce acasliveiaccsseiettydin Stars 329 2 3222 The Static POSC nenie ien nnrir 331 5 3 3 Calculation of Joint Centers co scscssieeakdecsisvast 335 5 3 4 Scaling the Mocap Model s sesnnnsseeseeseesseseeseee 336 5 3 5 The Marker Set ss sicecisvevicvaiecsdea ese sieus cases 338 5 4 Analog Configuration Files ccccccccceteesseesseeeteeeteentees 340 5 4 1 importVariables txt sewn wets cae nentom ioe 341 J42 DOLCE PIA calam haleacar Sas a e 345 Chapter 6 Tips on Using SIMM uu ecsseseeseeeee A 1 Chapter 7 SIMM Resources cccsccssssscseseeees B 1 PTE EP OV CNCLS ts ca corsa wei stot cad Ved gas E E needs aon ott B 1 Tid COIS aah tertiles th ee Cah at a rte hm aA tPA ra ta Osha B 16 7 3 Password txt amp vinikic aclathoulscrig etl apotataletvite eben B 16 PAS System INO INT osica a ds B 17 TD RONEN 5 cutnvses vied averse tease AE E S B 17 Index 1 Introduction 1 1 SIMM What it is SIMM Software for Interactive Musculoskeletal Model ing is a software system that enables you to create and analyze grap
143. ce called MULTIPLE_SCREENS that allows you to take advantage of multiple screens monitors on your computer If this preference is on Appendix A Tips on Using SIMM A 3 A 4 Appendix A Tips on Using SIMM the SIMM tool windows are created as separate top level windows They can be moved outside of the main SIMM window and they will have their own icons in the Windows task bar The model and plot windows are still constrained to the main SIMM window This option works best if you keep the main SIMM window on one screen and the tool windows on another screen because when you click anywhere in the main SIMM window or cause a new model or plot window to open the main SIMM window is popped above all of the tool windows This preference cannot be changed while SIMM is running it is checked only when SIMM is first launched You can right click on bones in the model window to display a pop up menu with options for changing the bone s drawmode material and other display options You can right click on muscles and on muscle points to display a pop up menu with display as well as editing options Use muscle groups If you have more than about 15 muscles in your model you will find it much easier to select the ones you want if they are divided into several groups In the lower extremity model provided with SIMM the muscles are grouped by function You could also group them by name the number of joints they span or any other crit
144. centers uses percentage offsets from the appro priate marker locations If medial 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 Calculation of shoulder joint centers uses the same technique as for hip center The reference length is the distance between the shoulder and elbow markers The off sets are specified as percentages of this distance The default values are shown in the example below Right Shoulder Inferior Displacement 12 5 Right Shoulder Anterior Displacement 1 25 Right Shoulder Lateral Displacement 2 5 Left Shoulder Inferior Displacement 12 5 Left Shoulder Anterior Displacement 1 25 Left Shoulder Lateral Displacement 2 5 Scaling the Mocap Model Once the locations of the OrthoTrak joint centers have been calculated from the static pose the Motion Module deter mines 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 5 3 Using the Mocap Model OrthoTrak does not create refer
145. ces contact forces and any other external forces in the motion data This optional parameter turns on or off the display of force trails A force trail consists of a white line representing the force at each time frame and a series of line segments con necting the tips of the white force vectors This optional parameter turns on or off the display of the forceplates that are specified in the motion header This optional parameter turns on or off the display of the foot prints that are specified in the motion header If you put this parameter in the header followed by an RGB color value see the example in Figure 3 24 SIMM will display a cursor in all plots of the motion data As you ani mate the motion the cursor will move along the plot data in sync with the display of the model This parameter specifies a motion event which will be shown in all plots of the motion data After the keyword event is the X coordinate usually the time in seconds fol lowed by the name of the event This optional parameter specifies the RGB color used to show the events in plots of motion data Events are shown as vertical lines with their names at the bottom Chapter 3 Input Files 291 3 5 Motion Files calc derivatives forceplate leftFootPrint right FootPrint 292 Chapter 3 Input Files movie This optional parameter specifies whether or not SIMM will calculate first derivatives of the motion data This option is most useful
146. ch motion is cur rent The motion realtime connection is always included in the list of motions that is cycled through and refers to the motion that is animated when SIMM is connected to Cortex or EVaRT in real time 2 5 2 5 1 model gt plot gt 2 5 Plot Maker Plot Maker The Plot Maker allows you to plot various computed prop erties of the muscle tendon actuators including muscle force moment moment arm and length You can create these plot curves for any set of muscles as a function of any generalized coordinate or motion variable In addition to generating data curves that are calculated from the musculo skeletal model there are also two ways you can read in and plot data that are stored in input files The first method involves plot data files see Section 3 6 Plot Files for more information and the second allows you to plot columns of data from motion files see Section 3 5 Motion Files for more information The Plot Maker window is shown in Figure 2 2 Selector Menu The model selector lets you choose which model you want to use to make plots Since some of the plotting options depend on the model each model has its own set of menus and forms to set the plotting options When you select a new model with the model selector the Plot Maker window is redrawn with the new model s menu settings If you never have more than one model at a time loaded into SIMM then you do not need to use the model s
147. ch you can click on with the left mouse button and drag along the shaft of the slider You can also click the left mouse button on either of the two arrow buttons to change the value more slowly If you click in the slider shaft away from the thumb the thumb will jump to where you clicked Toggle buttons control the on off yes no state of various parameters Clicking the left mouse button in the box tog gles the state between the two values When the state is on yes the toggle button is yellow When the state is off no the button is gray All tools have a selector menu at the top of the tool window The text above this menu shows the current model the model that the tool is currently working on and the current plot the plot that the tool is working on Below this text are selectors for changing the current model or plot You can change the current model with the model selector which is the box labeled model Clicking the left mouse button in this box pops up a menu of the models you have created You can then choose the one you want by releasing the but ton while the cursor is over its name You only need to use the model selector if you have more than one model at a time loaded into SIMM You can select the current plot in a similar fashion using the plot selector labeled plot If a tool does not operate on specific models e g Plot Viewer 2 2 2 2 Opening Files the model selector is not displayed in the header
148. checked a browse button is enabled that allows you to specify the name and location of the motion file Analog Data Analog data files contain forceplate and EMG data that was collected in syne with motion data When loading C3D files there are no separate analog files all of the analog data is contained in the C3D file When loading TRB TRC files you can load analog files only if they correspond to the cho sen 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 Other wise you should select the analog file as well in the file browser The same holds for XLS files which are not actu ally analog files but are treated similarly XLS files can contain other data corresponding to the recorded motion Chapter 5 Motion Module 321 5 2 Opening Tracked Marker Files forceplate data 322 Chapter 5 Motion Module such as kinetic data calculated 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 forceplate 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 Forceplate data in an ana
149. command splits the selected polygon displayed in green by adding a vertex at the center of it and forming tri angles using that vertex and each edge of the original poly gon This command works only if there is one selected polygon 2 15 Bone Editor iti Foyet bm s Vimiti o model gt help F a do boolean bone 1 gt operation gt bone 2 gt norm bone 1 tibia_r asc tibia_r femur_r asc femur_r bone asc ground Bone editing boolean and bone loading options split polygon dd to t d change segment gt delete polygons a segment groun ge seg scroll edges new bone name bone asc load bone flip normals delete vertices unselect polygons Norm options unselect vertices convexify polygons vertex tolerance 0 0000000 triangulate move bone 1 to gt 8 angle tolerance 0 00 separate bones write bone 1 fill holes tx 0 00000 preserve normals delete bone 1 yy 0 00000 tz 0 00000 bone export gt selected vertex 44 of 145 coordinates 0 039000 0 082205 0 007241 5X polygons 74 75 76 95 96 97 sy selected polygon 56 of 286 show normals SZ Figure 2 22 Bone Editor window Chapter 2 Tools 139 2 15 Bone Editor delete polygons scroll edges split edge flip normals delete vertices unselect polygons move bonel to gt write bone 1 delete bon
150. constraint object is attached defined as the par ent segment When you select this item a pop up menu of the model s body segments is displayed Choosing a seg ment from this menu will reassign the current constraint object to the selected segment The constraint object s over all position will not change when it is assigned to a new seg ment However when the model is put in motion the constraint object will follow the movement of the new seg ment to which it is attached Constraint objects and points cannot both be assigned to the same body segment so in the pop up menu the segment s on which the points are defined will be grayed out This command saves the current state of all constraint objects in the model to a buffer It can be used in combina tion with the restore all button to help you undo changes made while editing constraint objects This command restores the most recently saved copy of all of the current model s constraint objects It can be used in combination with the save all button to help you undo changes made while editing constraint objects This command deletes the current constraint object from the model 2 13 Constraint Editor Model Right Shoulder model gt constraint object f object name scapulothorax1 segment gt segment thorax save all radius x 0 1470 sphere lt 0 2079 4 cylinder ellipsoid Z 0 0944 P delete restore all constrain to quadrant
151. creating scripts to batch process several motion trials This preference specifies whether or not to save an HTR file when importing a TRB TRC C3D file HTR files cannot be read into SIMM but they can be useful if you want to import the joint angles that SIMM calculates into another software package This preference is used to initialize the appropriate checkbox in the motion import dialog box but you can change it as you load individual motion trials This preference specifies the name of the HTR file to create when importing a TRB TRC C3D file For most applications you do not want to explicitly set this preference because every time you import a motion trial the saved HTR file will have the same name unless you browse for a different name Instead do not define this preference and let SIMM deter mine an appropriate HTR file name for each motion trial that you import This preference is useful primarily when creating scripts to batch process several motion trials This preference specifies whether or not SIMM will update the model pose and refresh the display as it performs inverse kinematics on each frame of data in a motion trial This preference specifies whether or not to load personal dat with each motion trial If this preference is set to yes SIMM Appendix B SIMM Resources B 9 B 1 Preferences MOCAP USE BAYES FILTER MOCAP ADAPTIVE MVCS MOCAP MIN FORCE C3D_ MARKER RESIDUAL THRESHOLD FORCEPLATE VERTICAL OFFSET
152. cs moments calculated for the specified gencoords Muscles that are not optimized but still included in the simulation will behave like regular mus cles and will apply forces to the body segments according to their specified activation patterns if any and force model If you want to output the activations of muscles that are not being optimized you must select them for output using the muscle activations output variable 2 17 2 17 1 model gt help 2 17 2 motion gt 2 17 Motion Editor Motion Editor The Motion Editor Figure 2 24 allows you to modify the motions linked to each model The currently selected motion can be renamed deleted cropped written to a file or have events added to it If plots have been created using these motions before they were edited these existing plots will not change to reflect the new motion characteristics the changes will only appear in newly created plots This tool can be useful if you want to compare several motion trials to each other because it allows you to normalize them accord ing to certain events such as heel strike and toe off Selector Menu The model selector lets you select the current model If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Motion Editor When you are done reading it close the window using its clos
153. cted vertex helping to show you how far the vertices have moved To move the selected vertices in the X Y and Z directions relative to the bone s current reference frame you can use the x y z and shift keys Pressing x translates the points in the negative X direction while pressing Shift and x translates them in the positive X direction Note the X Y and Z axes used for this command are the current axes of the bone If there are non zero rotations applied to the bone the bone s axes will not be the same as the body segment s axes To make them the same process the bone with norm to apply and then reset the current transform Dynamics Tool The Dynamics Tool is a graphical interface for running dynamic simulations created by the Dynamics Pipeline module These simulations are compiled as DLLs dynamic link libraries and can be loaded into SIMM for execution The Dynamics Tool allows you to set various parameters of the simulation such as the input motion for inverse dynam Chapter 2 Tools 149 2 16 Dynamics Tool 150 Chapter 2 Tools ics and the desired output variables e g moments pow ers The Dynamics Pipeline performs forward and inverse dynamics analyses using the same numerical method In both cases the equations of motion are integrated forward in time using a variable step integrator Forces and torques are applied to the body segments from gravity muscles ligaments ground reactions efc
154. ction by right clicking in the editing area to reveal a pop up menu with other editing commands Here is a list of the available com mands This command adds a control point to the function at the location of the cursor when you right clicked If you right click on an existing control point the menu item is add knot point and the point selected will be duplicated creating a knot This item is enabled only if you right click on a control point It deletes the point provided that there are enough remaining points to properly define the function e g two points for a linear function six for a GCV spline This command lets you change the type of the function that interpolates the control points The available types are step function zero order hold natural cubic spline 3rd order GCV spline Sth order and piece wise linear This command lets you specify which function in your model is used for this model component the component you chose for editing in another tool The submenu con tains a list of all of the functions defined in your model the one currently being used is indicated with a check mark Functions that are defined in the muscle file have an m before their numbers When you switch to a different func tion the previous one is not deleted even if it is not being used by any model component clone make new show hide crosshairs reset view control points reset view function enter XY coo
155. current tool in the Scripting window to the Motion Reporter The prompt changes to mr gt to indicate the change sets the current tool in the Scripting window to the Motion Editor The prompt changes to mt gt to indicate the change sets the current tool in the Scripting window to the Dynamics Tool The prompt changes to dt gt to indicate the change Chapter 2 Tools 199 2 21 Scripting Tool tool me move lt window gt x y move lt window gt x y width height refresh lt on off gt 200 Chapter 2 Tools exit 2 21 2 sets the current tool in the Scripting window to the Muscle Editor The prompt changes to me gt to indicate the change moves the specified window so that the upper left corner is at screen coordinates x y The origin of this coordinate system is the upper left corner of the SIMM application window with X going to the right and Y going down To specify the window enter the complete name as shown in the window s title bar enclosing it in double quotes if it contains spaces moves the specified window so that the upper left corner is at screen coordinates x y and resizes to the specified width and height The origin of this coordinate system is the upper left corner of the SIMM application window with X going to the right and Y going down To specify the win dow enter the complete name as shown in the window s title bar enclosing it in double quotes if it con
156. current working folder is usually the last folder from which you loaded a file or to which you saved a file so in general you should not override this default This preference specifies the name or IP address of the machine running Cortex to which you want to connect in real time When this option is on SIMM will read a start up script each time it is launched The file is named SJMM ssc and is located in your user application data folder eg C Users Peter AppData Local MusculoGraphics SIMM 7 0 SIMM ssc so each user can have his or her own start up script The file can contain commands to open and position tool windows as well as load models motions and plots If you customize this file by entering your own commands be sure to set WRITE STARTUP SCRIPT SET TOOLS TO NEW MODEL MULTIPLE SCREENS FASTER MUSCLE DRAWING B 1 Preferences WRITE STARTUP SCRIPT to no so that your modifications are not overwritten when you exit SIMM When this option is on SIMM will write a script each time the program is closed The file is named SJMM ssc and is written to your user application data folder eg C Users Peter AppData Local MusculoGraphics SIMM 7 0 SIMM ssc If the READ_STARTUP_SCRIPT preference is set to yes this file will be read by SIMM the next time the program is launched The file contains commands to open close and position tool windows so that the set up of the windows is preserved from one use of SIMM to the ne
157. d Output Options cee 153 2 16 3 Simulation esl lid aig ene pom eRenE Soe eRe a eeaD Ear aero Fe 154 2 16 4 Motion for Inverse Dynamics 0 6 155 2 16 5 Smoothing Low Pass Cutoff 00 0 156 2 16 6 System Parameters oss lt csgakdinvvakacdwadeedtevendiee 156 2 16 7 Simulation Execution ccccecssceesseeeees 158 2 16 8 Output Variables lt i2 c0chAesuueciant 159 Motion Editor seoooeeeenseseeeseessssrsserssressrrsreesse 163 2 17 1 Selector Menu Aisin Jcicatenaaeeeteieeseccteess 163 2 17 2 Command Menu n sssssonensnnensneesseeseeessssessnee 163 2 17 3 Cropping a Motion cccceesseeeteeereeeteees 166 2 17 4 Motion Events 35 25 Jsseisevcestsaesesscedeseovadeadonees 166 2 17 5 Playback Options ccceesceceseceseeeeeeeees 167 Motion Reporter soci retort Serena NEE 172 2 18 1 Generating a Report e ee eeeceeeeetteeeteee 174 2 18 2 Selector Menu vi tscttiecteteaeaat rte eas 176 2 18 3 Command Menu ic 22 acta lsedseascccavavatness 176 DNS ee OTITIS oes cent MG Tacs ce aus cece agate fea dn eh 179 2 18 5 Toggle Buttons cceceeeeseeteeeteeeteeteees 180 Skin Editor Sol ate os oon neato a a a Gone Ei 181 DAO Selector Men sor iiien a 182 2 19 2 Command Menu 00 cceee cece eececececccccceccceceeeeceee 183 2 19 3 Skin Attachments acnccensieacnesatinl ate ae 185 2 19 4 Group Weighting 22 Ggcsatececeads caterers eseduns nance 186 2 19 5 Model Window Commands
158. d SIMM ASCII file must contain the number of vertices num_vertices followed by the number of polygons num_polygons Then comes the vertex list whose length must be num_vertices Each line in this list contains the X Y and Z coordinates of a vertex Lastly there is the polygon list whose length must be num_polygons The first number in each line is the number of vertices nv in the polygon and the other numbers are the indices of the nv vertices The indices start at 1 and cor respond to the order in which the vertices are listed in the vertex list In the example shown the first polygon is a tri 260 290 0 062448 071901 0 057002 0 062417 062953 0 055540 0 045919 070017 0 069408 0 057682 053884 0 064535 e e Figure 3 2 Example bone file in old ASCII format 3 2 3 3 2 Bone Files angle formed by the first second and third vertices in the vertex list The second polygon is four sided using the third fourth seventh and eighth vertices Note when a musculoskeletal model is loaded into SIMM all of the model s bones that are specified in the old ASCII format are automatically processed with norm so that the vertex normal information is available For bones with many polygons this can add significantly to the time it takes to load a model Thus for large bone files it is recom mended that you convert them to the new SIMM ASCII format before adding them to your model SIMM Binary The third f
159. d also on the current acti vation level if the active component is turned on The tendon strain of the selected muscles Tendon strain is defined as the stretch of the tendon divided by the tendon slack length To compute tendon strain SIMM finds the static equilibrium force in the muscle tendon actuator Thus the tendon strain depends on the settings of the active and passive toggle buttons see Section 2 5 8 Toggle Buttons and also on the current activation level if the active compo nent is turned on The sum of the moments of all the selected muscles consid ering at each X value only those muscles that generate posi tive moment That is at each value in the selected generalized coordinate s range of motion the moment of each selected muscle is calculated All of the positive moments are then added together to get the total positive moment If a muscle generates positive moment for some generalized coordinate values and negative moment for oth ers its moment will be included in the sum only when it is positive The sum of the moments of all the selected muscles consid ering at each X value only those muscles that generate nega tive moment That is at each value in the selected generalized coordinate s range of motion the moment of each selected muscle is calculated All of the negative moments are then added together to get the total negative moment If a muscle generates negative moment for some generalized coordinate
160. d by a column of data representing one standard deviation from the mean output strides output strides normalized 2 19 2 19 Skin Editor This toggle button is active when the gait button is on It controls the output of motion files containing the individual strides that are found during report generation A motion file is written for each stride with a name constructed from the motion name and the stride identifier e g r2 for sec ond right stride The files are written to the folder containg the gait report This toggle button is active when the gait button is on It works the same way as the output strides button described above except that each stride is normalized to contain 101 time steps Skin Editor The Skin Editor allows you to create edit and export deformable skins A skin is similar to a polyhedral bone in that it consists of a set of vertices and a set of usually pla nar polygons using the vertices However in a skin each vertex can translate relative to all of the body segments as the joints of the model are moved The position of each skin vertex is calculated as the weighted sum of a set of attach ment points that are rigidly attached to the body segments For example in a skin that covers a leg model a skin vertex near the knee might have attachments on the thigh and the shank and possibly the patella as well As the knee flexes each attachment moves with its body segment The position of the
161. d cdsdaddaaledaesnstabaedaerea ai 37 2 5 2 Command Menu st s5ce5canotate setae ead cccayieeatoteeee 39 2 5 3 Generating Curves from a Model eee 40 2 5 4 Plotting Data from Motion Files 0 0 0 eee 4 iii DED Y Variables sfvaczacsstesiersscdisecich ata 42 2 5 0 XeVOtlaDles lt u aaa eae we 46 2 5 7 Options FOF is cdstin Aoscautereanidieneatn ars 47 2 5 8 Toggle Buttons yivccatscctssteceieanlsdasieseenied dacecets 50 DO DOWIE dO A a ear ibe 53 2 6 1 Selector Ment 2266 etek paialeateceteon ances 53 2 6 2 Command Menu 425s sec pineeecrn teAitetativeh aes 53 2 653 Dof FOM ina ssS rea dei eis 55 2 6 4 Transform Order ccceceeccecessceesseeeeseceeeseeeees 56 2 6 5 Rotation Axes Form i 5 20 scciesedeasacscdvvccesssnavene 56 21 M scle Editor noan arrei e e Later Tete 57 DRI Selector Menin inaen a isis 57 2 7 2 Command Menu ss nsoenssnnnssenssenseeossnseesseesseese 58 2 7 3 Global Parameter Commands 000008 60 2 7 4 Force Parameters Panel ic iiceisedivandeedeeoscti eas 61 2 7 5 Attachments Panel M53 ca sedecsveysaisectseieiea Son 64 2 7 6 Current Path Panel 2 7 35n Annies 66 2 7 7 Selected Attachments Panel isc ssccctdscciseacbese 67 2 7 8 Model Window Commands cccccceeeees 68 2 8 Gencoord Editor soo ckenasy wold tae hedebatosyama dn Seton eter san 71 DBA Select Meni sonarai nenii 72 2 8 2 Command Menu 5523555 edscdscchecacdsyeddedectieseceseesse 72 2 8 3 Toggle B
162. d chang ing their attachment locations and weights You can then save your changes back to a DAE or SKN file Selector Menu The model selector lets you select the current model If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Skin Editor When you are done read ing it close the window using its close box You will be able to re open it at a later time by selecting help again 2 19 Skin Editor BM Skin Editor Model Full Body Model model gt save skin restore skin unselect all tibia_r write skin Group 2 19 2 save skin restore skin skin gt name Muscle kin Skin vertex 35623 weight x WE Z 0 441 0 03786 0 00604 0 01659 ke ski gt i te femur_r 0 123 0 04677 0 40290 0 01782 patella _r 0 436 0 06806 0 00230 0 02306 export as bone Choose Segment weighting femur_r l Figure 2 26 Skin Editor window Command Menu When you select this item a pop up menu is displayed of skins in the current model Selecting a skin makes it the cur rent skin for editing Its properties can then be viewed and edited using the buttons and forms in the tool window This command saves the current state of the current skin in the model It can be used in combination with the restore skin button to help you undo changes made while editing skins This co
163. d deletes all of the selected markers from the model This command restores all of the selected markers in the current model The markers are restored from a buffer that was saved last time you used the save all or save selected commands When you first create a model SIMM saves copies of all of the markers so you can restore them back to their original form without having to save them first This command restores all of the markers in the current model The markers are restored from a buffer that was saved last time you used the save all or save selected com mands When you first create a model SIMM saves copies of all of the markers so you can restore them back to their original form without having to save them first This command unselects all of the selected markers in the current model Marker Parameters This field shows the name of the selected marker If more than one marker is selected this field is blank and inactive The names of the markers in your model should exactly match the names of the markers in the tracked marker files that you load into the model although case does not mat ter For models that are used as mocap models the names of the markers must match the marker names in the marker sets that OrthoTrak recognizes See Chapter 5 Motion Module for more information on mocap models and the OrthoTrak marker set Chapter 2 Tools 111 2 12 Marker Editor 112 Chapter 2 Tools segment offset weigh
164. d muscle groups SIMM then displays a dialog box for adding or deleting individual muscles from the group This command allows you to create a new muscle group which initially has no members When you select it SIMM displays a dialog box for specifying the name of the group You are not allowed to specify the name of an existing group when making a new muscle group Global Parameter Commands These commands control parameters that are not specific to a particular muscle This field contains the color factor which is used to color all of the muscles according to their lengths When the fac tor is 0 0 this technique is not used and the muscles are col ored according to their material properties as specified in the muscle file However when the factor is greater than 0 0 the muscles are colored red when they are shorter than 2 7 4 inherit from default make unique 2 7 Muscle Editor their resting lengths blue when they are longer than their resting lengths and white when they are near their resting lengths By changing the value of the color factor you can change the transitions between blue white and red A higher factor means that a muscle s color is more sensitive to length change so that it will turn red more quickly when lengthening and blue more quickly when shortening Force Parameters Panel The Force Parameters panel gives you access to all of the parameters that govern the force generating behavior of t
165. d_color 234 Chapter 3 Input Files same folder as the archive it will not be read when the model is loaded If this parameter is on SIMM will write a script file each time the model is saved or closed The file is created in the same folder as the joint file and has the same base name with the suffix ssc The file contains commands to restore the settings in the Model Viewer Plot Maker Motion Reporter Motion Editor and Dynamics Tool to the same values as when the file was created This parameter can be changed within SIMM by right clicking on the background in the model window and choosing edit model preferences from the pop up menu read_script file on Note model archives contain their corresponding script files within the archive When you save an archive its script file will be updated and stored within it When you close a model that came from an archive the script file inside the archive is not updated with the latest tool settings If there are loops closed kinematic chains in your model you can use this parameter to specify whether the inverse kinematics solver is on or off it is on by default Specify the desired state after the keyword on or of f If the solver is on and there are loops in the model SIMM will try to assemble the model so that all the loops are closed using the default configuration as a starting point See Section 2 8 5 Inverse Kinematics for more information inverse kinematics solver
166. damping activationl activation2 mass timescale enddynamicparameters Figure 3 20 Example definition of dynamic muscle parameters beginmuscle defaultmuscle tendon force length curve 17 3 4 Muscle Files A sample lower limb muscle rectus femoris is shown in Figure 3 22 The muscle path is defined by four points for illustration only it does not represent a realistic path The first point is a fixed point attached to the pelvis The second point is a moving muscle point in the pelvis frame Its X coordinate is a function 3 of the gencoord hip flexion its Y coordinate is a function 7 of the gencoord hip adduction and its Z coordinate is a constant 0 096 The third point is a via point defined in the femur frame and is included in the path only when knee_angle is between 120 and 80 degrees This is done so that the muscle path wraps over the femur when the knee is flexed beyond 80 degrees The fourth point is a fixed point attached to the patella The muscle is a member of two groups hip flexion and knee extension which means that the muscle name will appear in those two muscle group menus in the Model Viewer and Plot Maker The muscle definition also lists the values for the four muscle tendon parameters F M amp a Pennation angle must be specified in degrees Since the curves that specify the force length relations of the muscle must use this name for default muscle force length curve for
167. date with each frame of IK data as it is calculated How ever all SIMM commands e g to change the model view are still unavailable until the motion import is complete When this option is turned on SIMM will read personal dat with each motion trial and update the subject information in the Motion Reporter accordingly When this option is turned on SIMM will write to the gen erated motion the positions in the ground frame of all of the model s markers These are not the positions of the recorded markers in the input motion Instead after SIMM solves a frame of the motion the markers attached to the model are converted to the ground frame and added to the output motion This feature is useful if you want to keep a record of the closeness of the fit between the model markers and the recorded markers It is also useful if your recorded markers are noisy or have missing frames and you want your output motion to contain complete data for every marker for every frame For C3D import only This option allows you to choose from which parameter field in the C3D file to read the X axis units start at zero auto load analog files 5 2 Opening Tracked Marker Files names of the tracked markers Because the POINT LABELS field in a C3D file is limited to four characters some soft ware 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 n
168. del It saves the joint to a buffer so that you can restore it if you 2 6 3 rl r2 r3 tx ty tz 2 6 Joint Editor create a model SIMM saves copies of all of the joint descriptions so you can restore a joint back to its original form without having to save it first Dof Form The dof form on the left of the Joint Editor window gives you access to each of the six degrees of freedom dofs in the current joint see Section 3 3 3 Joints for a description of the six dofs If the dof is a constant you can change the value by selecting its field with the left mouse button and then typing in a new value You can change it to a function by right clicking on the field and selecting function and then a generalized coordinate from the pop up menu If the dof is a function you can right click on the field and choose from the pop up menu to change it to a constant change the gen eralized coordinate used in the function or send the func tion to the Function Editor for editing If you change a dof from a constant to a function SIMM creates a new function to use for the dof This new function is given two control points whose X values are 360 0 and 360 0 and whose Y values are just below and just above the value of the dof when it was constant If you change a dof from a function to a constant its value is initially set to the average of the Y coordinates of the function s control points If you have closed loops in your model and the I
169. del If the subject mass is specified in per sonal dat in the field Weight that value will be used to initialize the field in the dialog box Chapter 5 Motion Module 333 5 3 Using the Mocap Model preserve mass distribution load personal dat read marker names from save JNT file save MSL file 334 Chapter 5 Motion Module This field specifies whether or not the mass distribution in the unscaled mocap model should be preserved in the scaled model the alternative is to scale the mass of each body seg ment based on its geometric scaling For more information on scaling mass parameters see Section 5 3 4 Scaling the Mocap Model Whichever method you choose the final mass of the scaled model will always be equal to the mass specified in the subject mass field only the distribution of that mass among the various body segments will be different 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 personal 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 origin offsets 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 o
170. derivative controller to determine the moments necessary to drive a model to follow the input motion Consult the Dynamics Pipeline manual for more information about this feaure This field shows which function is currently being used as the gencoord s restraint function used during dynamic sim ulations and for inverse kinematics with closed loop models when the gencoord is unclamped If the gencoord has no restraint function you can right click on this field and select make new from the pop up menu SIMM will create a new function based on the gencoord s range of motion and use it as the restraint function If this field shows the index of a function e g f 1709 you can right click on the field to display a pop up menu with three options Choose edit to send the function to the Function Editor for editing choose make new to create a new function and use it as the genco ord s restraint function and choose delete to remove the function as the gencoord restraint function the function itself is not deleted Chapter 2 Tools 75 2 8 Gencoord Editor 76 keys 2 8 5 inverse kinematics Chapter 2 Tools The keys display show you which keys control the current gencoord See Section 2 4 6 Model Window Viewing Com mands for a description of how keyboard keys can be used to change a gencoord s value Inverse Kinematics The inverse kinematics IK toggle button allows you to turn loop solving on and off When the
171. ders 30 model based script file specifying in joint file 233 moment arm defined 43 moment defined 42 moment maxforce defined 44 Motion Editor 163 172 command menu 163 information header region 163 176 motion files 286 297 opening 13 saving 17 specifying in joint file 232 287 Motion Module 311 345 importing IKS files 327 opening analog data files 321 opening C3D files 312 opening TRB C files 312 opening XLS files 321 real time import 324 motion objects 293 296 defined 287 specifying in joint file 268 specifying in motion file 293 Motion Reporter 172 181 command menu 176 output file form 179 subject information form 179 motions adding events 166 animating 30 33 cropping 166 deleting 165 displaying continuously 23 dividing into steps 165 editing 165 normalizing 164 playback options 167 saving to files 164 smoothing 165 movie files 303 movies 27 28 auto loading 318 auto movie mode 27 choosing AVI file 27 Index 5 motion movies 28 using default file name 27 Muscle Editor 57 71 command menu 58 force parameters panel 61 information header region 57 model window commands 68 moving muscle attachment points 70 selecting muscle attachment points 69 muscle files 277 286 opening 12 saving 17 specifying in joint file 232 277 muscle force functions editing 61 muscle groups in dynamic simulations 157 muscle menu defined 8 muscle orientation defined 45 muscle parameters activation defined 63 editing 62 ma
172. des normalized K pl_wn7 Figure 2 25 Motion Reporter window Chapter 2 Tools 173 2 18 Motion Reporter 174 Chapter 2 Tools 2 18 1 ing directory the DLL the output variables the system parameters and the smoothing parameters must all be set appropriately before creating the report Because the dynamic simulations are performed through the Dynamics Tool you have an opportunity to customize them For example in a standard gait report you might include graphs of EMG activity for the few muscles that were recorded With the Motion Reporter and Dynamics Tool you can choose to include all of the muscles in the simula tion and optimize their activations to generate the inverse dynamics moments The gait report will then contain graphs of estimated activations for all of the muscles with some guided by the input EMG If the gait option is turned off SIMM will not perform any cropping or vetting of the motions before creating the report It will assume that each selected motion is of the same activity with approximately the same starting and ending positions It will perform a dynamic simulation on each motion if needed and then normalize it to contain 101 time steps It will then calculate means and standard devia tions of all of the selected report variables If the gait option is turned on SIMM will assume that each motion represents one or more walking strides indicated by heel strike and toe off events
173. displayed containing a list of the motions that have been linked to the current model When you select one of the motions the model begins at the cur rent time value of that motion and proceeds at the rate spec ified in the motion speed field The start button is changed to read stop to indicate that the motion is active If the oop motion checkbox is turned off for this motion in the Motion Editor the animation will stop when it reaches the last frame of motion data If Joop motion is on the animation will continue until you click on the stop button Because this procedure repeatedly draws the model in the model window it can slow down the computer making it difficult Chapter 2 Tools 23 2 4 Model Viewer 24 look at gt drawmode gt Chapter 2 Tools to execute commands in other windows So although you can start an animation and then open other tools and make plots for example this is not advised You should also avoid changing the model view while the animation is pro ceeding If you need to change the view of the model stop the animation first then restart it after positioning the model appropriately This command lets you change the body segment that is fixed in space for display purposes only The origin of this segment will not move as you flex the joints in your model but it may rotate about its origin as the joints move This command is particularly useful if you want to zoom in on a body segment that
174. dron that already has correct or cus tomized normals that norm would modify e g because the polyhedron has holes or portions that are inside out The number in this field is the tolerance that norm uses to remove duplicate vertices All vertices within tolerance of each other are merged into one vertex A tolerance value of 0 0 will turn off vertex tolerance checking These fields specify the X Y and Z translations of the bone within its segment s reference frame These fields specify the X Y and Z rotations of the bone within its segment s reference frame These rotations are applied in a body fixed manner in the order X then Y then Z i e an Euler XYZ rotation It is recommended that you apply one rotation at a time so that the axis of each rotation remains parallel to one of the axes of the body segment s reference frame These fields specify the X Y and Z scale factors of the bone relative to its original size 2 15 5 p 5 2 15 Bone Editor Model Window Commands Bones polygons NURBS patches and polyhedron vertices can be selected and edited using keyboard and mouse com mands in the model window To use these commands you must first set the tool mode to the Bone Editor by clicking on the Bone Editor icon in the heads up display HUD on the left side of the model window To indicate that all key board and mouse commands are being directed to the Bone Editor the icon will be highlighted with
175. duplicate vertices All vertices that are within num units of each other will be merged into one vertex A value of 0 0 which is the default stops norm from checking for dupli cate vertices fill in holes in the polyhedra As norm processes a polyhe dron it will find holes in it and attempt to fill them in with Chapter 4 Norm 307 308 Chapter 4 Norm es num con tri CCW rn opt triangles If the polyhedron contains large holes norm may have difficulty filling them this option lets you specify the maximum allowable length for edges in the polyhedra If norm finds any edges with a length greater than num it will subdivide them until they are shorter than this length Norm does not create additional polygons during this process it just inserts vertices into existing edges make all of the polygons in the file convex Norm will split off pieces of concave polygons making new triangles until all of the polygons are convex triangulate all of the polygons in the file Norm will divide all polygons with four or more edges into triangles tells norm that all polygons are ordered in a counter clock wise direction i e the vertices within each polygon are specified counter clockwise If you use this option norm will not reorder any polygons but will calculate vertex nor mals assuming that all of the polygons are counter clock wise tells norm that all polygons are ordered in a clockwise direction i e
176. e bone export gt 140 Chapter 2 Tools This command deletes the selected polygons There is no way to undo this operation except by reloading the bone file However in some cases you may be able to fill in holes created by deleting polygons by running norm on the bone with the fill holes option This command lets you change the selected edge of the selected polygon by scrolling through them It works only if there is one selected polygon This command splits the selected edge in half causing each of the two polygons which use it to be split into two pieces This command reverses the directions of the normal vectors for the selected polygons It then recomputes the vertex nor mals for the bone This command deletes all of the currently selected vertices This command unselects all selected polygons on bone 1 including those that are hidden using the F10 key This command moves bone to the chosen body segment It leaves the bone in its current position relative to the rest of the model but transforms the vertex coordinates so that they are expressed in the new segment s reference frame It then runs norm on the bone using the current set of parame ter values in the norm options region This command writes bone to a file It displays a file browser to let you specify the name and location of the file This command deletes bone 1 This operation cannot be undone This command allows you to export grou
177. e model using the restore pose command in the Model Viewer Chapter 2 Tools 73 2 8 Gencoord Editor 74 Chapter 2 Tools 2 8 4 value tolerance default value Gencoord Form The gencoord form in the lower left corner of the Gencoord Editor window contains numerical fields for the gencoord properties The current value of the gencoord is displayed in this field If the gencoord is part of a loop changing its value will cause the inverse kinematics solver to try to keep the loop closed by changing the other gencoords in the loop while keeping the current gencoord constant If it cannot find a solution at the current gencoord value it will find the clos est one If the current gencoord is locked its value cannot be changed by typing in a new value If the gencoord is clamped you cannot change its value to a number outside its specified range The tolerance of a gencoord is used when the gencoord is set to a new value If the difference between the new value and the current value is less than the tolerance the new value is ignored and the gencoord remains unchanged This tolerance feature can be useful when you are importing a motion which contains identical or similar gencoord values for some periods of time By setting the tolerance of each gencoord to say 0 5 degrees small changes in gencoord values will not result in the joint transformation matrices being recalculated thus saving some computation time This
178. e percent of gait cycle at which it occurs in the motion New events created using this feature will not appear in any existing plots but will appear in any new plots created from the motion When you select this item a pop up menu of existing events is displayed The first item in the pop up menu new event creates a new event named event_x adds it to the current motion at time 0 0 and makes it the current event for edit ing name x coord 2 17 5 show markers show marker trails lines 2 17 Motion Editor This field contains the name of the event Events that SIMM calculates are labeled r or l for right and left followed by hs for heel strike and to for toe off This field contains the value of the X coordinate at which the event occurs For motions that have been normalized the X coordinate is percent of gait cycle For most other motions the X coordinate is time in seconds Playback Options The checkboxes on the right side of the Motion Editor win dow allow you to change some display and evaluation options when animating a motion Each option is described below This option toggles the display of marker data in the motion which are usually shown as blue spheres This option does not affect the display of the markers attached to the model the pink spheres If there is no marker data in the motion this option is grayed out You can right click on the check box to display a dialog box sh
179. e them left and right left mouse button 2 9 3 2 9 Plot Viewer These keys allow you to zoom independently in the X and Y directions within the plot window Pressing the x key will zoom in in the X direction on a part of the plot and press ing the x key and the Shift key will zoom out and simi larly for the y key When you click the left mouse button in a plot window a cross hair is placed at the cursor location and the coordi nates of that point are displayed next to it You can place up to 30 cross hair points in each plot window As you zoom in on a particular cross hair using the i key the precision of the displayed coordinates is increased so that you can more accurately note the point s location To remove all cross hair points from the plot right click in the plot window and choose the delete points option Live Plot Curves A live plot curve is a plot of a muscle property that is updated automatically whenever any property of the muscle changes Live plot curves are very useful when creating and modifying muscles because you can instantly observe the effects of moving an attachment point or a wrap object or changing any other property on the length moment arm or force of the muscle To make a plot curve live right click on the curve name in the plot key and choose live from the pop up menu A lower case l will be displayed on the left side of the key to indicate that the curve is live Whenever any ch
180. e Section 3 3 3 Joints for an explanation of the loop joint When the loop is properly enforced the points on the two segments are coincident and the distance is zero When the loop is not properly enforced the loop joint disarticu lates and the two points are separated by a certain distance This parameter specifies how large a distance is considered acceptable Its value can also be specified in the joint file as described in Section 3 3 Chapter 2 Tools 717 2 9 Plot Viewer 78 2 9 2 9 1 delete points of interest delete labels reset view calculate mean of all curves show motion cursor hide motion cursor Chapter 2 Tools Plot Viewer The Plot Viewer lets you change the views of the plots With this tool you can zoom in on a particular region of a plot curve as well as display the coordinates of any point in a plot The tool window available in previous versions of SIMM has been replaced with a pop up menu that is dis played when you right click in the plot window Thus you can now access all of the Plot Viewer commands from within the plot window The commands in the pop up menu are described in the next section and the other available commands are described in Section 2 9 2 Pop up Menu This command deletes all of the points of interest that have been added to the plot using the left mouse button as described in Section 2 9 2 This command deletes all of the labels that have been added to the p
181. e box You will be able to re open it at a later time by selecting help again Command Menu When you select this item a pop up menu is displayed of motions linked to the model Selecting a motion makes it the current motion for editing Its properties can then be viewed and edited using the forms and sliders in the tool window Chapter 2 Tools 163 2 17 Motion Editor la I Motion Editor Model Gait Model model gt motion save to file normalize smooth divide into strides delete motion delete event edit motion save to file normalize 164 Chapter 2 Tools name lhs coord 1 1948 Mame walk2 events playback options J show markers marker trails lines marker trails points J show foot prints gj show force plates gj show external forces jj loop motion show force trails E show joint torques J show moments show joint forces cropping Figure 2 24 Motion Editor window This command allows you to save the current motion to a file When you select it a file browser will let you choose the output file to create or overwrite This command normalizes the current motion so that it con tains 101 time frames It fits a natural cubic spline to each column of data and evaluates it at 101 evenly spaced inter vals It also adds a new column called percent to the motion with values from 0 0 to 100 0 This column becomes the new X column meaning that it
182. e by selecting help again Command Menu Select this command to create a new wrap object or to select an existing wrap object for editing When you select this item a pop up menu of existing wrap objects is displayed The first item in the pop up menu new wrap object creates a new wrap object named Wrap _1 adds it to the current model and makes it the current wrap object for editing The Chapter 2 Tools 83 2 10 Wrap Editor 84 segment gt muscles gt save all restore all delete Chapter 2 Tools remaining items in the pop up menu allow you select exist ing wrap objects for editing Select this command to change the body segment to which the current wrap object is attached defined as the parent segment When you select this item a pop up menu of the model s segments is displayed Choosing a segment from this menu will reassign the current wrap object to the selected segment The wrap object s overall position will not change when it is assigned to a new segment How ever when the model is animated the wrap object will fol low the movement of its new parent segment This command lets you choose the set of muscles that wrap over the current wrap object When you select this item a pop up menu of the muscle groups is displayed Choosing a muscle group from this menu causes it to appear at the bot tom of the Wrap Editor window If the chosen muscle group is already displayed at the
183. e current motion speed setting and how long it takes to display one frame of data After creating the movie SIMM will modify the frame rate of the movie file so that it plays back at the speed specified by this preference For example if MOTION MOVIE _SPEED is defined as 50 0 the resulting movie will play at 50 of the motion s original speed as defined by the time column If this preference is not specified or is not a positive number the motion speed Appendix B SIMM Resources B 13 B 1 Preferences CONFIRM REPORT SIMULATIONS NORM_IMPORT_ TOLERANCE AUTO MOVIE FRAME RATE SKIN _EXPORT_TO MAYA B 14 Appendix B SIMM Resources setting in the Model Viewer is used to set the playback speed of the movie This preference specifies whether or not to display a confir mation dialog box that must be dismissed before generating a motion report If this preference is on the dialog is displayed when generate report is selected if the report requires the run ning of at least one dynamic simulation to calculate kinetics variables This preference specifies the vertex tolerance when importing certain bone files into SIMM When a bone file is read into SIMM if it does not already contain a normal vector for each vertex then it is processed by Norm to calculate them During processing Norm merges all vertices that are within NORM_IMPORT_ TOLERANCE of each other If this preference is not specified the default vertex tolerance is 0
184. e currently ignored by SIMM A complete description of the OBJ format can be found on various web sites including http en wikipedia org wiki Obj Note when a musculoskeletal model is loaded into SIMM all of the model s bones that are specified in the Wavefront OBJ format are automatically processed with norm to Object chair obj Vertices 1098 Faces 1585 MATO LAGNA G O S927 BO CA059S Vie 9 Onley eet 49338 500i 49109 71910 vn 1 640098 4 029196 10 036920 W SS 9IOTHS 19 205900 Woo SIS2 U l Bl pA E DBLP Appl Figure 3 3 Example bone file in Wavefront OBJ format 3 2 5 3 2 Bone Files ensure that the vertex normal information is complete For bones with many polygons this can add significantly to the time it takes to load a model Thus for large bone files it is recommended that you convert them to the SIMM ASCII format before adding them to your model STL SIMM also supports bone files in both the ASCII and binary STL formats both are identified with the st file suffix This is a format originally developed for stereolithography CAD systems but is also commonly used when reconstruct ing 3D objects from 2D medical image data An example of the ASCII STL format is shown in Figure 3 4 A polyhe dron is specified as a series of unconnected facets usually solid facet normal 0 432299 0 719353 0 543736 outer loop vencen IZ e AGIG00 VOL S2AOO IL AAO sye syal venter LAs 5 WO A500
185. e defined in the joint file see Section 3 3 for details SIMM will automatically read and write a script file for that Chapter 2 Tools 19 2 4 Model Viewer 20 2 4 2 4 1 model gt Chapter 2 Tools model If you want to save a model script file manually e g after specifying various tool settings for a model with read_script_file turned off make the model window the active window and select File Save Model Script from the menu bar SIMM will create a script file in the same folder as the joint file with the same base name as the model but with the suffix ssc The file will contain commands to restore the settings in the Model Viewer Plot Maker Motion Reporter Motion Editor and Dynamics Tool to the same values as when the file was created Model Viewer The Model Viewer allows you to change the views of the musculoskeletal models You can rotate scale and translate a model into any viewing perspective as well as choose which muscles to display on the bones There are also com mands to display shadows of the body segments and start or stop a continuous animation of a model Figure 2 1 You can also create TIFF images or AVI movies of the model window using this tool Some of the viewing commands that are available from within the Model Viewer window can also be performed by pressing keys while the model window is the active i e topmost window These key sequences serve as short cuts so that you can
186. e desired ellipsoidal wrapping technique The three techniques hybird mid point and axial are described in detail in Section 2 10 5 Ellipsoidal Wrapping Methods The method you choose with these radio buttons will be used for this muscle only When you choose the wrapping method in the Wrap Editor it will set the method for all muscles which are associated with that wrap object Current Path Panel This panel shows the attachment points that define the path of the current muscle in the current body position These points are determined by using the current generalized coor dinate values to calculate the locations of the moving points the on off state of the via points and whether the muscle wraps over any wrap objects The list is updated in realtime as the body moves or as you edit the attachment points The first three columns show the XYZ coordinates of the points with respect to the body segments to which they are attached The next column shows the body segment and the last column shows the type of attachment point 2 7 7 2 7 Muscle Editor Current Path The list of active points for deltoid2_r X WE Z 0 004610 0 136110 0 005600 0 021910 0 005250 0 054220 0 003857 0 015762 0 041186 0 001986 0 012206 0 035376 0 005753 0 000809 0 012058 0 025360 0 000200 0 009440 Segment Type humerus_r fixed DELT2pt2a_r moving scapula_r wrap delt2_r scapula_r wrap delt2_r scapula_r fixed scapula_r fixed Figure 2 6
187. e filtered signal The calculated values are stored in the motion file in an auxiliary data column that is linked to the EMG column e g semimem_r and semimem r aux When this option is off the moving window smoothing algorithm described below is used instead These parameters are used to smooth EMG data when the use Bayes filter for EMGs option is turned off When SIMM uses this type of processing it rectifies the signal then smooths it using a moving average algorithm The window size for the moving average is specified by the EMG moving save HTR file save motion file 5 2 3 5 2 Opening Tracked Marker Files window size field and the number of times that the algo rithm is applied to the data is specified by the EMG smooth ing passes field Save Options 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 another software pack age 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 allows you to save a SIMM motion file contain ing 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
188. e folder containing the bone files used in the model SIMM will look in this folder first to find each bone file but if a particular file is not found SIMM will search in other folders as well Thus SIMM might open some bone files from one folder and other ones from another folder The complete list of folders SIMM will search for bone files is given in Section 3 2 Bone Files This parameter can be changed within SIMM by right click ing on the background in the model window and choosing edit model preferences from the pop up menu bone_path bones If this parameter is on SIMM will read a script file each time it loads the model This file must be in the same folder as the joint file and must have the same base name with the suffix ssc This file can contain any SIMM script com mands but it is designed to contain commands to specify settings in the tools It is particularly useful for specifying the output variables for the Motion Reporter and Dynamics Tool so that you do not need to reselect them each time you load the model This parameter can be changed within SIMM by right clicking on the background in the model window and choosing edit model preferences from the pop up menu read_script file on Note model archives contain their corresponding script files within the archive If there is a separate script file in the Chapter 3 Input Files 233 3 3 Joint Files write script file inverse kinematics solver backgroun
189. e 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 options for importing the static average from frame to frame subject mass 5 3 Using the Mocap Model static c3d Options markers 56 frames 550 data rate 120 0 Hz Mocap Model D GaitAnalysis Model G aitModel jnt Browse Import Static Trial Static C3D file OK __ Cancel Cancel average from frame 1 to frame 550 subject mass 175 000 V preserve mass distribution read marker names from POINT LABELS Export Scaled Model I save JNT file I save MSL file ii Figure 5 2 Static Trial Import Dialog Box pose In many cases you will want to use the default set tings for these options so you can simply click the OK but ton to import the motion The following list describes each option in the dialog 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 initial ized to 1 and the number of frames in the file meaning that all frames will be averaged If frames in the chosen sequence are missing some markers locations for markers that are present will still be used in the average This field allows you to specify the mass of the motion cap ture subject The units should be the same as the units used in the mocap mo
190. e selected muscles This length depends only on the locations of the muscle attach ment points and the current configuration of the model s joints The origin to insertion length of the selected muscles divided by their respctive lengths in a neutral position By default the neutral position is the anatomical position all gencoord values equal to zero However if the USE_DEFAULT POSE FOR NORMALIZATION preference is set musculotendon velocity moment arm moment arm numerical gt 2 5 Plot Maker to yes then instead of the anatomical position SIMM will use the default pose of the model This Y variable is useful when you want to compare muscle lengths between differ ent subjects during an activity The contraction lengthening velocity of the muscle tendon actuator When plotting versus a gencoord the velocity will always be zero When plotting versus a motion the genco ord velocities from the motion data will be applied to the model in order to calculate musculotendon velocity The moment arm of the selected muscles with respect to the chosen generalized coordinate The generalized coordinate is chosen from the moment arm submenu which appears when you move the cursor off the right side of the moment arm selection You cannot compute the moment arm of a muscle with respect to a motion variable so the submenu lists only true generalized coordinates The moment arm depends only on the locations of the muscle attachment p
191. e which format the bone file is in SIMM can import all of the five formats but can only output bone files in the ASCII format see Sec tion 2 15 Bone Editor for information on writing bone files SIMM comes with a conversion utility called norm that can also import all five bone file formats as well as out put three of them ASCH old ASCH and binary Norm is located in the directory where the SIMM executable resides In addition to converting between different file for mats norm processes bone files by calculating vertex nor mals checking the vertex and polygon lists for inconsistencies and optionally translating and rotating bones and filling holes in their surfaces see Chapter 4 Norm for details To locate bone files that are referenced in a joint file SIMM searches the folders in the following list in the order shown If a particular folder does not exist or the bone file is not found in it SIMM proceeds to the next folder in the list 1 the folder specified by the bone path parameter in the joint file 2 the folder bones in the folder containing the joint file 3 the folder containing the joint file Chapter 3 Input Files 223 3 2 Bone Files 224 Chapter 3 Input Files 3 2 1 4 the folder specified by the BONES FOLDER preference this preference if not defined by the user defaults to Simm Resources bones 5 the folder Simm Resources mocap bones SIMM ASCII The first bone file format is t
192. each gencoord that you include you must specify all of the parameters name value velocity clamped state and locked state For each muscle that you include you must specify name activa tion visibility state It is recommended that you no longer specify default_value in a gencoord definition in a JNT file or activation or visi ble in a muscle definition in a MSL file If you do SIMM will add attempt to add those parameter values to the default pose of the model whether the default pose is user defined or SIMM generated If they are already defined in the default pose SIMM will ignore the values specified in the gencoord and muscle definitions When you save a JNT file SIMM will output the default pose but not the default_values in the gencoord definitions or the activation and visible settings in the muscle definitions In order words if you do not define a default pose in the JNT file SIMM will build one using values specified in the gencoord and muscle definitions If you do define a default pose all conflicting values specified in the gencoord and muscle def initions will be ignored And when exporting a model all pose related values are written to the default pose and not to the gencoord and muscle definitions Chapter 3 Input Files 275 3 3 Joint Files Pose representing mid stance of right foot during gait beginpose right stance gencoord lower torso TX 0 427888 1 265419 unclamped unlocked gencoord lower t
193. ear transform in 2 13 Constraint Editor Transforming Constraint Objects The collection of controls labeled transform can be used to move and rotate the current constraint object within its par ent segment s frame of reference The current constraint object s transformation can be modified interactively in the model window or it can be modified precisely by entering values in the translate or rotate fields of the Constraint Edi tor window INTERACTIVE CONSTRAINT OBJECT TRANSFORMATION The current constraint object can be moved rotated and scaled using the model window commands described in the previous section or by entering specific values into the numerical fields in the Constraint Editor window as described below NUMERICAL CONSTRAINT OBJECT TRANSFORMATION To apply precise transformations to the current constraint object first enter the distances and angles to transform by in the translate and rotate fields then click the button below the text fields one or more times to apply the transform If the transform in local frame radiobutton is selected then the specified transform will be applied relative to the constraint object s local XYZ axes Otherwise the transform will be applied relative to the constraint object s parent segment s XYZ axes To apply the inverse transform click the but ton The values you enter into these fields remain there even after they are applied To clear all values from the translate and ro
194. eater than sign on the right side of the item box For example the model selector which displays a pop up menu of the models is labeled model gt A muscle menu is a special type of menu Muscle menus group muscles according to group names assigned in the muscle file e g hip flexors see Section 3 4 Muscle Files When you click the left mouse button on one of the items in a muscle menu the corresponding muscle is selected and the box to the left of the muscle name is highlighted When you click the left mouse button on that item again the mus cle is unselected Several of the tools display the muscle menus but selecting a muscle in one tool s menu does not mean that it is selected in another tool s menu For example the Model Viewer and Plot Maker each display separate copies of the same muscle menus When you select a mus cle in the Model Viewer it changes the model view but does not select the muscle within the Plot Maker If you want to generate a plot curve for that muscle you must also select it from the muscle menu in the Plot Maker To make it easier to select and unselect large groups of mus cles the title bar of each muscle menu also has a special function If one or more muscles in a menu are unselected then clicking the left mouse button in the title bar of that menu causes all of the muscles to be selected If all of the muscles are already selected then when you click in the title bar they become unselected
195. ect the use of model window viewing commands If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Model Viewer When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again Command Menu This command restores the camera view of the current model to one that you had previously saved When you select this command a pop up menu of the available views is displayed Selecting one will restore the camera view to the one saved in that buffer See the save camera command for directions on saving a camera view This command saves the current camera view of the model to a buffer When you select this command a pop up menu of the current view buffers is displayed Selecting one will save the current model view to that buffer overwriting the previous one You can also select make new camera from the menu to create a new camera view See the restore cam era command for directions on how to restore the camera once you have saved it This command restores the pose of the model to one that you had previously saved A model pose contains the values and velocities of all of the gencoords as well as the activa tions and display state visible invisible of all of the mus cles When you select this command a pop up menu of the available po
196. ects associated with the deformity will be adjusted such that their individual deform percentages match the defor mity slider s percentage Holding down the Alt or Ctrl keys and clicking the reset button just above the deformity sliders will automatically reset all deformity sliders to their default values In addition to controlling multiple deform objects you may find it useful to set up deformity sliders to control individual deforms This allows you to specify a meaningful range of values for a specific deform control the deform s default value when the model is first loaded and adjust the deform object s percentage without having to make it the current deform object To create or modify deformity sliders you must edit the model s joint file manually then reload the model There is no way to add remove or modify deformity sliders interac tively within SIMM Deform Tips Techniques and Caveats The following list describes each element of a SIMM model that is deformed when it falls within the outer box of a deform object 1 bone surfaces Bone vertices for all bones in the segment are deformed However bone vertex normals are not deformed Therefore you may notice irregular shading of deformed bone surfaces 2 distal joint centers The origin of each joint emanating from the segment is deformed However the joints DOFs and kinematic functions are not deformed Chapter 2 Tools 107 2 12 Marker Editor 108 Chap
197. ects that involve the same gencoords the IK solver will solve the loop_tolerance 2 8 Gencoord Editor loops and constraints simultaneously That is when a gen coord value is changed or joint kinematics are modfied the IK solver will adjust all of the other gencoords in order to enforce all loops and constraint objects at the same time In some cases having loops and constraint objects that involve the same gencoords may make finding a solution more diffi cult because there are more constraints on the gencoords that can be adjusted If this problem arises you may want to soften the constraint objects by adjusting the weight of the constraint points as described in Section 2 13 6 Constraint Point Attributes Note if you turn off the IK solver using the inverse kine matics toggle button SIMM will still enforce the constraint objects This parameter specifies the acceptance level for the solu tions that the solver module reaches when implementing the loop constraints It does not affect the speed or accuracy of the loop solving Rather it is a cutoff value specifying whether or not the solution is acceptable If it is not accept able a dialog box may be presented indicating that the loop constraint is not satisfied this notice appears only when loading or editing a model not when changing gencoord values This tolerance value corresponds to the distance in model units between the two segments of the loop joint se
198. ed the results calculated so far are stored in the motion 2 16 8 gencoord values gencoord velocities gencoord accelerations muscle activations muscle lengths muscle forces 2 16 Dynamics Tool Output Variables The checkboxes in this region specify which variables are calculated during the simulation and saved in the output motion When the initialize button is pressed the output motion is created with the appropriate columns to hold all of the selected variables These columns are initially filled in with zeros and are overwritten with the simulation results as each time frame is calculated To select or deselect an output option click the left mouse button on the checkbox To select individual model components for each output option click the right mouse button on the checkbox and choose components from the dialog box For example if you right click on gencoord values SIMM will display a dialog box allowing you to select which gencoord values you want to output If you right click on muscle lengths SIMM will display a dialog box of the muscles in the model Below is a list of the available output variables the values of the generalized coordinates In most cases you will want to keep this option on so that you can see the results of the simulation However one case if which you would not is when you are outputting gencoord moments corr See the description of that option for details the velocities of the genera
199. ed in the Dynam Chapter 2 Tools 63 2 7 Muscle Editor 64 Chapter 2 Tools 2 7 5 ics Pipeline manual To change the value of one of these parameters click on its field and type in a new value If the field is grayed out it means that this parameter is inherited from the default muscle and cannot be edited If you want to modify the parameter for this muscle only then you must first right click in the field and choose make unique from the pop up menu This will give the muscle its own copy of the parameter from the default muscle which you can now edit by left clicking on the field To remove the muscle s own copy of the parameter and instead have it inherit it from the default muscle choose inherit from default from the pop up menu If you want to edit the default muscle s copy of the parameter you must first select the default mus cle using the muscle button Attachments Panel This panel gives you access to all of the parameters that define the paths of the muscles At the top of the panel are the fixed via and moving attachment points The checkbox to the left of each attachment point allows you to select and deselect the point To change the body segment to which a point is attached click on the name of the current segment and choose a new one from the pop up menu For each X Y and Z coordinate of an attachment point if the coordinate is a constant you can change the value by selecting its field with the left
200. eform object within a segment Figure 3 15 shows a typical auto reset deform object specification Deform Object Fields These fields specify the dimensions of the deform object s inner box All bone vertices distal joint centers muscle attachment points and wrap objects within the deform object s inner box will receive the full effect of the object s deformation These two keywords must each be followed by three numbers that specify an XYZ coordinate in the deform object s reference frame The default values for innermin are 0 03 0 03 0 03 and the default values for innermax are 0 03 0 03 0 03 These fields specify the dimensions of the deform object s outer box The object s deforming effect is limited to the region enclosed by its outer box These two keywords must each be followed by three numbers that specify an XYZ coordinate in the deform object s reference frame The default values for outermin are 0 04 0 04 0 04 and the default values for outermax are 0 04 0 04 0 04 deform my auto reset deform autoreset yes translationonly yes innermin 0 05 0 44 0 08 innermax 0 05 outermin 0 07 0 45 0 1 outermax 0 07 0 05 0 08 0 1 0 1 xyz body rotation POSITION 33 6900 25 6600 16 1100 translation POSITION enddeform 0 0153 0 0279 0 0287 Figure 3 15 Example of an auto reset deform Chapter 3 Input Files 265 3 3 Joint Files xyz_ body rotation POSITION translation POSITION xyz_ body
201. eginpoints 0 029 0 031 0 096 segment pelvis 3 hip flexion 7 hip adduction 0 096 segment pelvis 0 033 0 403 0 001 0 012 0 043 0 001 endpoints begingroups hip flexion knee extension endgroups segment femur ranges 1 knee angle 120 80 segment patella wrapobject distal femur ell midpoint range 2 1 max_force optimal fiber length tendon_slack_length pennation_ angle min thickness 0 004 max thickness 0 008 780 0 Newtons 0 0840 meters 0 3460 meters 5 0 degrees min material muscle min max material muscle max endmuscle 282 Chapter 3 Input Files Figure 3 22 Example muscle definition 3 4 Muscle Files current activation level when calculating muscle forces see Section 2 5 Plot Maker for more details You can also optionally specify the minimum and maxi mum thicknesses and materials of the muscles At an activa tion of 0 0 a muscle will be drawn with material min_material and a thickness of min_thickness At an activation of 1 0 material max_material will be used and its thickness will be max_thickness For activations between 0 0 and 1 0 a linear combination of the min and max values for the material and thickness will be used If you do not specify values for these parameters SIMM will calculate reasonable defaults To indicate that the muscle should wrap over a wrap object defined in the model s joint file you must specify an associ ation between the muscle
202. eight segment tolerance cl 0 0900 0 1800 0 0520 1 0000 r scapula 0 001 c2 0 0950 0 1400 0 0700 2 0000 r scapula 0 001 c3 0 0550 0 0900 0 0550 1 0000 r scapula 0 002 endpoints endconstraintobject Figure 3 18 Example constraint object A constraint object is defined by a geometric primitive e g sphere fixed to one body segment and one or more points fixed to other body segments The points are constrained to remain on the surface of the geometric primitive at all times The fields in a constraint object definition shown below Chapter 3 Input Files 271 3 3 Joint Files constrainttype segment xyz_ body rotation translation object dimensions 272 Chapter 3 Input Files specify the size position and orientation of the geometric primitive as well as the locations of the points Constraint Object Fields This field specifies the type of the geometric primitive The available types are sphere ellipsoid cylinder and plane If no type is specified the default type sphere is used This parameter specifies the body segment to which the geometric primitive constraint object is attached This parameter specifies the orientation of the constraint object as an XYZ Euler rotation The orientation is calcu lated by first applying the X rotation around its local X axis then the Y rotation around its new local Y axis and finally applying the Z rotation around its new local Z axis If the rotation is
203. eir visibility Even if the markers are not visible they are still used by the Motion Module when importing tracked marker files Model Window Commands Markers can be selected and edited using the buttons and parameter fields in the Marker Editor window However the marker button only allows you to select one marker at a time while it is often desirable to select and modify a set of markers at the same time e g all of the right ASIS mark ers The muscle editing commands in the model window described below allow you to do this Chapter 2 Tools 113 2 12 Marker Editor 114 Chapter 2 Tools Markers can be selected and edited using keyboard and mouse commands in the model window To use these com mands you must first set the tool mode to the Marker Editor by clicking on the Marker Editor icon in the heads up dis play HUD on the left side of the model window To indi cate that all keyboard and mouse commands are being directed to the Marker Editor the icon will be highlighted with a yellow frame and the title bar of the Marker Editor will be highlighted in yellow SELECTING MARKERS To select markers press and hold the S key While this key is pressed the HUD text box in the lower left corner of the model window displays Selecting markers N selected where N is the number of markers currently selected As you move the cursor around the model window if it hovers over a marker the marker will be highlighted with
204. elected skin vertex yellow sphere on a line between its two attach ments green spheres each fixed to a different body segment The relative weights of the two attachments determine the location of the skin vertex on the line In editing mode the skin vertex can be dragged along the line to change the attachment weights The right image shows a skin vertex with three attachments which form a triangle The location of the skin vertex is determined by the relative weights of the three attachments and in eduting mode the vertex can be dragged anywhere inside the triangle to change the weights Chapter 2 Tools E EDITING SKIN VERTICES To edit the group of selected skin vertices press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Mov ing skin vertices and attachments Each selected vertex is displayed with a yellow sphere and each of the vertex s attachments is displayed with a greenish blue sphere with a line to the origin of the body segment it is attached to If the vertex has only one attachment then the attachment sphere is coincident with the vertex sphere and you will see only the latter If the vertex has two attachments a line is drawn between them and the skin vertex is located somewhere along the line depending on the weights If the vertex has three attachments a triangle is drawn between them and the 2 20 2 20 Function Editor skin verte
205. elector The plot selector lets you choose the plot to which you will add curves Before you have made any plots the pop up menu contains one item called new Initially new is the cur rent plot and it indicates that if you generate any curves a new plot window will be created to display the curves When you create a new plot window by this method the Chapter 2 Tools 37 2 5 Plot Maker Model Lower Extremity Plot none model gt plot gt help f Plotting hip_adduction moment vs hip_adduction Ee y variable gt TNE delete curves muscles gt plot title hip_adduction moment vs hip_adduction curve name segment gt step size 1 0000 motion curve gt activation 1 000 xmin 50 000 x max 30 000 y min y max scale 1 offset l active actoverride Bl passive J isometric J glut_min1 J glut medi H glut min3 E _ glut_med2 J quad_fem iliacus J glut_med3 _ gem _ psoas J glut_min1 _ peri J glut_med1 _ glut_min2 J glut_med3 lt lt done gt gt J glut_min3 lt lt done gt gt _ sar Bt _ glut_maxl _ peri lt lt done gt gt Figure 2 2 Plot Maker window 38 Chapter 2 Tools help 2 5 2 make curves delete curves muscles gt 2 5 Plot Maker window is given a title see below and the current plot is changed to this new one Clicking on the help button opens a window containing helpful text about the Plot Maker When you are done read in
206. ely 24 fixed segment defined 242 flat_shading defined 239 force mattes adding to body segment 129 force defined 44 form defined 9 editing 9 forward dynamics 150 Function Editor 189 195 functions 249 254 G gait toggle button 180 gait events calculating 317 Gencoord Editor 71 77 command menu 72 dof form 74 information header region 72 generalized coordinate groups defining in joint file 248 slider display 25 generalized coordinates 245 248 clamping 30 73 default value 74 247 defining restraint functions 247 locking 30 73 restoring from buffer 72 saving to buffer 72 slider display 25 specifying velocities 293 tolerances for 74 typing in values 74 gouraud_ shading defined 239 gravity in dynamic simulations 157 specifying in joint file 236 H hot keys 35 I IKS files 327 image capture see snapshots inertia matrix specifying for body segments 129 inertial parameters setting 129 inverse dynamics 150 inverse kinematics defined 76 specifying in joint file 234 turning on off 76 isometric toggle button 52 Index 3 J Joint Editor 53 command menu 53 dof form 55 information header region 53 rotation axes form 56 transform order 56 joint files 231 268 opening 12 saving 17 joints 243 245 restoring from buffer 54 saving to buffer 54 L ligaments 286 linear function defined 249 live model update 318 live plot curves 81 look at command 24 M making movies see m
207. ence 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 have been deter mined 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 Motion Module reads the length from personal dat If there are no foot length mea surements 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 infor mation consists of the name of the OrthoTrak segment and X Y and Z reference numbers that correspond to the unscaled 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 tha
208. ent for the Deform Editor Any newly created deform objects will be Chapter 2 Tools added to this segment The name of the current segment is displayed to the right of the button deform object gt save restore delete 2 11 3 segment object name 2 11 Deform Editor Select this command to create a new deform object or to choose an existing deform object for editing When you click this button a pop up menu of all deform objects assigned to the current segment is displayed The first item in the pop up menu new deform object creates a new deform named Untitled adds it to the current body segment and makes it the current deform object for editing The remaining items in the pop up menu allow you select exist ing deform objects for editing This command saves a snapshot of the current state of all deform objects in the model It can be used in combination with the restore button to help you undo changes made while editing deform objects This command restores the most recently saved snapshot of the current model s deform objects It can be used in combi nation with the save button to help you undo changes made while editing deform objects This command deletes the current deform object from the model Deform Object Attributes The panel to the right of the Deform Editor command menu can be used to edit the current deform object s attributes This field displays the name of the Deform Edi
209. ent points press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Moving muscle points net move seg X Y Z where X Y and Z are the distances that the points have moved rela tive to the body segment seg If all of the selected muscle points are attached to the same body segment then seg is that segment Otherwise seg is the ground frame To trans late the selected points in the plane of the screen press and hold down the left mouse button anywhere in the model window and move it to drag the points in that direction A green arrow is also drawn in the model window starting at the original location of the first selected point helping to show you how far the points have moved To move the selected attachment points in the X Y and Z directions relative to their respective body segments use the X y Z and Shift keys Pressing x translates the points in the negative X direction while pressing Shift and x trans lates them in the positive X direction Note if multiple attachment points are selected and they are attached to dif ferent body segments then the x y and z keys will move all of the points along the axes of the ground frame RIGHT CLICKING ATTACHMENT POINTS You can right click on an attachment point to display a pop up menu with several editing options The options allow you to select unselect the point for editing create a new point before or aft
210. enu item creates a single snapshot image of the cur rent model window If a file already exists with the current snapshot file name it is automatically overwritten so be careful The function key F12 will also take a snapshot of the active model window auto snapshot This menu item puts SIMM in auto snapshot mode In this mode SIMM will create a snapshot image each time the current model window is refreshed To exit this mode select auto snapshot again to disable it SIMM helps you to 26 Chapter 2 Tools movie gt choose movie file use default movie file name auto movie 2 4 Model Viewer remember by playing a snapshot sound each time a snapshot file is created In addition to these menu items if the current model has any motions linked to it then these motions will be listed at the bottom of the snapshot pop up menu Selecting one of these motions will cause the motion to be played back start ing at the current motion value and using the current gear A snapshot image will be created for each frame of motion until the end of the motion To stop this process you can click the stop button or select the motion s menu item in the snapshot pop up menu again The movie command allows you to easily animations of the SIMM model window into AVI movie files When you select the movie command a pop up menu is displayed The menu contains the following items This menu item displays a file browser dialog that allows
211. er Plot Maker Motion Reporter Dynamics Tool and Motion Edi Chapter 2 Tools 195 2 21 Scripting Tool 196 Chapter 2 Tools Scripting AP MODEL gt open_mocap init100 trb gt open walk1 trb ol mt set motion walk1 walkl_rl gt normalize t motion walk1_l1 normalize gt tool pm J gt semimem_r on pm gt semiten_r on gt make gt semimem_ on gt semiten_ on gt make open C Program Files MusculoGraphi norm_musculotendon_length is NormalHamstrings plt Figure 2 29 Scripting Tool window tor and the save restore functions in the Muscle Editor These allow you to batch process motion trials perform inverse dynamics analyses on them and create plots of mus cle lengths or other motion variables e g for gait analysis More script functions will be available in future versions of SIMM The Scripting Tool uses a current tool and a current folder to help parse commands that you enter When you enter a command the first word in it is checked to see if it is a top level command such as open save or close If it is the Scripting tool parses and executes the command If it is not the command is passed on to the current tool such as the Motion Editor or Plot Maker This tool then parses and exe 2 21 1 open open lt filel gt lt file2 gt open_mocap open_mocap lt filename gt close lt model gt close lt plot gt save jnt lt filename gt lt model gt
212. er have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Gencoord Editor When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again Command Menu This command lets you select which gencoord s properties you want to edit When a gencoord is selected its properties can be viewed and edited using the toggle buttons and num ber fields in the tool window This command saves the current gencoord of the current model It saves all of the gencoord s properties to a buffer so that they can be restored if you make changes that you later want to undo When you first load a model SIMM saves copies of all the gencoords so you can restore them back to their original form without having to save them first This command restores a previously saved gencoord description Selecting it restores the current gencoord s properties from a buffer that was saved last time you used the save current command When you first create a model SIMM saves copies of all of the gencoords so you can restore a gencoord back to its original form without having to save it first 2 8 3 restraint active clamped locked 2 8 Gencoord Editor Toggle Buttons This button allows you to toggle the restraint function of the current gencoord from active to inac
213. er this point delete the point select the muscle for editing hide the display of the muscle hide the display of all muscles except this one and delete the mus cle Note you can right click on any attachment point with out holding down any keyboard keys and without first clicking on the Muscle Editor icon in the HUD 2 8 Gencoord Editor The Gencoord Editor lets you view and edit properties of the generalized coordinates such as their ranges and default values It also lets you create and modify restraint functions for the gencoords which are used by the inverse kinematics solver as well as by the Dynamics Pipeline 2 8 Gencoord Editor ps Gencoord Editor Model Dynamic Mocap Model model gt name knee_flex_r gencoord gt save current restore current JJ restraint active J clamped locked value tolerance CEEE range min range max PD stiffness restraint 0 000000 0 000000 0 000000 10 000000 150 000000 0 000100 f 1709 keys none Figure 2 8 Gencoord Editor window Chapter 2 Tools 71 2 8 Gencoord Editor 72 2 8 1 model gt help 2 8 2 select gencoord gt save current restore current Chapter 2 Tools Selector Menu The model selector lets you choose which model s genco ords to view and edit When you choose a new model with the model selector the Gencoord Editor window is redrawn with the settings of the new model If you nev
214. ere are the SIMM defaults for the built in force motion object Forceplate Objects Forceplates are special motion objects that are defined in the header of the motion file and are not driven by columns of motion data Their position and color are constant throughout the motion so each one can be fully specified in the header with XYZ scale factors an X YZ translation and an XYZ Euler rotation The bone file used to display force plates is forceplate asc located in the Resources bones folder in your SIMM installation When the SIMM Motion Module imports a TRB TRC C3D file and creates a motion it calculates the proper forceplate information from the ana log data so you normally do not need to specify these val ues yourself Chapter 3 Input Files 295 3 5 Motion Files 296 Chapter 3 Input Files 3 5 4 Foot Print Objects Like forceplates foot prints are also special motion objects that are defined in the header of the motion file and are not driven by columns of motion data Their position and color are constant throughout the motion so each one can be fully specified in the header with a scale factor an XYZ transla tion and an XYZ Euler rotation The bone files used to dis play foot prints are JeftFootPrint asc and rightFootPrint asc located in the Resources bones folder in your SIMM installation When the SIMM Motion Module imports a TRB TRC C3D file and creates a motion it calcu lates the proper foot print inf
215. erion that you want Use body segment groups and generalized coordinate groups to make large models easier to navigate and display Try to keep muscle names short When SIMM reads in a muscle file it scans for the longest muscle name then makes every muscle group menu wide enough to hold that name This is done so that it is easy to position many group menus at once in a window To avoid large menus that run beyond the window borders try to limit muscle names to 10 letters In addition to selecting delete from the Plot Maker command menu there is another way to delete plot curves Pressing the Delete or the Backspace key in a plot or plot key window will delete all of the selected curves from the plot To delete a model click the close box in the upper right corner of the model s window or press the Delete or Backspace keys in the model s window If the display of your model is too slow e g for smooth animation try changing the drawing mode for some of the body segments For small polygons flat shading is often indistinguishable from gouraud shading but is usually faster For example when viewing an entire human skeleton you can probably use flat shading for the hand and foot bones without affecting the quality of the display a great deal When displaying shadows of the body segments you usually want the shadows to be cast on a world object such as the floor or a wall When setting the locations of the shadows
216. es and not use this option add num units to all vertex X coordinates add num units to all vertex Y coordinates add num units to all vertex Z coordinates rotate all vertex coordinates num degrees around the X axis rotate all vertex coordinates num degrees around the Y axis rotate all vertex coordinates num degrees around the Z axis scale all vertex X coordinates by a factor of num scale all vertex Y coordinates by a factor of num scale all vertex Z coordinates by a factor of num For the tx ty and tz options you can specify certain key words instead of entering an actual number These are explained below Shown are the options only for tx but the options are the same for ty and tz Chapter 4 Norm 309 310 Chapter 4 Norm tx min tx max tx mid translate the origin of the object along the X axis so that the smallest X coordinate is 0 0 i e find the smallest X coordi nate among all the vertices and subtract it from all the X coordinates translate the origin of the object along the X axis so that the largest X coordinate is 0 0 i e find the largest X coordi nate among all the vertices and subtract it from all the X coordinates translate the origin of the object along the X axis to the mid point between the smallest and largest X coordinates i e average the smallest and largest X coordinates and subtract this value from all X coordinates The geometric operations are all implemented as space
217. ess of the actual weight value the Motion Module treats all markers equally This checkbox controls whether or not the marker is visible in the model window Even if the marker is not visible it is still used by the Motion Module when importing motion files This checkbox controls whether or not the marker is fixed Fixed markers are optional markers whose X Y and Z off 2 12 4 radius visible 2125 2 12 Marker Editor sets in the mocap model are not automatically calculated when the static trial is processed Rather the offsets in the marker definition in the joint file are used to position the marker on the model These offsets are scaled with the body segment however Thus they are fixed to a certain region of the bone surface even as the bone is scaled to fit the motion subject The fixed not fixed property of a marker is rele vant only to the mocap model since this property is used only when recalculating offsets during processing of the Static trial Global Parameters This field contains the radius of the markers in the model It affects only the display of the markers in the model win dow it does not affect any marker offset calculations that the Motion Module performs when loading a mocap model This checkbox controls the visibility of all of the markers in the model window It is a convenience feature that allows you to turn all of the markers on or off without selecting them individually and changing th
218. eting 118 restoring 118 saving 118 specifying in joint file 270 transforming 123 constraint points creating 124 tolerance 126 contact objects adding to body segments 130 creating markers 110 cropping motions 166 D def_bone 239 255 256 default_value of generalized coordinates 74 247 of materials 258 Deform Editor 93 108 attributes panel 97 command menu 96 information header region 95 model window commands 99 tips and techniques 107 transform panel 101 deform objects auto reset deform objects 104 combining multiple 95 103 creating 97 defined 93 deformity sliders 95 106 deleting 97 Index 2 editing attributes 97 inner and outer boxes 93 specifying in joint file 263 tips and techniques 107 transforming 101 deformities specifying in joint file 267 deleting bones 140 deleting markers 111 drag and drop of input files 15 drawmode flat_shading 239 gouraud_ shading 239 none 239 of body segment groups 24 outlined 239 setting in Segment Editor 128 setting interactively 24 solid_fill 239 specifying in joint file 238 wireframe 239 dynamic preferences 157 dynamics input and output options 153 output variables 159 running in SIMM 149 smoothing input data 156 Dynamics Tool 149 162 information header region 153 E ellipsoid wrapping methods 90 92 axial 92 hybrid 91 midpoint 91 specifying in Wrap Editor 87 events deleting 165 F fiber length defined 44 fixed segment changing interactiv
219. evels and kinetic data when importing a motion SIMM uses a configuration file named forceplate data EMG data other data 5 4 1 5 4 Analog Configuration Files importVariables txt to determine which analog variables to import from an analog file and how the data for each vari able 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 interpret analog data as one of three types These variables specify voltages representing force or moment components as measured by a forceplate trans ducer Given the voltages generated by a forceplate 6 chan nels for an AMTI or Bertec forceplate 8 channels for a Kistler forceplate SIMM can calculate and display a force location and vector for the forceplate These variables define activation levels for one or more muscles 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 muscles during an animation Any variables that are not forceplate or EMG data are clas sified as other data SIMM does not perform any calcula tions on these data variables but they may be included in SIMM plots importVariables txt The file importVariables txt file contains a list of variable names and attributes When SIMM processes an analog data file or an OrthoTra
220. f the Norm pro gram which is described in detail in Chapter 4 Chapter 2 Tools 137 2 15 Bone Editor 138 2 15 1 model gt help 2 15 2 do boolean norm bone 1 split polygon Chapter 2 Tools Selector Menu The model selector lets you select the current model If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Bone Editor When you are done read ing it close the window using its close box You will be able to re open it at a later time by selecting help again Command Menu Most of the operations in the command menu work on the bone specified by the bone 1 button This bone is called the current bone which is not the same as the current segment The boolean operations work on two bones specified by the bone 1 and bone 2 buttons This command executes the specified boolean operation between bone and bone 2 The output bone is given the name that is in the new bone name field and is stored in the current segment which can be changed using the change segment button This command runs norm on bone 1 Any transformations you have done to the bone are integrated into the bone file the bone vertices are transformed and the normals are recomputed The translation and rotation fields are then reset to 0 0 and the scale fields are reset to 1 0 This
221. f your time will be spent choosing the proper size and placement for each object The inner box and outer box fields described in Section 2 11 3 allow you to specify the size and shape of the current deform object In addition to specifying the size and shape of your deform objects you will need to transform them into position and then transform them again to actu ally apply a deformation to the model The inner and outer boxes of the current deform object can be moved rotated and resized using the model window commands described in the previous section or by entering specific values into the numerical fields in the Deform Edi tor window as described below The collection of controls labeled transform can be used to position the current deform object within its parent seg ment s frame of reference in position mode and to apply a deform by moving and rotating the deform object s inner box in deform start and deform end mode Chapter 2 Tools 101 2 11 Deform Editor 102 Chapter 2 Tools transform translate rotate body fixed rotation translation transform in x 0 00 0 0000 y 0 00 0 0000 B T clear local frame z 0 00 0 0000 clear transform in y parent frame reset Figure 2 15 Deform Object Transform Panel Numerical Deform Object Transformation To apply precise transformations to the current deform object first enter the distances and angles to transform by in the translate and r
222. face of a geometric primitive a k a constraint object on a second segment This mechanism is useful for creating joint kinematics that are too complex to be modeled with a traditional SIMM joint For example in the shoulder two or more points on the scapula can be constrained to remain in contact with the ribcage which is represented as an ellip soid Once this constraint is activated when you change the value of one of the generalized coordinates in the shoulder SIMM will adjust the values of the other generalized coor dinates in order to satisy the constraints This process is similar to the inverse kinematics algorithm that keeps loops together Each constraint is made up of a constraint object associated with a specific body segment in the model and one or more constraint points on different body segments A segment may have more than one constraint object attached to it Constraint objects and points are defined within the refer ence frame of their associated segment and follow the movement of that segment Constraint objects can take the form of planes spheres cylinders or ellipsoids Selector Menu The model selector lets you choose which model s con straint objects you wish to edit When you select a new model with the model selector the Constraint Editor win dow is redrawn with the new model s settings If the current help 2 13 2 constraint obj ect gt 2 13 Constraint
223. feature is especially useful when you are importing a motion in real time with the Motion Module and want the SIMM animation to be as fast as possible The default value for tolerance is 0 0 The default value of a gencoord is the value that is reverts to when you select the restore ge values command in the Model Viewer When you change the default value of a gen coord that is used in a loop the inverse kinematics solver will re evaluate the loop s default configuration potentially range min range max PD stiffness restraint 2 8 Gencoord Editor changing one or more gencoord s default values so that the loop remains closed If default values of other gencoords in the loop are changed a message window will pop up to alert you to the new default values You can then choose to 1 accept and save the new default values 2 view but not save the values as defaults or 3 discard them The range of the gencoord is displayed in the range min and range max fields Both values can be changed by selecting the appropriate field with the left mouse button and then typing in a new value Changing the range does not change the restraint function if any so you may need to edit the gencoord s restraint function after changing its range This field holds a stiffness value that is used by the Dynam ics Pipeline when calculating gencoord moments corr while performing a dynamic simulation This calculation uses a PD proportional
224. ff the gait checkbox turns on off the standard deviations checkbox turns on off the output strides checkbox Chapter 2 Tools 207 2 21 Scripting Tool output_norm_strides lt on off gt generate 2 21 5 set model lt model gt working dir lt folder gt dll lt filename gt input_file lt filename gt output_file lt filename gt start_time lt time gt end_time lt time gt step_size lt time gt motion lt motion gt kinematics_cutoff lt frequency gt forces_cutoff lt frequency gt 208 Chapter 2 Tools turns on off the output strides normalized checkbox generates the motion report using all of the current settings Dynamics Tool Commands The following commands are available in the Scripting Tool when the Dynamics Tool is the current tool enter the com mand tool dt to make the Dynamics Tool the current tool sets the Dynamics Tool to the specified model specifies the directory to be used for the dynamic simulation for input and output files specifies the DLL to be used for the simulation specifies the input motion file for the simulation specifies the output motion file created by the simulation specifies the start time of the simulation specifies the end time of the simulation specifies the step size reporting interval of the simulation specifies which of the motions already linked to the model to use as input to the simulation specifies the low pass cutoff frequency
225. for a different name Instead do not define this preference and let SIMM determine an appro priate HTR file name for each motion trial that you import This preference is useful primarily when creating scripts to batch process several motion trials This preference specifies whether or not to save a muscle file for the scaled model when importing a static trial This pref erence is used to initialize the appropriate checkbox in the static import dialog box but you can change it as you load individual static trials This preference specifies the name of the muscle file to create when importing a static trial For most applications you do not want to explicitly set this preference because every time you import a static trial the saved muscle file will have the same name unless you browse for a different name Instead do not define this preference and let SIMM determine an appropriate HTR file name for each motion trial that you import This preference is useful primarily when creating scripts to batch process several motion trials TOOL PREFERENCES This option causes the Plot Maker to change its X variable and Y variable settings according to the current plot If you have several plots on the screen which involve different X and Y variables then when you use the plot selector to set the Plot Maker to a particular one the X and Y variable settings USE DEFAULT POSE FOR NORMALIZATION SNAPSHOT FILE NAME SCRIPTING CURRENT F
226. g between your name and SIMM The mapping con sists of the name of your marker followed by the keyword marker followed by the SIMM keyword for that marker For example to use right asis as the name of the right ASIS marker use this mapping right asis marker RASIS For a complete list of the built in names for each critical marker see the document MotionModuleMarkers pdf located in the folder S7 MM Documentation For a complete list of the SIMM keywords for each critical marker look at the bottom of importVariables txt in SIMM Resources mocap misc This keyword specifies a data channel that exists simply to be included in SIMM plots This keyword may be option ally 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 5 4 2 5 4 Analog Configuration Files forcepla cal When importing analog data from ANB ANC files SIMM uses the same calibration file as Cortex and OrthoTrak for processing forceplate 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 forceplate s refer to Appendix C of the OrthoTrak manual Note forcepla cal is not used for C3D import since C3D files contain the necessary calibration information for the force plates Chapter 5 Motion Module 34
227. g it close the window using its close box You will be able to re open it at a later time by selecting help again Command Menu Select this command to create data curves from a model according to the plotting parameters you have chosen see Section 2 5 3 Generating Curves From a Model for more details The number of curves added to a plot when make curves is selected depends on the sum option see Section 2 5 8 Toggle Buttons If the swm option is off then one curve will be added to the plot for each selected muscle If the sum option is on then the individual muscle curves will be summed and the result one curve will be added to the plot Selecting this command deletes all of the selected curves in the current plot window To select or unselect a plot curve click the left mouse button on the curve name in the plot key This toggles the curve between being selected and unselected When the curve is selected the region around the curve name is highlighted in white when unselected the region is black You can also delete selected curves in a plot by pressing Backspace or Delete while the plot or plot key window is the active window This command lets you choose the muscles that will be used to generate plot curves When you select this item a pop up menu of the muscle groups is displayed Choosing a muscle group from this menu causes it to appear at the bottom of the Plot Maker window If the chosen muscle group is already disp
228. h type of output Selector Menu The model selector lets you select the current model If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Motion Reporter When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again Command Menu This command lets you select which gencoord values you want to include in the report Clicking on the button dis plays a dialog box containing all of the gencoords in the model gencoord moments gencoord powers joint forces external forces muscle activations 2 18 Motion Reporter This command lets you select which gencoord moments you want to include in the report Clicking on the button dis plays a dialog box containing all of the gencoords in the model This command lets you select which gencoord powers you want to include in the report Clicking on the button dis plays a dialog box containing all of the gencoords in the model This command lets you select which joint reaction forces you want to include in the report Clicking on the button dis plays a dialog box containing all of the joints in the model This command lets you select which external forces usu ally ground reaction forces you want to include in the report Clicking on the butt
229. he accuracy of the least squares solver module within SIMM This module is used by the Motion Module to solve frames of marker data and by SIMM to implement closed loops and constraint objects For both uses the module adjusts the model s gencoords iteratively until the markers loops and or constraints collectively called solver ordinates are satisfied to within the specified accuracy or until the speci fied maximum number of iterations has been reached The accuracy value corresponds to the sum of the squares of the errors between the current solver ordinates and the ideal loop_tolerance marker visibility marker radius 3 3 Joint Files ordinates Decreasing this value will cause the solver mod ule to iterate longer and return a more accurate solution The solver_method allows you to choose between the Leven berg Marquardt method specified by tm and the Gauss Newton method specified by cn of least squares solving The latter method is usually faster but can be less robust when some marker data is missing Shown below are the parameters with their default values solver method LM solver_accuracy 0 0001 solver_max_iterations 100 This parameter specifies the acceptance level for the solu tions that the solver module reaches when implementing the loop constraints It does not affect the speed or accuracy of the solver module Rather it is a cutoff value specifying whether or not the solution is acceptable If it
230. he muscles Muscle Force Functions At the top of the panel are thumbnails for the five functions used in the force model They are the force length curve of tendon T F L the active force length curve of the muscle fibers A F L the passive force length curve of the fibers P F L the force velocity curve of the fibers F V and the excitation pattern of the muscle EXC When you right click on one of the thumbnails SIMM displays a pop up menu with the following options This option is activated if the muscle is not currently inher iting the function from the default muscle It changes the property so that it does use the same function that the default muscle uses The function that it had been using is not deleted even if it is no longer used in the model This option is activated if the function is currently being inherited from the default muscle It makes a copy of the default function and uses it only for this muscle Chapter 2 Tools 61 2 7 Muscle Editor 62 edit default function edit function make new function Chapter 2 Tools This option is activated if the function is currently being inherited from the default muscle It sends the function to the Function Editor so that it can be edited This option is activated if the function is not currently being inherited from the default muscle It sends the function to the Function Editor so that it can be edited This option is activated only if there is no
231. he Muscle Editor is the current tool enter the com mand tool me to make the Muscle Editor the current tool sets the Muscle Editor to the specified model sets the Muscle Editor to the specified muscle saves all muscles saves the current muscle save lt muscle gt restore all restore current restore lt muscle gt 2 21 Scripting Tool saves the specified muscle restores all muscles restores the current muscle restores the specified muscle Chapter 2 Tools 219 3 Input Files 3 1 Introduction A musculoskeletal model is specified with three types of input files The bone files Section 3 2 contain lists of polygons that define the bone surfaces The joint file Section 3 3 specifies the kinematics of the joints and the characteristics of the body segments The muscle file Section 3 4 contains lists of coordinates that describe the muscle lines of action and the parameters needed to com pute isometric muscle forces SIMM scans these input files and creates a data structure that represents the musculoskeletal model When SIMM scans the joint and muscle files it ignores all text between the delimiters and so you can include comments in the files to help you document your model Bone files which cannot contain comments can be preprocessed with norm see Chapter 4 before being loaded into SIMM This chapter describes how to create a musculoskeletal model using input files Examples from the lowe
232. he abso lute value of the data If it is turned off then the data is not modified before plotting Note that this option does not reverse the sign of the data points but rather takes their absolute values so be careful when using it while creating curves that have positive as well as negative data points The current setting of rectify has no effect if you are plotting data from plot data files or columns of data from motion files This toggle button lets you choose whether or not to plot the active component of muscle force Turning it on means that the force from the active force length curve of the muscle will be included when computing muscle tendon force The current setting of active has no effect if you are plotting data from plot data files or columns of data from motion files This toggle button lets you choose whether or not to plot the passive component of muscle force Turning it on means that the force from the passive force length curve of the muscle will be included when computing muscle tendon force The current setting of passive has no effect if you are plotting data from plot data files or columns of data from motion files This toggle button controls the use of the universal activa tion level in the options form When it is turned on the acti vations of all of the muscles used for plotting will be set to the value shown in the activation field of the options form This does not change their values in the muscle
233. he force plates in the model window when a motion trial is first imported into SIMM A typical value is 0 001 1 mm so that the force plates are visible slightly above the floor It does not affect the force calculations nor the display of the force vector in the model window If this preference is not specified a value of 0 001 is used MOCAP STATIC SUBJECT MASS MOCAP_STATIC LOAD PERSONAL DAT MOCAP STATIC PRESERVE MASS DISTRIBUTION MOCAP STATIC MARKER NAME SOURCE MOCAP STATIC SAVE JOINT FILE B 1 Preferences STATIC TRIAL IMPORT PREFERENCES This preference specifies the mass of the subject when importing a static trial to create a subject specific model The value is used to initialize the appropriate field in the static import dialog box but you can change it as you load individ ual static trials This preference specifies whether or not to load personal dat when importing a static trial This file can contain informa tion about subject parameters e g body mass foot length MVIC values and model calculations e g hip and shoulder center positions For more information on personal dat see Section 5 3 Using the Mocap Model This preference is used to initialize the appropriate checkbox in the static import dia log box but you can change it as you load individual static trials This preference specifies when importing a static trial whether or not the mass distribution in the unscaled model should be
234. he recommended format for new musculoskeletal models It is an ASCII format that was customed developed for SIMM and an example is shown in Figure 3 1 This format is identified with the asc file suffix The first line in the bone file must be the string NORM_ASCII The second line contains the number of verti ces num_vertices followed by the number of polygons num_polygons The third line contains the bounding box of the bone The six number are respectively X min X max Y min Y max Z min and Z max Then comes the ver tex list whose length must be num_vertices Each line in this list contains the X Y and Z coordinates of a vertex and the X Y Z coordinates of the vertex normal The utility program norm can compute vertex normals for you see Chapter 4 Norm for more details Lastly there is the poly gon list whose length must be num_polygons The first number in each line is the number of vertices nv in the polygon and the other numbers are the indices of the nv vertices The indices start at 0 and correspond to the order in which the vertices are listed in the vertex list In the example shown the first polygon is a triangle formed by the first second and third vertices in the vertex list The second polygon is four sided using the third fourth sev enth and sixth vertices When listing the indices for a poly gon you should order them so that they walk around the perimeter of the polygon You can specify
235. hen select a body segment the target segment from the combo box located under the Group weighting label Now when you press the and buttons next to the combo box the attachment weights of the selected skin ver tices are adjusted as follows For each selected skin vertex if the vertex has an attachment on the target segment its weight is increased by 10 if the button was pressed and decreased by 10 if the button was pressed If the selected skin vertex does not have an attachment on the target seg ment then if the button was pressed the vertex s attach ments are not changed If the button was pressed a new attachment is added to the vertex The location of the attach ment is the current position of the skin vertex expressed in the target segment frame and the attachment weight is set to 0 05 In all cases after the weights of the target segment attachments have been changed the weights of all other attachments for the selected skin vertices are adjusted so that the weight total for each vertex is 1 0 2 19 5 2 19 Skin Editor Model Window Commands Skin vertices can be selected and edited using keyboard and mouse commands in the model window To use these com mands you must first set the tool mode to the Skin Editor by clicking on the Skin Editor icon in the heads up display HUD on the left side of the model window To indicate that all keyboard and mouse commands are being directed to the Skin Editor the
236. hics 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 ligaments develop force thus generating moments about the joints SIMM allows you to analyze and test a musculoskeletal model by calculating 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 system you can quickly explore the effects of changing musculoskeletal geometry and other model parameters Since the software can be used to study many different musculoskeletal structures it can enhance the productiv ity of investigators working on diverse problems in bio mechanics SIMM provides a framework that organizes the parameters of a model and allows people to work together on a modeling project The moving three dimen sional images of anatomical structures that you can create are extremely valuable when developing a model and when communicating the results of an analysis Chapter 1 Introduction 1 1 2 Applications 2 Chapter 1 Introduction 1 2 Applications SIMM has a wide variety of applications Here are a few examples Biomechanics researchers are using SIMM to create mod els of the human elbow
237. his controls whether the gencoord moments are displayed as arrows or as translucent spheres When displayed as arrows the arrow for each gencoord is drawn along the gencoord s axis with the length representing the magnitude of the moment When displayed as spheres a red sphere is displayed for each moment centered on the origin of the child segment of the gencoord s primary joint This option toggles the display of all motion objects that are not covered by the above options such as the spheres used to represent mass center positions in motion files created by dynamic simulations This option toggles the looping of the motion playback If turned on the motion will wrap around to the beginning when it gets to the end The motion will thus loop continu ously until you stop it This option controls whether or not to enforce constraint objects while animating the motion If the motion contains complete gencoord data that already satisfy the constraint objects then you can turn off this option so that SIMM does not recalculate them If your model does not contain any constraint objects this option is grayed out This option controls whether or not loop constraints are enforced while animating the motion If the motion contains complete gencoord data that already satisfy the loop con straints then you can turn off this option so that SIMM does not recalculate them If your model does not contain any closed loops of body segments th
238. hold down the left mouse button anywhere in the model window and move it to drag the markers in that direction A green arrow is also drawn in the model window starting at the original location of the first selected marker helping to show you how far the markers have moved To move the selected markers in the X Y and Z directions relative to their respective body segments you can use the X y z and Shift keys Pressing x translates the markers in the negative X direction while pressing Shift and x trans lates them in the positive X direction Note if multiple markers are selected and they are attached to different body segments then the x y and z keys will move all of the markers along the axes of the ground frame RIGHT CLICKING MARKERS You can right click on a marker to display a pop up menu with several editing options The options allow you to select unselect the marker for editing hide the display of the marker hide the display of all markers except this one and delete the marker Note you can right click on any marker without holding down any keyboard keys and without first clicking on the Marker Editor icon in the HUD Chapter 2 Tools 115 2 13 Constraint Editor 116 2 13 2 13 1 model gt Chapter 2 Tools Constraint Editor The Constraint Editor allows you to create and edit con straints in the model These constraints provide a way of constraining points on one body segment to remain on the sur
239. hout having to change the drawmode of each indi vidual segment in the limb Note There is another method for changing the drawmodes of bones and world objects If you right click on a bone or world object in the model window SIMM will display a pop up menu Using this menu you can change the object s drawmode and material as well as turn on and off the dis play of the segment axes and object s normal vectors You can also set the camera to look at that segment as if you had used the look at command This command allows you to control which gencoord slid ers are visible in the Model Viewer window If your model contains a large number of gencoords it can be tedious to quickly locate an individual gencoord slider amongst all the others When you select the gencoord command a pop up menu of the gencoords is displayed Selecting items in this menu toggles the visibility of the gencoord s slider in the Model Viewer Furthermore if gencoord groups are defined in the model then the gencoord menu will be organized by these groups This makes it easy to quickly toggle the visi bility of several gencoord sliders at a time Note when a model is loaded SIMM checks to see how many gencoords are in the model If there are more than 50 gencoords in the model then SIMM hides all gencoord slid ers by default to avoid filling the Model Viewer window with too much information The snapshot command allows you to easily capture still
240. hs per second divided by max contraction velocity Thus the range of the func tion s abscissa should be 1 0 to 1 0 and its ordinate should Chapter 3 Input Files 279 3 4 Muscle Files 280 Chapter 3 Input Files be 1 0 for a velocity of 0 0 When a muscle contracts it is defined to have a negative velocity If you will be using your musculoskeletal model in dynamic simulations you need to add a section to the muscle file defining the names of the muscle parameters needed by the dynamic muscle model consult the Dynamics Pipeline manual for details An example is shown in Figure 3 20 You then need to specify values for these parameters in the muscle definitions Note Case is significant when entering text into muscle files All SIMM keywords e g beginmuscle endmus cle must be in lower case letters You are free however to use upper as well as lower case letters for naming the mus cles and SIMM will display these names exactly as you type them into the muscle file You can define a default muscle which contains the parameters that are usually identical for every muscle e g the normalized force length curves If a particular muscle definition does not contain a certain parameter or curve the parameter or curve is inherited from the default muscle This greatly reduces the amount of information that you have to specify in each muscle definition A sample default muscle is shown in Figure 3 21 VA ORO
241. icon will be highlighted with a yellow frame and the title bar of the Skin Editor will be highlighted in yellow Note you cannot select or unselect entire skins with model window commands You must use the skin button in the Skin Editor to select the current skin for editing SELECTING SKIN VERTICES To select a skin vertex press and hold the S key While this key is pressed the HUD text box in the lower left corner of the model window displays Selecting skin vertices As you move the cursor around the model window if it hovers over a skin vertex the vertex will be highlighted with a yel low wireframe sphere and its index will be shown in a tool tip box If you then left click on the vertex it will be added to the group of selected skin vertices If you click on an already selected vertex it will be unselected You can also box select skin vertices by pressing and holding down the left mouse button and dragging the cursor to form a rectan gle around the vertices you want to select or unselect As you select and unselect vertices the Skin Editor window updates to show the number of vertices selected and the weights and locations of their attachments If the selected vertices do not have the identical attachment segments weights or locations the corresponding fields in the GUI are blank indicating that multiple values are present Chapter 2 Tools 187 2 19 Skin Editor 188 Figure 2 27 The left image shows a s
242. if your motion contains gencoord data but you also want to plot gencoord velocities SIMM will use the specified X column to calculate derivatives so if the X col umn is not time you will not get meaningful results This parameter specifies a forceplate object that will be dis played as the motion is animated The built in forceplate motion object a unit cube is used for the display and it is scaled translated and rotated into the proper position based on the specified values After the keyword forceplate are the XYZ scale factors the XYZ position of the forceplate origin in the world reference frame and the XYZ Euler rotation from the world frame When the SIMM Motion Module imports a TRB TRC C3D file and creates a motion it calculates the proper forceplate information from the ana log data so you normally do not need to specify these val ues yourself These parameters specify left and right foot print objects that will be displayed as the motion is animated The built in foot print motion objects are used for the display and they are scaled translated and rotated into the proper posi tions based on the specified values After the keyword leftFootPrint or rightFootPrint are the single scale factor the XYZ position of the foot print origin back of the heel in the world reference frame and the XYZ Euler rota tion from the world frame When the SIMM Motion Module imports a TRB TRC C3D file and creates a motion it calcu
243. ifferent range of the X variable ankle_angle Model Archive Files A model archive is a compressed file containing all of the files associated with a model including joint file muscle file bones files and any motion files currently linked to the model It contains everything needed to load the model back into SIMM at a later time To create a model archive select File Export Model Archive from the SIMM menu bar To open an archive select File Import Model Archive from the menu bar Model archive files cannot be opened in other software applications However because everything is in one file it is a good way to share models with other users or to backup your models before modifying bone files or other components that are typically shared among models 3 8 Script Files 3 8 Script Files A script file is a text file of commands that can be executed by the Scripting Tool Section 2 19 Scripting Tool lists all of the available commands An example is shown in Figure 3 27 You can create a script file in any text editor and load it into SIMM in one of three ways You can select File Open in the menu bar and choose the script file you can type load lt filename gt into the Scripting Tool and you can drag and drop the file onto any SIMM window For drag and drop the window on which you drop the file affects how the commands are executed as explained in Section 2 2 1 Drag and Drop cd D GaitAnalysis MotionData subject0
244. ight of an attachment controls how closely the skin vertex follows it when the joints move The sum of the weights for all attachments for each skin vertex must equal 1 0 If you click on the weight field for an attachment and enter a value the weights of the other attachments if any will automatically be adjusted so that the sum is 1 0 If more than one skin vertex is selected and those vertices have attachments with different weights than the other selected vertices the weight fields will be blank If you click on a blank weight field and enter a value the weight for that attachment for all selected vertices will be changed to that value Chapter 2 Tools 185 2 19 Skin Editor 186 Chapter 2 Tools XYZ 2 19 4 The XYZ coordinates of an attachment specify the location of the point in the reference frame of the body segment it is attached to If more than one skin vertex is selected and those vertices have attachments with different coordinates than the other selected vertices the X Y and or Z fields will be blank If you click on a blank field and enter a value the coordinate for that attachment for all selected vertices will be changed to that value Group Weighting The group weighting feature in the Skin Editor allows you to proportionally change attachment weights for a group of skin vertices which can be helpful for smoothly deforming the skin around a joint To use it first select a group of skin vertices T
245. ill be ignored System Parameters This button lets you choose which muscles you want to include in the dynamic simulation If the use muscle groups box is checked and there are optimization groups defined for the muscles see below each muscle name will be col ored according to the groups it is in This button lets you choose the normalization option for the output motion created by the dynamic simulation Normal ization of the output can be useful if you want to compare several dynamic analyses to each other By default normal ization is off and the output motion will contain the appro gravity gt preferences gt use muscle groups 2 16 Dynamics Tool priate number of data frames as specified by the simulation time parameters The option 0 0 gt 0 99 will result in the output motion containing 100 frames of data In addition a reference number will be added to each frame of data ranging from 0 0 to 0 99 The option 0 0 gt 99 0 will also result in 100 frames but the reference number will range from 0 0 to 99 0 Normalization does not affect the accuracy or step size of the numerical integration during the simula tion It only affects the time interval between the frames of data stored in the output motion This button lets you specify the direction of the gravity vec tor In general you should specify the gravity vector in your joint file in which case that value is used to initialize the parameter
246. images from the SIMM model window in TIFF image for Chapter 2 Tools 25 2 4 Model Viewer mat When you select the snapshot command a pop up menu is displayed The menu contains the following items choose snapshot file This menu item displays a file browser dialog that allows you to specify the name and location of the next snapshot image to be created by SIMM By default SIMM will create snapshots starting with the filename snapshot_0001 tif Each subsequent snapshot file will have the numeric portion of the filename incremented by one e g snapshot_0002 tif snapshot_0003 tif etc When you select choose snapshot filename to specify a different snapshot filename SIMM examines the filename you enter to see if it contains a num ber If so SIMM uses that number as its snapshot counter Finally SIMM will make sure that the name of each snap shot file it creates ends with tif This identifies the file to other programs as a TIFF image file include alpha channel This menu item allows you to specify whether SIMM should include an alpha channel in the snapshot images it creates By default SIMM creates a 24 bit RGB image with out an alpha channel If this menu item is selected SIMM will create a 32 bit RGBA image that includes z depth val ues as an alpha mask By including an alpha channel SIMM snapshot images can be combined with other images of 3D scenes using third party compositing software take snapshot F12 This m
247. in dow makes SIMM pause for the specified number of seconds This can be useful if you are making a script for giving a demo or for waiting after issuing the initialize command in the Dynamics Tool to give SIMM time to load the simula tion DLL in another thread before issuing the run com mand simwait lt model gt moviewait lt model gt param lt model gt lt param gt lt value gt system lt DOS command gt tool mv tool pm tool mr tool mt tool dt 2 21 Scripting Tool makes SIMM wait until the dynamic simulation using the specified model has finished This can be useful if you re making a script that runs a series of simulations or you want to execute commands only after a simulation has fin ished e g plotting results makes SIMM wait until the movie being created is finished writing to the file sets the specified model parameter preference to the speci fied value The two parameters that are currently supported are read_script_file and write_script_file runs the specified DOS command and waits until it is fin ished This is useful if for example you want to move or make a copy of a data file after outputting it from SIMM sets the current tool in the Scripting window to the Model Viewer The prompt changes to mv gt to indicate the change sets the current tool in the Scripting window to the Plot Maker The prompt changes to pm gt to indicate the change sets the
248. 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 voluntary contraction resulting in a smooth muscle excitation level that varies 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 ana log file to scale that muscle s EMG data thus each muscle s excitation will peak at 1 0 sometime during the motion The file importVariables txt located in SIMM Resources mocap misc or in the folder with your motion data contains mappings between typical EMG channel names and the muscle names in the mocap model It does not contain any MVC values See Section 5 4 1 importVariables txt for information on how to add MVC values to this file In most cases however it is sufficient to not specify them and use SIMM s default scaling method Other data is contained in XLS files and can represent any motion variable 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 calculates and stores in its spreadsheet XLS format It may also include motion events such as toe off and heelstrike that are stored at the top of the XLS file SIMM does not perform any calcula tions on
249. in this tool However if you want to change it from the default you can do so with this button If you select the custom option a dialog box will pop up allowing you to specify the x y and z coordinates of the gravity direction vector This button will display a dialog box with a list of the dynamic preferences that were defined in the joint file These can be edited using either the checkbox to turn pref erences on or off or editing the values in the fields provided This checkbox lets you choose whether or not the muscles included in the simulation should be grouped during static optimization If selected all the muscles in each optimiza tion group will be assigned the same activation level An optimization group is a muscle group whose name ends in opt When use muscle groups is selected all of the mus cle selection dialog boxes in the Dynamics Tool show the muscle names in a separate color for each group and with the group number after the name If there are muscles in the simulation that are not in an optimization group they will be optimized individually Chapter 2 Tools 157 2 16 Dynamics Tool 158 2 16 7 initialize pause resume reset Chapter 2 Tools Simulation Execution This button initializes the dynamic simulation A copy of the current model is sent to the simulation which checks to make sure it matches the one built into the DLL If the num ber and connectivity of the body
250. increase the display of your model making the ani mation playback much smoother This option is on by default When this option is on SIMM will display the frequency of the model display in the lower left corner of the model win dow but only when animating a model using the start but ton in the Model Viewer This frequency value shown in frames per second depends on the performance of your graphics card and the complexity of your model This option is off by default When this option is on SIMM will display the number of polygons per second it is drawing in the lower left corner of the model window but only when animating a model using the start button in the Model Viewer This value depends on the performance of your graphics card and the complexity of your model This option is off by default This preference specifies whether or not to display informa tion in the model window about the motion being animated If it is on SIMM will show the motion name current time and current frame in the lower right corner of the model win dow MOTION TRIAL IMPORT PREFERENCES This preference specifies the model to use as the generic unscaled model when importing a static trial to create a sub ject specific model This preference specifies the offset from the local maximum of the marker trajectory to the time of the heel strike event A heel strike event is defined as a transition from positive to negative in the distance between the
251. ion In this mode you can translate the inner and outer boxes together by clicking on an edge of the outer box and dragging it You can rotate the inner and outer boxes together by clicking on one of the circles on the outer box s faces and spinning it Lastly you can resize each box inde pendently of the other by clicking on one of the corner edge or face handles and dragging it Deform start mode is for specifying the starting position of the deformation In this mode you can only translate and rotate the inner box To do so click on the box or one of the face circles and drag it Deform end mode is for specifying the ending position of the deformation In this mode you can only translate and rotate the inner box To do so click on the box or one of the face circles and drag it As you hover the cursor over a han 2 11 5 2 11 Deform Editor dle in any of these deform modes a tool tip describes the handle s function RIGHT CLICKING DEFORM OBJECTS You can right click on a deform object to display a pop up menu with several editing options The options allow you to select the object for editing activate deactivate it hide its display hide all deform objects other than this one and delete the object Note you can right click on any deform object without holding down any keyboard keys and with out first clicking on the Deform Editor icon in the HUD Transforming Deform Objects When adding deform objects to a model most o
252. ions Edit Preferences You can also save the current set of prefer ences back to the file using Option Save Preferences File Individual preferences can also be defined or changed using the Scripting Tool see Section 2 18 for details Here is a description of each preference in SIMM Appendix B SIMM Resources B 1 B 1 Preferences SIMM FOLDER RESOURCES FOLDER OUTPUT FILE FOLDER CORTEX MACHINE READ STARTUP SCRIPT B 2 Appendix B SIMM Resources GENERAL PREFERENCES This preference specifies the folder containing the SIMM executable program It is used to help set the values for other preferences if they are not fully specified For exam ple if the MOCAP_MODEL preference is set to a relative path name then it is assumed to be relative to the SIMM_FOLDER In general you should not specify SIMM_FOLDER in your preferences file instead letting SIMM define it at start up to be the folder containing SIMM exe This preference specifies the folder containing the primary SIMM resource files such as password txt and prefer ences txt In general you should not specify this preference in your preferences file instead letting SIMM define it at start up to be SIMM_FOLDER Resources This preference specifies the destination folder for the Plot Maker when creating a muscle orientation file and for the Bone Editor when saving a bone file The default value is which means that the current working folder will be used The
253. ir default values are shown in Fig ure 3 10 Cameras Cameras formerly known as model views define the posi tion and orientation or pose of a camera relative to the model Once you have loaded a model into SIMM you can set the camera pose to any of the poses that you specified in the joints file by using the restore camera command see Chapter 3 Input Files 257 3 3 Joint Files Figure 3 10 SIMM s default materials 258 Chapter 3 Input Files 3 3 9 Camera Pose begincamera posterior 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 2 0 3 1 0 1 0 endcamera 3 3 Joint Files Section 2 4 2 Command Menu for details An example camera definition is shown in Figure 3 11 Each camera is specified by a name and a 4x4 transformation matrix The 3x3 matrix in the upper left corner specifies the rotations of the model around the axes of the world reference frame The first three numbers in the last row of the matrix specify the translation in the X Y and Z directions from the origin of the world frame the Z translation should always be nega tive You can enter cameras directly into a joint file if you know the exact coordinates but it is usually easier to manip ulate the camera interactively within SIMM use the save camera command see Section 2 4 2 Command Menu to save the transformation matrix to a buffer then write the model to a file so that you have the precise 4x4 matrix saved to a file You ca
254. ir own DLLs but can choose from several pre built DLLs that come with the software fi Dynamics Tool Iti Foyet RG s Vimmkti Level model gt 2 16 Dynamics Tool input amp output options m working dir D Models GaitModel dynamics bro owse dil Models GaitModel dynamics simulation dll browse ij input file Wodels GaitModel dynamics walk2_IN mot browse Output file odels GaitModel dynamics walk2_CUT mot browse simulation time endi 3 8750000 motion for inverse dynamics walk2 motion smoothing low pass cutoff kinematics 10 Hz include forces 25 Hz include EMG none Hz include system parameters muscles 0 selected normalize gt none gravity gt E preferences Step 0 0083333 output variables right click to select individual model components gt gencoord values system ener g Vy SY 8y y gencoord velocities gt joint reaction forces y gencoord accelerations joint reaction torques muscle activations gt gencoord moments gt muscle lengths gencoord moments corr muscle forces gt gencoord powers v muscle velocities spring forces y fiber lengths Pap muscle moment arms V fiber velocities muscle moments contact forces total muscle moments mass center positions optimized muscle activations mass center velocities simulation execution initialize Figure 2 23 Dynamics Tool window Chapter 2 Tools 2 16 Dy
255. irst load a model SIMM saves copies of all of the muscles so you can restore them back to their original form without having to save them first This command restores all of the muscles in the current model from the buffer that was saved during the last save all or save current command When you first load a model SIMM saves copies of all of the muscles so you can restore them back to their original form without saving them first This command adds an attachment point to the current mus cle It displays a pop up menu letting you choose where to Chapter 2 Tools 59 2 7 Muscle Editor 60 delete attachments gt delete muscle edit group gt make new group Chapter 2 Tools 2 7 3 color factor add the new point in the list of existing points and what body segment it will be attached to This command lets you delete attachment points It displays a pop up menu with two primary options You can delete an attachment point on the current muscle by selecting the first option the name of the muscle and then selecting a point from the submenu You can delete all selected attachment points on all muscles in the current model by selecting the second option all selected attachments This command deletes the currently selected muscle The default muscle cannot be deleted This command allows you to edit the members of the mus cle groups Click on it to display a pop up menu of the cur rently define
256. is This can be help ful when verifying a new joint definition or when visualiz ing moment arm calculations The keyword loopjoint should no longer be needed in a joint definition now that SIMM includes an inverse kine matics IK solver If you have loops of body segments in your model the IK solver will find gencoord values that sat isfy the loop constraints and keep the loops closed If you turn the IK solver off or if it cannot find a configuration which keeps the loops closed SIMM will display your model with one of the joints in the loop broken This so called loop joint will be ignored for display and plotting purposes so you won t be able to animate the joint or plot muscle properties as a function of the joint s gencoords To specify which joint should act as the loop joint put the key word loopjoint in the joint definition In most cases how ever it is recommended that you do not specify loop joints and instead allow the IK solver to control the loops in your model Generalized Coordinates Generalized coordinates are degrees of freedom in the mus culoskeletal model The definition of the generalized coor dinate knee angle from the femoral tibial joint definition Chapter 3 Input Files 245 3 3 Joint Files 246 Generalized Coordinate begingencoord knee angle begingroups right leg lower body endgroups range 0 0 120 0 keys k_key default_value 30 0 wrap restraint 19 active yes
257. is fixed but the segment is allowed to rotate about its origin if the joints in your model allow this If you define a segment named ground then this segment is automatically marked as the fixed segment Otherwise the segment whose name appears first in the joint file is marked as the fixed segment Note that segment names are used in joint definitions as well as segment definitions so the order in which you enter joints may also matter For example in the sample lower extremity file supplied with SIMM pelvis is the first body segment referenced in the joint file so that segment is the fixed segment When you flex adduct or rotate the hip the femur rotates with respect to the pelvis which remains fixed in the world reference frame If the joint file were altered so that the femur were referenced first then the pelvis would rotate with respect to the femur If you explicitly define a ground segment you can define its characteristics just like you can with any other body seg ment You can specify one or more bone files so that you can see the ground segment in the model window You can interactively change the fixed segment using the look at command in the Model Viewer see Section 2 4 2 Command Menu for details When you select a body seg ment with this command that segment becomes the new fixed segment If you write the model to a file however this new fixed segment is not marked as such in the output file 3 3 3
258. is far from the origin of the ground frame and then rotate the view locally around this body segment Note to Dynamics Pipeline users The look at command does not affect the ground segment used for calculating dynamics Regardless of which segment is treated as ground for display purposes the dynamics ground segment will always be the fixed segment in the SIMM model see Sec tion 3 3 2 Fixed Segment for more details This command gives you control over the display of the body segments and world objects When you select this command a pop up menu of the body segments is dis played After selecting one of them or one of the four groups of objects at the bottom of the menu roll off to the right to select one of drawing styles The six styles are gouraud shaded filled polygons smooth shading flat shaded filled polygons flat shading solid fill filled poly gons no shading outlined white polygons with high lighted edges wireframe hollow polygons and none no display Furthermore if body segment groups are defined in the model then the drawmode pop up menu will be organized by segment groups This makes it easy to quickly gencoords gt snapshot gt 2 4 Model Viewer change the draw mode of several body segments at a time For example if you are working with a multi limbed model you may want to group the body segments by limb In doing so you could quickly change the drawmode of an entire limb wit
259. is not accept able a dialog box may be presented indicating that the loop constraint is not satisfied this notice appears only when loading or editing a model not when changing gencoord values This tolerance value corresponds to the distance in model units between the two segments of the loop joint see Section 3 3 3 Joints for an explanation of the loop joint When the loop is properly enforced the points on the two segments are coincident and the distance is zero When the loop is not properly enforced the loop joint disarticu lates and the two points are separated by a certain distance The loop tolerance parameter specifies how large a dis tance is acceptable Shown below is the parameter with its default value Once the model has been loaded into SIMM this parameter can be changed via the Gencoord Editor loop tolerance 0 0001 These parameters specify properties of all of the markers in the model Marker_radius is the radius of the spheres used to represent the markers in the model window It affects Chapter 3 Input Files 237 3 3 Joint Files 238 Chapter 3 Input Files 3 3 1 only their display it does not affect any marker offset calcu lations that the Motion Module performs when loading the model Marker visibility controls the visibility of all of the markers in the model window It is a convenience fea ture that allows you to turn all of the markers on or off with out selecting them individually and cha
260. is option is grayed out Chapter 2 Tools 171 2 18 Motion Reporter 172 Chapter 2 Tools show movie 2 18 This option toggles the display of the movie if any associ ated with the motion See Section 3 9 Movie Files for information on how to load movies into SIMM and link them to motions Motion Reporter The Motion Reporter Figure 2 25 allows you to create reports from sets of motions A report is an Excel file con taining means and standard deviations of various variables calculated from the motions This tool can create reports of any kind of motion e g walking running golf swing but has some additional features designed specifically for creat ing gait reports The report file that the Motion Reporter creates is a binary Excel file with the data organized into sheets e g one for angles one for moments one for muscle lengths You can post process or format the data any way you want by extracting it from this file However if you create reports using the Gait Model that comes with SIMM in the Mod els GaitModel folder there is a corresponding Excel graphs file containing formatted graphs that look like a stan dard gait report This file is called GaitModel_report xls It links to a file called GaitModel_data xls to get the subject specific report data and it links to NormalData xls to get data for normal gait which it also displays in the graphs Thus if you use the Motion Reporter to create a file ca
261. is very important so that the restraint function has a value of exactly zero between 25 and 55 degrees World Objects World objects are polygonal surfaces that are fixed to the world reference frame They can be used to enhance the dis play of a model by providing a setting for the musculoskele tal structure Typical examples include a floor walls stairs or a bottom bracket and seat for a cycling model A sample world object is shown in Figure 3 8 The file that contains the object s surface description must be in the same format as a bone file see Section 3 2 Bone Files and can be pro cessed with norm see Chapter 4 Norm before being loaded into SIMM You can translate scale and rotate the object in the bone file using the origin scale and rota tion parameters as shown in the figure The origin defines the location of the origin of the world object in the world reference frame Rotation defines the XYZ Euler rotation between the world reference frame and the refer ence frame of the world object which is implicitly defined by the vertices in the bone file To control the appearance of a world object assign a mate rial to it in the same way that you do for a body segment If WORLD OBJECT floor beginworldobject floor filename floor asc origin 0 0 0 9 0 0 scale 0 5 0 5 0 5 rotation 90 0 0 0 0 0 material floor material drawmode flat shading texture file carpeting tif 3 3 Joint Files you do not assign
262. it the current bone bone 1 first make sure the b but ton next to the Bone Editor icon in the HUD is highlighted then press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Editing bone1 followed by some text describing the type of editing being performed To translate the bone in the plane of the screen press and hold the left mouse button anywhere in the model window The HUD text box will update with translating to confirm translation mode Also a green arrow is also drawn in the model window starting at the original location of the bone s origin helping to show you how far the bone has moved Drag the cursor to move the bone in that direction and release the left mouse button when you are done To scale the bone uniformly in X Y and Z press and hold the middle mouse button with the cur sor anywhere in the model window The HUD text box will update with scaling to confirm scaling mode Also a mea surement bar is drawn over the model starting at the origin of the bone and ending at the cursor The current XYZ scale factors are shown at the end Drag the cursor to increase or decrease the scaling factors and release the middle mouse button when you are done To rotate the bone about the seg ment s X Y and Z axes press and hold the right mouse but ton with the cursor anywhere in the model window The HUD text box will update with rotating to confirm r
263. k XLS file it consults the importVari ables txt file to decide which variables to import and how to interpret them The file can also contain alternate definitions of the critical markers in the mocap model These are the markers that have to be included in your motion capture Chapter 5 Motion Module 341 5 4 Analog Configuration Files force plate 342 Chapter 5 Motion Module marker set in order for SIMM to automatically scale the model to fit the subject The default version of this file is located in SIMM Resources mocap misc You can customize the file and leave it in this folder or you can put a copy in the folder containing your motion data When SIMM processes a motion trial it first looks in the motion data folder for importVariables txt If it is not found there SIMM then looks in SIMM Resources mocap misc 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 import 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
264. kine matic functions select File gt Save Joints To save the model s muscles select File gt Save Muscles Use the Win dows file browser to specify the name and location of the joint or muscle file to be written If you do not specify a jnt or msl file name extension for the file SIMM will add the appropriate one to the file name you specify To create a motion file for a model either the model s win dow must be the active i e topmost window or if a tool window is active it must be set to that model Select File gt New Motion and use the Windows file browser to specify Chapter 2 Tools 17 2 3 Saving Files 18 Chapter 2 Tools plot files the name and location of the motion file to be created SIMM will automatically add a mot extension to the file name for you if necessary When you click OK in the file browser the new motion file will be created with a motion header but without any motion frames To add motion frames to the new file you must repeatedly position the model by adjusting its generalized coordinate values then select File gt Add Motion Frame Each time you select Add Motion Frame from the File menu a new row of informa tion containing the model s current generalized coordinates will be appended to the motion file When SIMM first creates a motion file it gives the motion a default name and sets the datarows variable to 200 see Section 3 5 Motion Files After saving your motio
265. l lt filename gt lt model gt save plt lt filename gt lt plot gt save smm lt filename gt lt model gt 198 load lt filename gt pref lt name gt lt string gt cd lt folder gt pwd wait lt of seconds gt Chapter 2 Tools saves the specified model to the specified muscle file SIMM does not notify you if this action overwrites an exist ing file saves the specified plot to the specified file SIMM does not notify you if this action overwrites an existing file saves an archive of the specified model to the specified file SIMM does not notify you if this action overwrites an exist ing file loads and executes the specified script file Script files are ASCII text files with lists of commands with each com mand on its own line in the file sets the preference named name to the value string sets the current folder of the Scripting Tool to the specified folder This is the folder that is used when opening and sav ing files When you open a file by specifying a relative path name SIMM will look for it in the current folder When you save a file by specifying a relative path name SIMM will save it to the current folder You can use the command cd to move the current folder up one level e g from C SIMM models to C SIMM When SIMM is first launched the current folder is set to the value of the prefer ence SCRIPTING CURRENT FOLDER prints the name of the current folder in the Messages w
266. lack length the maximum length at which the tendon develops no force This parameter is used to find tendon strain which scales the X coor dinates of the tendon s force length curve maximum isometric force that the muscle fibers can produce active component This parameter scales the Y coordinates of the tendon s force length curve and of the muscle s active and passive force length curves optimal fiber length the fiber length at which max imum active isometric force is generated This parameter scales the X coordinates of the muscle s active and passive force length curves pennation angle the angle at which the muscle fibers insert on the tendon or bone As pennation angle increases the amount of muscle force that is transmitted through the tendon to the bone is decreased level of activation which can range from 0 0 to 1 0 This parameter scales the active component of iso metric muscle force Dynamic Parameters Form If the muscle has dynamic parameters defined for use with the muscle models in Dynamics Pipeline simulations SIMM will display them in a form on the right side of the Force Parameters panel labeled dynamic If you do not plan to use this model for dynamic simulations then you can ignore this form You cannot add or delete dynamic parame ters in the Muscle Editor but you can change their values for the selected muscle via this form To add or delete parameters edit the muscle file as describ
267. layed The first item make new muscle creates a new muscle named 58 Chapter 2 Tools save current restore current save all restore all add attachment gt 2 7 Muscle Editor Muscle _X adds it to the current model and makes it the current muscle for editing The muscle is attached to the first segment in the model and is given two arbitrarily posi tioned attachment points The muscle properties are inher ited from the default muscle if there is one If there is not then selecting make new muscle will create a default mus cle The remaining items in the pop up menu allow you to select existing muscles for editing This command saves a copy of the current muscle in the current model It saves it to a buffer so that you can restore it if you make changes that you later want to undo When you first load a model SIMM saves copies of all of the mus cles so you can restore them back to their original form without having to save them first This command restores the current muscle in the current model from the buffer that was saved during the last save all or save current command When you first load a model SIMM saves copies of all of the muscles so you can restore them back to their original form without saving them first This command saves all of the muscles in the current model It saves them to a buffer so that you can restore them if you make changes that you later want to undo When you f
268. layed at the bottom selecting it again will turn Chapter 2 Tools 39 2 5 Plot Maker 40 motion curve gt segment gt Chapter 2 Tools 2 5 3 it off You can click on individual muscles in any of the dis played group menus to select or deselect them for plotting This command lets you create plot curves from the data in motion files see Section 3 5 Motion Files When you select this command a pop up menu of motions is dis played After choosing a motion SIMM will display a win dow with checkboxes for all of the data columns in the motion The items are organized into tabs such as Genco ords Muscle Activations and Force Plates You can select any number of items to plot although each plot in SIMM is limited to 60 curves When you press OK the curves will be added to the current plot This command lets you choose the body segment to be used with the muscle orientation Y variable For each selected muscle with an attachment point on this body segment the vector describing the muscle line as it attaches to that body segment is defined as the muscle orientation Consult Sec tion 2 5 5 Y variables for more details Generating Curves from a Model Use the following technique to plot computed properties e g moment force length of the muscles in a model See Section 2 5 5 Y variables for a complete list of the muscu lotendon properties that you can plot 1 Ifyou have more than one model loaded i
269. lculate derivatives show markers calculate gait events 5 2 Opening Tracked Marker Files 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 calcu lating derivatives 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 deriva tives of any force or EMG data in the analog file if pres ent These derivatives can then be plotted using the motion curves command in the Plot Maker see Section 2 5 2 for more details To calculate derivatives SIMM uses the time column in the motion data and assumes that its units are sec onds If there is no time column or if it is not in seconds the derivatives that SIMM calculates will not be correct 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 spherical 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 locations These
270. le once the right thigh refer ence frame has been oriented within the static pose marker cloud the exact positions of the critical markers attached to the right thigh can be measured directly from the static pose and entered into the mocap model thus overwriting what ever offsets were in the model input file After the offsets of all the critical markers have been deter mined in this fashion the mocap model is fit to the static pose marker cloud as described in Section 5 1 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 critical 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 determines the offsets of the critical markers which the OrthoTrak algorithms can defin itively 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 Analog Configuration Files SIMM can include analog data such as ground reaction forces EMG activation l
271. lect polygons or patches first make sure the p button next to the Bone Editor icon in the HUD is highlighted then press and hold the S key While this key is pressed the HUD text box in the lower left corner of the model window displays Selecting polygons or Selecting patches As you move the cursor around the model window if it hovers over a polygon or patch on bone 1 the polygon patch will be highlighted in blue and its index will be shown in a tool tip box If you then left click on the polygon patch it will be highlighted in green and added to the group of selected objects If you click on an Chapter 2 Tools 147 2 15 Bone Editor 148 OBE OBE ce Chapter 2 Tools already selected polygon patch it will be unselected You can also box select polygons patches by pressing and hold ing down the left mouse button and dragging the cursor to form a rectangle around the ones you want to select or unselect EDITING POLYGONS PATCHES Selected polygons and patches cannot be edited using model window commands To delete or flip the normals of polygons and patches use the buttons in the Bone Editor window To translate polygons select and edit the appropri ate vertices as described in the next section Control points of NURBS surfaces cannot be edited SELECTING VERTICES To select polygon vertices first make sure the v button next to the Bone Editor icon in the HUD is highlighted then press and hold the S ke
272. lected the icon will be highlighted with a yellow frame and the title bar of the Model Viewer will be highlighted in yellow You can then use the following commands to change the view of the model and to articulate the joints Pressing this key moves the model in towards you making it larger Pressing this key moves the model out away from you mak ing it smaller Pressing this key moves the model to the left within the model window Pressing this key moves the model to the right within the model window Pressing this key moves the model up within the model window Pressing this key moves the model down within the model window To move the joints of a model you can press the keys that are listed in the definitions of the generalized coordinates see Section 3 3 4 Generalized Coordinates When you press these keys while the model window is the active win dow the values of the generalized coordinates will change For example pressing the k key changes the value of knee_angle in the sample lower extremity model and thus flexes and extends the knee The speed and direction of the gencoord movements work the same way as the model rota tions described above If you keep the keys pressed to con tinue changing a gencoord you will eventually reach the end of the gencoord s range When this happens the value of the gencoord will stop changing and the model will stop F2 F3 F4 F5 F6 2 4 Model Viewer moving However
273. length of 0 0 This tells SIMM to treat the muscle as a tendon only element using the tendon force length curve to calculate its force By specifying a tendon force length curve that models the mechanical behavior of ligamentous tissue the muscle will thus behave as a ligament As with muscles ligaments can span any number of body segments and can wrap over wrap objects Because ligaments are created using a modified muscle definition they will be listed as muscles in the SIMM graphical interface but you can use muscle groups to differentiate them from normal muscles Motion Files Motion files contain lists of joint angles that describe motions of musculoskeletal models Once loaded into SIMM motions can be linked to the models already loaded The motion variable e g gait_cycle is treated as a gener alized coordinate It can be used to animate the model and 3 5 Motion Files can serve as the independent variable when making plots You can also create plots of any column of motion data using the Plot Maker see section 2 5 4 Command Menu In addition to specifying joint angles during a motion you can also specify muscle activation levels Because the thick ness and color of each muscle depends on its activation you can use a motion file to not only playback the kinematics of an animation but also to display the relative activity levels of the muscles used to create the motion An example motion file is shown in Figure 3
274. lick on make curves to add the plot to the curve The events for the motion will not be displayed in the plot since the X axis is not time X variables The possible independent X variables are the current model s generalized coordinates and the motion variables that are linked to the model You can also select an individ ual column of motion data as the X variable see below When you choose an X variable SIMM sets the xmin and xmax fields in the options form see Section 2 5 7 Options Form to the full range of motion for the generalized coordinate or motion variable If you want to plot computed muscle properties over a smaller range you should edit these form fields before generating your plot curves motion curve 2 5 7 plot title 2 5 Plot Maker This item in the X variable pop up menu lets you plot one column of motion data versus another The submenu con tains a list of the motions linked to the current model and each of those has submenus giving you access to all of the columns of motion data To use this option you must select a motion curve as both the Y variable and the X variable The selected curves do not have to be from the same motion but they must contain the same number of data points Once you have selected both click on make curves to add the plot to the curve The events for the motion will not be displayed in the plot since the X axis is not time Options Form This field contains the title of the
275. lized coordinates the accelerations of the generalized coordinates the dynamic activation levels of the muscles This will not be the same as the excitation levels if the muscle model used in the dynamic simulation models non linear activa tion dynamics most models do the musculotendon lengths of the muscles in the simulation the dynamic forces in the muscles in the simulation Chapter 2 Tools 159 2 16 Dynamics Tool muscle velocities fiber lengths fiber velocities contact forces mass center positions mass center velocities System energy joint reaction forces joint reaction torques gencoord moments 160 Chapter 2 Tools the velocities of the muscles in the simulation the fiber lengths of the muscles in the simulation the fiber velocities of the muscles in the simulation the forces applied by the rigid body contact detection algo rithm and or the NURBS spring contact detection algo rithm This includes the impulses applied during penetrating contact and the forces applied during resting contact the X Y Z coordinates of the location of each segment s mass center This is usually needed only when you create a new SIMM model and want to double check that it has been assembled correctly in the dynamics code the X Y Z components of the velocity of each segment s mass center This is usually needed only when you create a new SIMM model and want to double check that it has been assembled correctl
276. lled GaitModel data xls and put it in the same folder as GaitModel_report xls you can then open GaitModel_report xls in Excel select the option to update links and see the report data in the updated graphs If you choose to include kinetic variables in a report moments powers joint forces the Motion Reporter works 2 18 Motion Reporter in conjunction with the Dynamics Tool to perform dynamic simulations that calculate those variables Thus to report kinetic variables you must have the Dynamics Pipeline Module or the FIT Module and have already set up the Dynamics Tool with the appropriate parameters If the Motion Reporter needs to perform a dynamic simula tion on a motion it will do so using the current settings in the Dynamics Tool except for the motion for inverse dynamics which it will set automatically Thus the work f E Motion Reporter nem Model Gait Model model gt gencoord values output file GaitModel_data xls gencoord moments gencoord powers Subject Information joint forces name Charlie Bucket iz external forces examiner Andrew Payne scle activations ayy muscle BESS OPES Study initial evaluation S y lengths MOADE ENEH height 1 580 m weight 52 800 ke age 12 0 muscle forces id a87fe62b9 o A Bien Eip muscle velocities generate report BSneT AS a motions to include in report gait gt pl_wn8 J standard deviations pl_wn5 output strides F i pl_wn6 output stri
277. llowed by the X Y and Z sizes respectively radius 0 2 0 3 0 2 This parameter may be used to disable the constraint object If its value is no or false then the constraint object will have no effect on the model This parameter may be used to disable the display of the constraint object s shape in the model window If this Chapter 3 Input Files 273 3 3 Joint Files quadrant constraint points 274 Chapter 3 Input Files parameter s value is no or false then the constraint object will not be visible in the model window but it will still be enforced This parameter may be used to limit the constraint object to one half of the geometric primitive When the object is lim ited in this way the constraint points are required to remain in contact with the selected half of the object The valid quadrants are x x y y Z or z for spherical and ellip soidal constraint objects and x x y or y for cylindrical constraint objects Constraint points are specified between the keywords beginpoints and endpoints You can define any number of points attached to any body segments However the more points you define the more difficult it will be for SIMM to find a set of gencoord values which satisfy the constraint In practice two or three points is usually suffi cient to create the desired constraint on the motion Each point is defined by its name its X Y Z position in the body segment s reference frame its
278. log file are voltages measured by forceplate transducers These voltages are converted into forces using a calibration file forcepla cal This file is the same one used by 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 S MM Resources mocap misc If you have only one forceplate configuration for your motion capture system it is preferable to put force pla cal in SIMM Resources mocap misc rather than copy ing it into every folder of motion data Note C3D files that contain force plate data also contain the calibration information for the plates Thus there is no seprate calibration file that SIMM reads when importing C3D files SIMM also uses another configuration file importVari ables txt to map forceplate channels to SIMM variables This file is located in SIMM Resources mocap misc it can also be placed in the folder with your motion data and con tains mappings for typical channel names for up to six for ceplates You will only need to change this file if you use more than six forceplates or use forceplates that have exotic channel configurations This file is used when loading ANB ANC files and when loading C3D files See Section EMG data other data 5 2 Opening Tracked Marker Files 5 4 1 importVariables txt for information on how to mod ify this file SIMM displays EMG data by varying the sizes and colors of the corresponding muscles
279. lot Maker deleting 39 making live 81 naming 48 rectifying 51 plot files 298 300 opening 14 saving 18 Plot Maker 37 52 command menu 39 generating curves from a model 40 information header region 37 offset field 50 options form 47 plotting data from motion files 41 scale field 50 toggle buttons 50 180 X variables 46 Y variables 42 plot points creating 81 plot selector defined 10 Plot Viewer 78 81 plot window commands 80 plots adding labels 80 calculating means 78 creating see Plot Maker deleting 39 deleting labels 78 deleting points 78 resetting view 78 saving to files 80 sending to model windows 80 showing auxiliary data 79 showing cursor 78 showing data points 79 showing events 79 showing grid 79 showing zero line 79 polygons selecting 147 preferences in dynamic simulations 157 preferences file 1 Q quick solve defined 316 Index 7 R real time import see Motion Module rectify toggle button 51 restoring body segments 128 camera positions 22 generalized coordinates 72 joints 54 markers 111 model poses 22 muscles 59 skins 183 restraint functions 251 making active inactive 73 S saving body segments 128 bone files 19 camera positions 22 current muscle 59 generalized coordinates 72 joint files 17 joints 54 markers 110 model archive files 19 model poses 23 motion files 17 muscle files 17 muscles 59 plot files 18 script files 19 skins 183 Index 8 saving files 17 scaling plot
280. lot using the add label menu item described below This command resets the view of the plot to its initial view The plot curves are zoomed and or translated so that they are all visible within the window This command calculates the mean and standard deviation of all curves currently in the plot and adds the results to the plot as a new curve It is useful if you are plotting joint angles or muscle lengths for several subjects or motion tri als and want to compute their averages All of the curves in the plot must have the same X values in order to calculate their mean This command toggles the display of the cursor in the cur rent plot The cursor is the vertical bar in the plot that shows show events hide events show grid hide grid show data points hide data points show crosshairs hide crosshairs show Y 0 show auxiliary data hide auxiliary data 2 9 Plot Viewer the current value of the motion variable that was used in creating the plot The cursor is visible only if the plot is a function of some motion and if the motion file header con tains the cursor parameter see Section 3 5 Motion Files for details on specifying a plot cursor This command toggles the display of motion events Motion events are vertical bars in plots that mark certain events in the motion that was used to create the plot Motion events are visible only is the plot is a function of some motion and if the motion file header contai
281. lp you undo changes made while editing This command restores the most recently saved copy of the function It can be used in combination with the save button to help you undo changes made while editing This parameter is enabled when the function being edited is a GCV spline which supports smoothing The smoothing algorithm is a low pass filter and the parameter value is the cutoff frequency all frequency components above this value are removed This parameter is the number of control points the function has If you type in a new value or move the slider to change it the function will be resampled at regular intervals so that it has the specified number of control points This parameter is particularly useful when editing data col umns from motions see Section 2 17 2 for details These columns typically contain hundreds of data points making it tedious to modify a portion of the function Instead of moving each of the original data points you can use the control points parameter to undersample the function and then modify the reduced set of points You do not need to restore the number of control points when finished SIMM will automatically resample the modified function to calcu late a data point for each time frame of the motion Chapter 2 Tools 191 2 20 Function Editor 192 Chapter 2 Tools 2 20 2 Function Editing When a function is displayed in the graph area you can add delete and move its control points
282. mand to change the segment to which the current constraint point is attached defined as the parent segment When you select this item a pop up menu of the model s segments is displayed Choosing a segment from this menu will reassign the current constraint point to the selected segment The constraint point s overall position will not change when it is assigned to a new segment How ever when the model is put in motion the constraint object will follow the movement of its new parent segment Con straint objects and points cannot both be assigned to the same segment so the parent segment of the associated con straint object will be grayed out save points restore points delete point 2 13 7 point name segment offset weight 2 13 Constraint Editor This command saves a snapshot of the current state of all constraint points for the current constraint object It can be used in combination with the restore points button to help you undo changes made while editing constraint objects This command restores the most recently saved snapshot of the current constraint object s points It can be used in com bination with the save points button to help you undo changes made while editing constraint points This command deletes the current constraint point from the model Constraint Point Attributes The panel to the right of the constraint point command menu can be used to edit the current point s attrib
283. me gt lt end_time gt crop_start lt time gt crop_end lt time gt reset_crop divide_strides delete delete lt motion_name gt delete lt event_name gt delete lt event_time gt 216 Chapter 2 Tools smooths all of the curves in specified tab of the current motion with the specified low pass cut off frequency smooths the specified curve in the specified motion with the specified low pass cut off frequency smooths the specified curve in the current motion with the specified low pass cut off frequency crops the current motion using the current crop settings crops the current motion using the specified start and end times crops the specified motion using the specified start and end times sets the start time for cropping to the specified time sets the end time for cropping to the specified time sets the start and end times for cropping to the start and end times of the current motion divides the current motion into strides creating a new motion with each one deletes the current motion SIMM does not prompt you to confirm the action deletes the specified motion SIMM does not prompt you to confirm the action deletes the event with the specified name from the current motion SIMM does not prompt you to confirm the action deletes the event with the specified time from the current motion SIMM does not prompt you to confirm the action delete all_motions delete all_events add_event
284. med pass word txt This file is created by SIMM as a convenience so you will not need to reenter your password each time you run the program SIMM attempts to create the file in the resources folder of your SIMM installation e g C Program Files x86 MusculoGraphics SIMM70 Resources password txt but if that folder is write protected it will create it in your user application data folder e g C Users Peter AppData Local Mus culoGraphics SIMM 7 0 password txt SystemInfo txt Each time SIMM runs it creates a file named SystemInfo txt containing information about your computer This informa tion can be useful when trying to resolve technical problems with SIMM If you request technical support by sending email to peter musculographics com please include a copy of SystemInfo txt with your message The file is located in your user application data folder e g C Users Peter App Data Local MusculoGraphics SIMM 7 0 SystemInfo txt Bones The bones subdirectory in the SIMM resources directory con tains the bone files used to display the SIMM demo model The bones in this directory are in the newer ASCII format If you want to use them in another model that you are devel oping you should copy them to a bones directory located in the directory containing your joint and muscle files see Sec tion 3 2 Opening Files for more details Appendix B SIMM Resources B 17 A act override toggle button 51 activation muscle
285. mmand restores the most recently saved copy of the model s current skin It can be used in combination with the Chapter 2 Tools 183 2 19 Skin Editor unselect all make skin gt write skin export as bone 184 Chapter 2 Tools save skin button to help you undo changes made while edit ing skins This command unselects all of the currently selected skin vertices in the current skin This command makes a skin from a static bone To make a skin select this command and choose a bone from the pop up menu SIMM will examine each vertex of the bone and calculate which body segments it is closest to The distance between a vertex and a body segment is defined as the shortest distance between the vertex and all of the vertices on all of the bones of the body segment If the vertex is more than three times closer to one body segment than all others it is given only one attachment with a weight of 1 0 Otherwise the vertex is given two attachments with weights proportional to the relative distances to the two body segments All of the calculations are performed with the model in its current pose so it is important to position the static bone and set all of the model s gencoord values appropriately before executing this command This command writes the current skin to a file A file browser is displayed allowing you to select the type of file DAE or SKN as well as the name and location This command
286. motion This parameter is optional but should generally always be specified The number of columns of data This parameter is required The number of rows of data This parameter is required The index of the column that will be used as the X axis when plotting motion data This will be usually be the time column but can also be a normalization column e g 0 0 to 100 or any other column in the file SIMM will automatically calculate the minimum and maximum values of the X column data to serve as the range of the Chapter 3 Input Files 289 3 5 Motion Files units keys wrap enforce loops enforce constraints show_markers 290 Chapter 3 Input Files motion variable If you do not specify x_column SIMM will use the column labeled time as the X column If there is no column with this label the first column as the X col umn This optional parameter specifies a units label that will be used when plotting motion data SIMM does not use it to convert any of the data it merely adds the label that you specify to the labels of the Y variables in the plots This optional parameter lets you specify one or two keys to animate the motion When you press these keys in the model window the motion will be animated at the motion speed specified in the Model Viewer If this parameter is specified the playback of the motion will wrap around to the beginning when it gets to the end The motion will thus loop continuously u
287. mporting a motion which contains identical or similar gencoord values for some peri ods of time By setting the tolerance of each gencoord to say 0 5 degrees small changes in gencoord values will not result in the joint transformation matrices being recalcu lated thus saving some computation time This feature is especially useful when you are importing a motion in real time with the Motion Module and want the SIMM anima tion to be as fast as possible By default the slider for each gencoord will be visible in the Model Viewer window If you want to hide the slider for a particular gencoord use the visible keyword with the value no Gencoord sliders that are initially hidden when the model is loaded can be made visible using the gencoords command in the Model Viewer The begingroups and endgroups keywords can be used to enclose the name s of one or more gencoord groups to which the gencoord belongs Organizing your generalized coordinates into groups can make it easier to navigate and display your model with the Model Viewer 3 3 5 3 3 Joint Files Functions Functions are used in SIMM for a variety of purposes such as constraining the motion within a joint kinematic func tions limiting the range of motion of the gencoords restraint functions specifying excitation patterns for mus cles excitation functions and specifying the movement of a muscle point relative to its body segment moving muscle point functions
288. muscle point In moving muscle points each of the X Y and Z components of the location can be a function of a general ized coordinate instead of being a constant For example you could define a muscle point in the pectoralis muscle to slide over the ribcage as the humerus elevates In addition to using via and moving muscle points to wrap a muscle over a constraint you can also use muscle wrapping objects for a more automated form of muscle wrapping Wrap objects are defined in joint files and can be spheres ellipsoids cylinders or torii Once one or more wrap objects are linked to a muscle SIMM will automatically wrap the muscle path over those wrap objects To link a wrap object to a muscle put the keyword wrapobject in the muscle definition followed by the object name as shown in Figure 3 22 For more information about creating and using wrap objects see Section 2 9 Wrap Editor and Sec tion 3 3 9 Wrap Objects The isometric force generating properties of a specific mus cle tendon actuator are derived by scaling a generic Hill based model To scale the generic model you must supply 3 4 Muscle Files four parameters and three curves The four parameters are peak isometric muscle force F s optimal muscle fiber length M pennation angle a and tendon slack length amp The three curves are the active and passive force length relations of muscle and the force length relation of tendon The active force le
289. n also create plots of kinematic variables and muscle proper ties and see the plots change in real time F 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 Note 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 time analog data is processed frame by frame without the bene fit of the full data set This has the following implications To set the baseline for the forceplates the first frame of force data is used as the zero level Thus when you first connect SIMM to Cortex you should make sure that nothing is on the forceplates If no MVC levels have been specified for some of the muscles a running tally of each muscle s maximum 326 Chapter 5 Motion Module 5 2 5 5 2 Opening Tracked Marker Files 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 IKS Files IKS files are a special type of input file for the Motion Mod ule They are identical in format to motion files MOT but they can be used as input to the Motion Module similar to TRC TRB and C3D files The unique feature of IKS
290. n size and color of the motion object See Section 3 5 3 Motion Objects for a description of how to specify these properties Motion objects are automatically displayed when any of their parameters appear as columns of data in a motion file However before a motion object can be referenced in a motion file it must first be defined in the joint file or be one of the motion objects built into SIMM SIMM provides six 268 Chapter 3 Input Files filename position scale xyzrotation beginmotionobject box filename unit _box asc position 0 0 0 0 0 5 scale 0 1 0 3 0 05 xyzrotation 0 0 45 0 0 0 material my red material drawmode flat shading vectoraxis z endmotionobject 3 3 Joint Files built in motion objects named force ball contact joint force joint torque and spring force that make it easy to visualize vectors and points in SIMM ani mations The ba11 object is represented by a sphere defined in the SIMM bone file wnit_sphere asc The other five objects are each represented by an arrow defined in the file arrow asc You can override the parameters of these shapes or define additional shapes by defining motion object in your joint file Motion Object Fields This field specifies the name of the bone file containing the motion object s shape This field specifies the starting X Y and Z position of the motion object in its parent segment s frame of reference The default values are 0 0 0 0 0 0 This field
291. n and displays it in the Function Editor If the motion contains kinematic data for a closed loop model it is recommended that you not edit data for genco ords in the loop Doing so will violate the loop constraint and the model will not move properly if IK is turned on SIMM will adjust all of the gencoords to satisfy the loop constraint Chapter 2 Tools 165 2 17 Motion Editor 166 2 17 3 crop reset 2 17 4 event gt Chapter 2 Tools Cropping a Motion You can change the range of an existing motion using this feature Start and end frames can be entered into the number fields or you can use the slider to move the start and end frames up and down until you have chosen the range you would like the model will move in the motion window accordingly Use the crop button to crop the motion when you are satisfied with the new range This command crops the motion between the two selected frames This operation cannot be undone Any parameter fields in other tools that are linked to the cropped motion will be updated accordingly e g the x min and x max fields in the Plot Maker Any existing plots of the motion will remain unchanged Before you have cropped the motion you can use this com mand to reset the crop limits back to the full range of the motion Motion Events You can create and edit events in a motion using this fea ture You can edit the event s name and the X coordinate e g tim
292. n enter up to five cameras in each joints file Wrap Objects Wrap objects are geometric primitives that automatically deflect muscles to prevent them from penetrating the wrap object Wrap objects are typically added to a model such that their surface approximates the surface of one or more of the model s bones The only required component of a wrap object definition is its name However you will usually want posterior is the name of this pose Figure 3 11 Example camera Chapter 3 Input Files 259 3 3 Joint Files 260 to specify its associated body segment and its placement within the segment s reference frame as well Wrap objects may be created interactively within SIMM using the Wrap Editor tool You may find it easier to create and modify wrap objects with the Wrap Editor rather than editing the joint file directly See Section 2 9 Wrap Editor for more information Example Wrap Object beginwrapobject hip wrapper wraptype ellipsoid segment pelvis xyz body rotation 20 0 0 0 0 0 translation 0 0826 0 0286 0 0808 radius 0 05 0 02 0 05 active yes visible no quadrant y endwrapobject Figure 3 12 Example wrap object Wrap objects are specified in the model s joint file How ever before a muscle can wrap over a wrap object the mus cle must be associated with that wrap object Associations between muscles and wrap objects are specified in the mus cle s definition in the muscle file see Secti
293. n in this panel are the ones that will move if you perform one of the editing com mands described in Section 2 7 8 and they will be the ones deleted if you press the delete attachment s button and choose all selected attachments It is often useful to see all of the selected points in one list so you can confirm that the proper ones are selected Even if a selected point is not visi ble e g when the muscle display is turned off or the point is hidden behind another object it will still be moved or deleted with the other selected points Model Window Commands Muscle attachment points can be selected and edited using the Attachments panel described in Section 2 7 5 However that panel operates only on the current muscle while it is often desirable to modify attachment points of different muscles at the same time The muscle editing commands in the model window described below allow you to do this Muscle attachment points can be selected and edited using keyboard and mouse commands in the model window To 2 7 Muscle Editor use these commands you must first set the tool mode to the Muscle Editor by clicking on the Muscle Editor icon in the heads up display HUD on the left side of the model win dow To indicate that all keyboard and mouse commands are being directed to the Muscle Editor the icon will be high lighted with a yellow frame and the title bar of the Muscle Editor will be highlighted in yellow SELECTING ATTACHM
294. n of the heel marker at heel strike and the position of the toe marker at toe off are calculated in the ground refer ence frame and the Z values are set to 0 0 so that the points are on the floor A foot print motion object is then scaled translated and rotated so that the back of its heel is at the heel marker position and the base of its second toe is at the toe marker position With this method the size of each foot print during a motion will be approximately equal to the size of the subject s foot but the foot prints in a motion may not all be the same size In fact if the subject slides or drags his her foot on the floor after heelstrike and before toe off the foot print will be much larger than normal Thus the size of the foot prints in addition to their locations can be used to help analyze the gait pattern This option toggles the display of force plates which are usually shown as blue rectangles on the floor Force plates are defined in the motion file header and are added there when a motion capture trial TRB TRC C3D file is imported into SIMM If there are no force plates defined in the header this option is grayed out This option toggles the display of external forces in the motion data These forces are usually ground reaction forces but also include any force expressed in the ground show force trails show body forces show joint forces 2 17 Motion Editor frame If there are no external forces in the mo
295. n the heads up display HUD on the left side of the model window To indicate that all keyboard and mouse commands are being directed to the Deform Editor the icon will be highlighted with a yellow frame and the title bar of the Deform Editor will be highlighted in yellow Chapter 2 Tools 99 2 11 Deform Editor 100 Chapter 2 Tools SELECTING DEFORM OBJECTS To select a deform object press and hold the S key While this key is pressed the HUD text box in the lower left cor ner of the model window displays Selecting deform objects As you move the cursor around the model window if it hovers over a deform object the object will be high lighted and its name will be shown in a tool tip box if the deform object is already the current object in the Deform Editor it will be unhighlighted when you hover over it If you then left click on the deform object it will be selected and the Deform Editor will update to show it as the current object You cannot select more than one deform object at a time EDITING DEFORM OBJECTS To edit the current deform object press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Editing current deform object After this message will be some text describing the type of editing you can perform on the object as dictated by the current mode Position mode is for speci fying which portion of the body segment undergoes the deformat
296. n to a file you may want to change its name or the value of datarows If the file contains fewer than 200 rows of data SIMM will print a warning when it reads the file but it will still load the motion correctly Thus you can check the motion right after creating it by loading the file back into SIMM by selecting File gt Open There is currently no way to edit frames of an existing motion and save the results to a file The Motion Editor allows you to crop motions and save them to a file but you cannot modify individual frames of data To accomplish this task you must use the Model Viewer to step through the motion frame by frame altering the model configuration where desired and writing each frame to a file with the Add Motion Frame command To save the contents of a plot window to a file either the plot window must be the active i e topmost window or if a tool window is active it must be set to that plot To save the plot select File gt Save Plot and use the Windows file browser to specify the name and location of the plot file to be written SIMM can write plot files in two formats tab model archive files bone files model script files 2 3 Saving Files delimited columns of data and Postscript If the file name you specify has a ps extension then SIMM will write the plot in Postscript format which can be sent directly to a Postscript printer Otherwise SIMM will write the plot data in tab delimited colum
297. n zero in the constraint object s local refer ence frame Model Window Commands Constraint objects can be selected and edited using key board and mouse commands in the model window To use these commands you must first set the tool mode to the Constraint Editor by clicking on the Constraint Editor icon in the heads up display HUD on the left side of the model window To indicate that all keyboard and mouse com mands are being directed to the Constraint Editor the icon will be highlighted with a yellow frame and the title bar of the Constraint Editor will be highlighted in yellow SELECTING CONSTRAINT OBJECTS To select a constraint object press and hold the S key While this key is pressed the HUD text box in the lower left cor ner of the model window displays Selecting constraint objects As you move the cursor around the model window if it hovers over a constraint object the object will be high lighted and its name will be shown in a tool tip box if the constraint object is already the current object in the Con straint Editor it will be unhighlighted when you hover over it If you then left click on the constraint object it will be selected and the Constraint Editor will update to show it as Chapter 2 Tools 121 2 13 Constraint Editor 122 Chapter 2 Tools the current object You cannot select more than one con straint object at a time EDITING CONSTRAINT OBJECTS To edit the current constraint object
298. namics Tool 152 Chapter 2 Tools These pre built DLLs include models of a full body with simplified shoulder motion and lumped mass hands a lower extremity model with lumped mass upper body and a right arm model with lumped mass hand When a DLL is created the following model properties are compiled into it and thus you cannot change any of them in your SIMM model without creating a new DLL e the number of body segments e the number of joints e the number of degrees of freedom in any joint e the order of rotations in a joint The following model properties are passed from SIMM to the DLL when the initialize button is pressed and thus you can change them in SIMM without needing to reload or rec reate a DLL e the number of muscles e any property of any muscle e the mass mass center or inertia of any body segment e the clamped and locked states and range of motion of any gencoord e the restraint moments at any gencoord e the orientations of any joint s rotation axes contact objects rigid body spring based and NURBS spring e force mattes for applying external forces to the body segments 2 16 1 model gt help 2 16 2 working dir DLL input file 2 16 Dynamics Tool Selector Menu The model selector lets you select the current model If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button ope
299. nd the parameters needed to compute muscle force Ligaments can also be defined in the muscle file SIMM scans these input files and creates a data struc ture that represents the musculoskeletal model There are also motion files that contain joint angle and other data rep resenting a motion and plot files which contain any data that can be calculated by the Plot Maker Each of these types of files is described in detail in Chapter 3 Input Files About the Manual This manual describes how to use SIMM to develop and analyze musculoskeletal models Chapter 2 Tools describes the user interface and the 15 software tools Chap ter 3 Input Files details how to define a musculoskeletal model Chapter 4 Norm describes the utility program that you use to preprocess bone files before loading them into SIMM Chapter 5 Motion Module describes an optional module that allows you to easily import data recorded by a motion capture system Appendix A contains some useful tips and caveats on using SIMM Appendix B describes how to customize SIMM to better fit your needs and preferences We recommended that you read both of the appendices before using SIMM to make your own musculoskeletal models Chapter 1 Introduction 5 1 6 SIMM Tutorials 6 Chapter 1 Introduction 1 6 SIMM Tutorials SIMM comes with sample leg arm and neck models built into the software and includes several tutorials that will introduce you to the basic capabili
300. ne which region of the segment will be deformed Once the boxes are attached to the segment the inner box may be freely transformed while the outer box remains stationary As the inner box is moved or rotated all bone vertices distal joint centers muscle points and wrap objects associated with the segment that lie within the inner box follow its movement exactly Elements of the body seg Figure 2 11 Attaching Figure 2 12 Applying Deform Boxes Deformation 2 11 1 model gt help 2 11 Deform Editor ment that lie between the walls of the inner and outer boxes experience a gradually decreasing amount of deformation Elements outside the outer deform box remain unaffected Complex deformities can be modeled by attaching multiple deform objects to a body segment Each deform object is responsible for deforming the particular region of the seg ment that it surrounds Taken together the deform objects act in a sequence the output of the first deform becoming the input of the second deform and so on Interactive trans formation of multiple deform objects can be coordinated by defining a deformity object in the model s joint file A deformity is simply a description of how to manipulate multiple deform objects at once Each deformity has an associated slider added to the bottom of the Deform Editor window Dragging a deformity s slider side to side causes all deform objects associated with the deformity to move through thei
301. ned to allow you to compare data derived from other sources e g exper imental data dynamic simulations with the data that SIMM computes from your model SIMM can also write out plot files containing curves that were computed from your mus culoskeletal model The format used for input and output is the same so you can create a plot with the Plot Maker save it to a file and load it back into SIMM at a later time Also because the format is tab delimited text you can easily import plot files into other software applications for addi tional analysis To save a plot in SIMM to a file make sure the plot window is the topmost window then select File Save Plot from the SIMM menu bar To load a plot file into SIMM select File Open from the menu bar and browse for the file An example plot file is shown in Figure 3 26 Comments are indicated by a hash mark All text on a line that fol lows a is ignored by SIMM when reading the file You can specify a title for the plot using the title keyword All text on the line following title is interpreted as the title of the plot You can specify plot curves individually or in a table format much like the columns of data in a motion file In the example in Figure 3 26 three curves are specified two in the first section and one in the next After the title the X and Y variables and curve name are specified for the first set of curves The name of the X variable is ankle_angle If yo
302. nents of each force and moment are display as concentric translucent red green and blue spheres If this preference is not specified forces and moments are displayed as arrows This preference specifies the size of the spheres when forces and moments are displayed as spheres using the DISPLAY FORCES AS ARROWS preference The radius of the sphere displayed in the model window for a given force com ponent is 0 05 times this preference times the magnitude of the component This preference specifies the default low pass cutoff fre quency when smoothing columns of data in motions This default value is used only when smoothing motion data with a script command that does not explicitly specify a cutoff fre quency or when the cutoff frequency is improperly specified in the motion smoothing dialog This preference specifies whether or not to suppress the dis play of most warning and confirmation dialog boxes in SIMM Specifically all dialogs that would be displayed while executing script commands will be suppressed as this prefer ence is meant to be used in conjunction with automated SIMM scripts This preference is used when creating a spring contact object from a NURBS bone It specifies the maximum allowable Appendix B SIMM Resources B 15 B 2 Colors B 2 B 3 B 16 Appendix B SIMM Resources distance between adjacent springs when placing them on the surface of the object If this preference is not specified a default
303. nging their visibility Even if the markers are not visible they are still used by the Motion Module when importing tracked marker files Both of these marker parameters can also be changed using the Marker Editor Shown below are the parameters with their default values marker visibility no marker radius 0 005 Body Segments A body segment consists of one or more bones fixed in a reference frame The only required component of a segment definition is a name You will usually want to specify one or more bone files as well however so that you can see the body segment in the model window Other optional compo nents include the segment s material properties drawmode shadow shadow color associated deform objects and dis play of the segment s reference frame Figure 3 3 Bones are specified using the keyword bone followed by the name of the bone file and optionally the material and drawmode for displaying the bone The material is used to set the color and lighting of the bone The drawmode gives you control over the shading of the bone s surface These optional drawmode and material identifiers can be placed in any order after the file name If you do not specify the mate rial or drawmode for a bone it will inherit the material or drawmode of the segment as specified with the drawmode and material keywords If no material is assigned to the 3 3 Joint Files body segment the default material def_bone is used See
304. ngth curve of muscle is scaled linearly by muscle activation which ranges from 0 0 no activation to 1 0 full activation All of the curves are defined by listing control points that are interpolated by nat ural cubic splines There are also some circumstances under which you can model the force velocity characteristics of the muscle ten don actuators When calculating muscle force during a motion sequence you have the option of estimating the velocities of the muscle fibers and using this information to scale the isometric force computations This process works by first finding the velocities of the generalized coordinates either taken from the motion file or calculated by differen tiating the generalized coordinate position data See Section 3 5 Motion Files for details Then muscle tendon velocity is calculated and this value is distributed to the fibers and tendon based on their relative stiffnesses The more compli ant element is assigned more of the velocity To use these force velocity features you need to specify two additional parameters in the definition of each muscle The first is max_contraction_velocity which defines the maximum contraction velocity of the muscle fibers in optimal fiber lengths per second a positive number The second is the normalized force velocity function for the muscle This defines the scaling factor for the isometric force as a function of the normalized fiber velocity optimal fiber lengt
305. not specified in the constraint object definition the default values are 0 0 0 0 0 0 This parameter specifies the position of the constraint object s origin with respect to the origin of its body seg ment It is expressed as an X Y Z translation vector The default values are 0 0 0 0 0 0 The dimensions of the constraint object are specified with several keywords depending on the type of the object as described below sphere The radius of the sphere is specified by the keyword radius followed by a single value radius 0 15 active visible 3 3 Joint Files cylinder The radius of the cylinder is specified by the keyword radius followed by a single value The height of the cylin der is specified by the keyword height followed by a single value radius 0 10 height 0 25 Note the height of the cylinder is used for enforcing the constraint The constraint points are required to remain on the section of the cylinder defined by the height value plane The width X dimension and the length Y dimension of the plane are specified by the keyword radius followed by the width and length respectively radius 0 2 0 3 Note the width and length of the plane are used for enforc ing the constraint The constraint points are required to remain on the section of the plane defined by these two val ues ellipsoid The sizes of the ellipsoid in the X Y and Z directions are specified with the keyword radius fo
306. nput files described in the previous sec tion plus those used by the Motion Module can be loaded into SIMM by dragging them from a Windows file explorer window and dropping them onto a SIMM window or the SIMM background Depending on the type of file SIMM uses the specific location of where you dropped it to deter mine how the file should be imported Here are the rules SIMM follows for drag and drop One or more JNT files can be dropped onto any SIMM win dow or the background SIMM will load each one as a new model A single MSL file can be dropped onto SIMM only if dropped with a single corresponding JNT file The JNT file will be loaded as a new model using the dropped MSL file for the muscle definitions instead of the muscle file speci fied in the JNT file if any One or more model archive files can be dropped onto any SIMM window or the background SIMM will load each one as a new model One or more motion capture files can be dropped onto SIMM If the files are dropped onto the SIMM background window each file will be treated as a static trial and used to load a new SIMM model using the Mocap Model as the generic model If the files are dropped onto a SIMM model window or tool window set to a specific model they will be treated as motion trials and will be loaded onto that model Note the Motion Module or C3D Module is needed for this feature One or more plot files can be dropped at the same time If they are dro
307. ns a texture In this case the entire texture will be replaced with the image dropped onto it Movie files can be dropped one at a time onto a SIMM model window to link them to a motion If more than one motion is in the model a dialog box will be displayed that allows you to select which motion to link the movie to If no motions are in the model an error message is printed IKS 2 3 joint and muscle files motion files 2 3 Saving Files One or more IKS files can be dropped onto a SIMM model or a tool window set to a specific model They will be treated as motion trials and will be loaded onto that model Note the Motion Module or C3D Module is needed for this feature Saving Files When saving joint muscle motion and plot files to disk you use the Windows file browser to specify the name and location of the file to write Use the browser to navigate to the directory where you want the file to go then either type the name of the file to create or select an existing file to be replaced When saving files to disk SIMM does not preserve any comments that may have been present in the original input file Be careful to avoid overwriting any existing SIMM files that contain useful comments To save a model s joints or muscles either the model s win dow must be the active i e topmost window or if a tool window is active it must be set to that model To save the model s segments joints generalized coordinates and
308. ns a window containing helpful text about the Dynamics Tool When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again Input and Output Options This specifies the directory to be used for the dynamic sim ulation This directory is used as the default location for the input and output files For inverse dynamics you should set the working directory before choosing the motion so that the paths for the input and output files will be set accord ingly see Section 2 16 4 Motion For Inverse Dynamics for more details This field specifies the DLL dynamic link library to be used for the dynamic simulation This DLL can either be one that you create using the Dynamics Pipeline or a pre built one that comes with the FIT Module Make sure to select the one that matches the model you have loaded into SIMM This field specifies the input file to be used for the dynamic simulation For forward dynamics this file is optional If used it can contain external forces and muscle excitation patterns that you want to apply during the simulation For most inverse dynamics simulations you do not need to specify an input file When you select a motion see Section 2 16 4 Motion for Inverse Dynamics SIMM will automat ically fill in the input file field with the name of a new file Chapter 2 Tools 153 2 16 Dynamics Tool 154 Chapter 2 Tools output file 2 1
309. ns and add a p t extension to the file name if necessary Tab delimited plot files are designed to be easy to read or import into word processing or spread sheet programs Note SIMM cannot read plot files in Postscript format Thus plots that you intend to load back into SIMM later should be saved in the tab delimited p t format A model archive is a compressed file containing all of the files associated with a model including joint file muscle file bones files and any motion files currently linked to the model To create a model archive use the File gt Export Model Archive command The archive will contain every thing needed to load the model back into SIMM at a later time Because everything is in one file it is a good way to share models with other users or to backup your models before modifying bone files or other components that are typically shared among models Bone files can be edited and saved using the Bone Editor This tool has a graphical interface to norm as well as some simple vertex and polygon editing functions After modify ing a bone you can save it to a file using the Bone Editor s write bone 1 command A model script file is a file of scripting commands that sets model specific parameters in the SIMM tools For example it contains commands to set the output variables in the Motion Reporter and the plot creation parameters in the Plot Maker If the read_script_file and write_script_file parame ters ar
310. ns in the report as gait strides If this button is turned on SIMM will divide each motion into left and right strides based on heel strike and toe off events It will then process and average the left and right strides separately and calculate all left side output variables from the left strides and all right side output variables from the right strides Right side variables are denoted by the suffix r e g knee_flex_r semimem_r hip r and left side variables are denoted by the suffix 1 Thus this gait option must be used in conjunction with a model that has appropriately defined components Additionally if SIMM performs simu lations on the strides to calculate dynamic variables such as moments and powers it will check to make sure that the stance portion of the stride occurs on a force plate If it does not that stride will be excluded from the motion report If the gait button is turned off SIMM will not crop or divide the motions based on events Also if it performs simula tions on the motions to calculate dynamic variables it will not check that all ground contact occurs on force plates It will process each motion trial without cropping normalize it to 101 time frames and then compute averages and stan dard deviations This toggle button lets you choose whether or not to include standard deviations in the motion report If it is turned on each column of output variables the means in the report file will be followe
311. ns one or more event parameters see Section 3 5 Motion Files for details on specifying a motion events This command toggles the display of the grid lines drawn on the background of the plot This command toggles the display of the data points that comprise each plot curve This command toggles the display of crosshairs that are drawn over the plot The crosshairs track the motion of the cursor as you move it over the plot with the XY coordinates of the intersection displayed as well Also if the crosshairs are close to a data point of one of the plot curves the cross hairs will lock onto the data point When this happens the XY coordinates change color to match the curve color and their values change to match the data point s XY values This command adjusts the Y range of the plot so that the horizontal axis Y 0 is shown This can be helpful if the plotted data has a small Y range far from the origin and you want to get a better perspective on the magnitudes of the plot values This command toggles the display of the auxiliary data if any for the plot curves Auxiliary data is specified in Chapter 2 Tools 79 2 9 Plot Viewer 80 add label save plot to file Chapter 2 Tools send to gt 9 o 5 w 2 F ba N motion files using the _aux suffix and is commonly used to specify the on off activation step function that corresponds to a channel of EMG data the Bayes filtered
312. nt s reference frame The fourth number is marker s weight in the marker tracking algorithm After the weight you can optionally specify whether the marker is fixed to the body segment fixed or whether its location can be adjusted by the Motion Module and whether it is visible or not in the model window visible invisible To use the model with the Motion Module s subject specific scaling features you must also specify scaling parameters for the segments These are specified with the gait _scale key word followed by the name of the reference segment and the segment s XYZ scale factors relative to the reference segment Read Chapter 5 Motion Module for details on how to specify these parameters and how they are used To use the model in dynamic simulations with the Dynam ics Pipeline or FIT Module you must also specify the iner tial parameters of each body segment Use mass to specify the mass and masscenter to specify the XYZ location of the mass center in the body segment s reference frame The inertia matrix is specified with inertia and the values should be with respect to the mass center of the segment and relative to the segment s reference frame Chapter 3 Input Files 241 3 3 Joint Files 242 Chapter 3 Input Files 3 3 2 Fixed Segment The fixed segment is the body segment that does not move in the SIMM display when you move the joints in your mus culoskeletal model That is the origin of this segment
313. ntil you stop it This optional parameter specifies whether or not to enforce loop constraints while animating the motion If the motion file contains complete gencoord data that already satisfy the loop constraints then you can set this parameter to no so that SIMM does not recalculate them If your model does not contain closed loops of body segments this parameter has no effect This optional parameter specifies whether or not to enforce constraint objects while animating the motion If the motion file contains complete gencoord data that already satisfy the constraint objects then you can set this parameter to no so that SIMM does not recalculate them If your model does not contain any constraint objects this parameter has no effect This optional parameter turns on or off the display of the marker data as the motion is animated Markers are usually show_marker trails show_forces show force trails show_force plates show _foot_prints cursor event event _color 3 5 Motion Files shown as blue spheres but you can change their display properties by modifying the default motion object This optional parameter turns on or off the display of the marker trails as the motion is animated A marker trail is a white line showing the trajectory of the marker during the entire motion This optional parameter turns on or off the display of the forces as the motion is animated This controls the display of forceplate for
314. nto SIMM use the model selector to make sure the current model is set correctly 2 If there are already some plot windows on the screen use the plot selector to choose which plot you want to add your new curves to If you want to make a new plot window choose the first item in the pop up plot menu labeled new If there are no plot 2 5 4 2 5 Plot Maker windows yet the plot selector is already set to new so you don t have to set it 3 Select the Y variable you want to plot e g force moment using the pop up menu that is displayed when you click on y variable 4 Select the X variable you want to plot against a joint angle or motion variable using the pop up menu that is displayed when you click on x variable 5 Select the muscles whose properties you want to plot Use the muscles command to display the appropriate muscle group menus then choose the muscles from these group menus 6 Set any other options like sum active passive and curve name 7 Click on make curves Note When plotting musculotendon properties that depend on activation e g moment force make sure that the mus cle activations are set correctly they might have been changed by a motion variable See the description of act override in Section 2 5 8 Toggle Buttons for additional details Plotting Data from Motion Files To plot columns of data from a motion file you can use the motion curve command described in Section
315. nverse dynamics simulations The definition of a GCV spline must have at least six control points and looks like this begingcvspline 20 0 0 5 10 0 2 5 23 7 8 2 35 0 5 8 endgcvspline Kinematic Functions Kinematic functions define translations and rotations between body segments as functions of the generalized coordinates For example the anterior posterior translation tx between the femur and the tibia is often modeled as a function of knee angle as shown in Figure 3 6 The knee_angle tx pairs are interpolated by a natural cubic spline When defining a kinematic function you should make sure that you define it over a large enough X range so that it is defined over the complete range of motion of every generalized coordinate that uses it If you do not SIMM will extrapolate the function but this might not give the desired results depending on the type of function The X coordinates like the range of motion of gencoords should be specified in degrees for rotational gencoords For transla tional functions you should use units that are consistent with the other lengths and translations that you specify in your model meters for most models Restraint Functions Restraint functions are used primarily for controlling genco ords during forward dynamic simulations performed with Chapter 3 Input Files 251 3 3 Joint Files the Dynamics Pipeline The functions define forces or torques that are applied to the
316. nverse Kinematics solver is on changing the complexity of a model will cause SIMM to re evaluate the loop configurations SIMM will try to find a configuration that closes all the loops If no solution is found an error message is displayed and the model is displayed with broken loops Chapter 2 Tools 55 2 6 Joint Editor 56 Chapter 2 Tools 2 6 4 2 6 5 Transform Order The transform order combobox allows you to change the order in which the dofs are processed when calculating the joint kinematics which define the transformation from the parent reference frame to the child reference frame Because the dofs are processed in a body fixed manner like an XYZ Euler rotation changing their order will change the joint transform The three translations tx ty tz are always pro cessed together and are shown simply as t in the order The order that is currently specified for the joint is shown in the combobox When you left click on it a pop up menu is displayed with all 24 possible orderings of the 4 elements For most joints you will want to specify the translation first For example when defining the hip joint between the pelvis and the femur first you want to translate from the ori gin of the pelvis frame to the center of the femoral head Then you want to rotate about that point using three orthog onal axes to define a ball and socket joint Rotation Axes Form The form in the lower left corner of the Joint Editor
317. o SIMM The main pur pose of norm is to compute surface normals for the polyhe dra in the files but it can also perform other functions such as removing duplicate vertices making the polygons con vex and translating or rotating the polyhedra These fea tures can be useful if you are creating new object files from medical image data or 3D digitization and you want to load them into SIMM Most of the functionality of norm is accessible via the Bone Editor tool in SIMM This graphical interface lets you view desired rotations translations and scales to a bone before they are applied with norm The Bone Editor also has sim ple polygon and vertex editing functions which norm does not However the stand alone version of norm contains some file conversion and advanced normal calculation func tions that are not accessible in the Bone Editor Before you begin modifying your bone files it is recommended that you learn about the Bone Editor and see if it can perform all the functions you will need If not then use the stand alone version of norm described below Norm is able to process object files which contain more than one object e g a single input file containing all of the ribs of an upper body model After reading in the file norm will separate out the individual polyhedra compute surface normals for each of them then write them all to the Chapter 4 Norm 305 306 Chapter 4 Norm specified output file The polyhedra in
318. odel jnt and solver dll solver dll may be hid den in the folder view because it is a system file Copy both files to the folder on the machine where Cortex resides you ll need to exit Cortex first if it is running This will guarantee that Cortex is using the same mocap model and the same scaling algorithms as SIMM uses Open the text file S MM Resources preferences txt in a text editor such as Notepad or Wordpad Locate the line that reads CORTEX_MACHINE lt hostnames and change the host 5 2 Opening Tracked Marker Files name to the name or IP address of your Cortex machine Save and close the file You can also set the CORTEX MACHINE preference in the Scripting Tool and then save the SIMM preferences so they will be restored the next time you launch SIMM see Section 2 18 for details If your motion capture system includes forceplates copy the file forcepla cal from your Cortex computer onto your SIMM computer and put it in the folder SIMM Resources mocap misc Each motion capture session 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 and load the appropriate capture file This will load the setup cal tracks trb trc and analog anb data for the capture Select File gt Skeleton Definitions gt Create SIMM Cal cium Skeleton JNT File Make sure
319. of the Baumgarte constraint stabilization parameter used by the dynamics code to enforce con straints Number must be greater than or equal to zero initializes the simulation runs the simulation if initialized pauses the simulation if running resumes the simulation if paused stops and resets the simulation Chapter 2 Tools 209 2 21 Scripting Tool gencoord_values lt name gt lt on off gt gencoord_values lt on off gt gencoord_velocities lt name gt lt on off gt gencoord_ velocities lt on off gt gencoord_accelerations lt name gt lt on off gt gencoord_accelerations lt on off gt muscle_activations lt name gt lt on off gt muscle_activations lt on off gt muscle_lengths lt name gt lt on off gt 210 Chapter 2 Tools adds or removes the specified gencoord to the list whose values will be written to the output motion if output of gen coord values is turned on Name can also be the name of a gencoord group or the word all turns on off the output of gencoord values If output is on only the selected gencoord values will be written to the out put motion adds or removes the specified gencoord to the list whose velocities will be written to the output motion if output of gencoord velocities is turned on Name can also be the name of a gencoord group or the word all turns on off the output of gencoord velocities If output is on only the selected gencoord velocities will
320. oints and the current configuration of the model s joints It is calculated using the partial velocity method described This option is similar to the moment arm Y variable described above but uses a change in length technique to calculate the values To calculate the moment arm for a given gencoord and body position a central difference tech nique is used with the muscle length calculations The length of the muscle is calculated at the desired body posi tion and at positions corresponding to the gencoord value plus delta and the gencoord value minus delta A quadratic function is fit to these three data points and the slope at the midpoint is used as the moment arm This technique is use ful if your model includes closed loops or constraint objects which can interfere with the partial velocity method of cal culating moment arms Chapter 2 Tools 43 2 5 Plot Maker 44 fiber length norm fiber length force moment max_force gt tendon length Chapter 2 Tools The fiber length of the selected muscles To compute the fiber length of a muscle SIMM finds the static equilibrium force in the muscle tendon actuator Thus the fiber length depends on the settings of the active and passive toggle but tons see Section 2 5 8 Toggle Buttons and also on the current activation level if the active component is turned on The fiber length of the selected muscles divided by their respective optimal fiber lengths To compute
321. on off gt muscle lengths lt name gt lt on off gt 206 Chapter 2 Tools Motion Reporter Commands The following commands are available in the Scripting Tool when the Motion reporter is the current tool enter the com mand fool mr to make the Motion Reporter the current tool sets the Motion Reporter to the specified model turns on off output to the motion report of the value of the specified gencoord Name can also be the name of a genco ord group or the word all turns on off output to the motion report of the moment of the specified gencoord Name can also be the name of a gen coord group or the word all turns on off output to the motion report of the power of the specified gencoord Name can also be the name of a genco ord group or the word all turns on off output to the motion report of the reaction forces of the specified joint Name can also be the word all turns on off output to the motion report of the external forces acting on the specified body segment Name can also be the word all turns on off output to the motion report of the activation of the specified muscle Name can also be the name of a mus cle group or the word all turns on off output to the motion report of the length of the specified muscle Name can also be the name of a muscle group or the word all muscle forces lt name gt lt on off gt muscle_velocities lt name gt lt on off gt motions lt name
322. on 3 4 1 Mus cles Muscle wrap associations may also be specified within SIMM using the Wrap Editor tool The fields in a wrap object definition shown below specify the size posi tion and orientation of the geometric primitive as well as method of wrapping Wrap Object Fields wraptype This parameter specifies the type of geometric primitive to use for the wrap object The valid types are sphere cyl Chapter 3 Input Files segment xyz_ body rotation translation object dimensions 3 3 Joint Files inder ellipsoid and torus If no wrap type is specified the default type sphere is used This parameter specifies the body segment to which the wrap object is attached This parameter specifies the orientation of the wrap object as an XYZ Euler rotation The orientation is calculated by first applying the X rotation around its local X axis then the Y rotation around its new local Y axis and finally applying the Z rotation around its new local Z axis If the rotation is not specified in the wrap object definition the default val ues are 0 0 0 0 0 0 This parameter specifies the position of the wrap object s origin with respect to the origin of its body segment It is expressed as an X Y Z translation vector If no translation is specified the default values are 0 0 0 0 0 0 The dimensions of the wrap object are specified with sev eral keywords depending on the type of the object as described below
323. on displays a dialog box contain ing all of the force mattes in the model external forces expressed in the ground frame are applied to the body seg ments using force mattes This command lets you select which muscle activations you want to include in the report The output activation for each muscle is the average of its activation for each motion trial The activation for a particular motion trial depends on sev eral factors If there is no EMG data for a muscle its activa tion is whatever it is set to in the Muscle Editor default 1 0 If there is EMG data but the muscle is not included in the dynamic simulation of that motion trial then the activa tion is the smoothed EMG signal If the muscle is included in the simulation its activation is calculated using the input excitation and the equations for activation dynamics The input excitation is the EMG signal if any the specified excitation pattern if any or whatever the activation level specified in the Muscle Editor Lastly if the dynamic simu lation calculates optimized muscle activations then the acti Chapter 2 Tools 177 2 18 Motion Reporter 178 muscle lengths muscle forces muscle velocities generate report Chapter 2 Tools vations written to the motion report will be the optimized ones This command lets you select which muscle lengths you want to include in the report Muscle lengths are calculated from the kinematic data
324. ons and automatically computes a deforming transformation that restores the seg ment s origin to its original undeformed position If the seg ment s reference frame is defined such that its origin coincides with the center of its proximal joint then the result of an auto reset deform will be to restore the elements within its inner box to their original undeformed position For an auto reset deform to behave correctly the following conditions must be met 1 the origin of the body segment must coincide with the center of the segment s proximal joint 2 the inner box of the auto reset deform must contain the origin of the body segment and 3 the auto reset deform must be the last deform object in the segment s list of deforms In the hip joint example the femur segment would be mod eled such that its reference frame and proximal joint were centered within the femoral head An auto reset deform whose inner box surrounded the femoral head would be added to the end of the femur s deform list The auto reset deform s outer box would surround all of the femur except the distal joint With this setup the auto rest deform would move and rotate the femoral head back into the acetabulum with its deforming effect gradually decreasing along the length of the femur The knee joint would remain unaffected Chapter 2 Tools 105 2 11 Deform Editor 106 by the auto reset deform because it would lie outside of the auto reset deform s ou
325. ontact detection works consult the Dynamics Pipeline manual NURBS spring NURBS spring objects are used only by dynamic simula tions and they are used in conjunction with NURBS objects to model contact between a NURBS surface and a mesh of springs A NURBS spring object consists of a spring infor mation file with suffix spr that contains position normal and stiffness information about the springs You can make a spring object using the make springs obj button in the Bone Editor To learn more about how NURBS based con show mass center show segment axes show normals show inertia show all mass centers show inertia 2 14 Segment Editor tact detection works consult the Dynamics Pipeline man ual The interface in the Segment Editor does not let you define all of the properties necessary to set up NURBS based con tact detection for dynamic simulation but it does let you define and view the contact objects Once you have defined and positioned them appropriately in your model you will need to edit the joint file and enter the NURBS contact pairs NURBS contact pairs specify which objects can con tact which other objects Display Parameters This toggle button lets you turn on and off the display of the current segment s mass center location If the mass center is not specified the button is deactivated This button lets you toggle the visibility of the current seg ment s reference frame in the model window
326. ool Figure 2 4 You cannot edit the force length curves of the muscles or tendons with the Muscle Editor but read Appendix A Tips and Caveats for details on how to edit these curves interac tively in SIMM Selector Menu The model selector lets you select which model s muscles you can change with the Muscle Editor If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Muscle Editor When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again Chapter 2 Tools 57 2 7 Muscle Editor B Muscle Editor Model Lower Extremity model gt name semimem muscle Force Parameters Attachments Current Path Selected Attachments current restore current save all restore all delete attachment s gt Its 0 3590 add attachment gt force delete muscle Fmo 1030 00 lmo 0 0800 global parameters EEn 15 00 color factor 0 00 act 1 0000 edit group gt dynamic make new group amecae mass damping activation1 activation2 fatigue_factor recovery_factor muscle_model Figure 2 4 Muscle Editor window 2 7 2 Command Menu This command lets you create a new muscle or choose an existing muscle for editing When you select this item a pop up menu of existing muscles is disp
327. or locating the center of the model window which is also the center of the perspective transformation that is applied to the model view Model Window Viewing Commands All of the commands described in this section can be used to change the view of a model without opening the Model Viewer window Just activate the window of the model you want to move and press the appropriate keys The com mands described at the beginning of this section can be used even if the Model Viewer icon in the heads up display Chapter 2 Tools 31 2 4 Model Viewer 32 Chapter 2 Tools HUD is not selected The commands that do require the icon to be selected are described at the end and are indi cated as such There are two methods of changing the view of the model within the model window The first method which operates when the trackball toggle button in the Model Viewer win dow is turned on works as follows Pressing the Ctrl key and the left mouse button will pan the view within the model window As you move the cursor in any direction the model will follow Pressing the Ctrl key and the middle mouse button lets you zoom in and out of the model Mov ing the cursor to the right will zoom in and moving it left will zoom out Press the Ct r1 key and the right mouse but ton to rotate the model with a trackball method Imagine a trackball superimposed on the model window and you can move it using the cursor Moving the cursor in some direc tion
328. ord moments adds or removes the specified gencoord to the list whose powers will be written to the output motion if output of gen coord powers is turned on Name can also be the name of a gencoord group or the word all turns on off the writing of gencoord powers to the output motion If output is on only the powers of the selected gen coords will be written to the output motion turns on off the writing of spring forces to the output motion specifies the number of spring forces to include in the out put motion Space will be made in the motion file to hold Chapter 2 Tools 213 2 21 Scripting Tool moment_arms lt name gt lt onloff gt moment_arms lt on off gt muscle_moments lt name gt lt on off gt muscle moments lt on off gt total muscle moments lt name gt lt on off gt total muscle moments lt on off gt optimized_muscle_activations lt name gt lt on off gt 214 Chapter 2 Tools this many spring forces If more than this number of springs generate force during a time frame of the simulation only the first num of them will be output adds or removes the specified muscle to the list whose moment arms for all gencoords will be written to the output motion if output of muscle moment arms is turned on Name can also be the name of a muscle group turns on off the writing of muscle moment arms to the out put motion If output is on only the moment arms of the selected muscles will be w
329. organized into sheets If you are using the Gait Model that comes with SIMM you should name this file GaitModel_data xls The Gait Model includes an Excel file of formatted graphs called GaitModel_report xls This graphs file links to GaitModel_data xls to get the data for the graphs as well as NormalData xls for normal data Thus if you generate a report called GaitModel data xls you can then open GaitModel_report xls in Excel select the option to update links and see the report data in the updated graphs Subject Information Form The name of the subject or patient The name of the examiner technician supervising clinician physical therapist etc A brief description of the study or condition The height of the subject This value is not used for any model calculations it is merely copied to the motion report The weight of the subject This value is not used for any model calculations it is merely copied to the motion report The age of the subject The subject ID This can be any string of characters or num bers The date the motion trials were collected The format day month year is preferred but since this information is not Chapter 2 Tools 179 2 18 Motion Reporter 2 18 5 gait standard deviations 180 Chapter 2 Tools used by SIMM and merely copied to the motion report month day year is also acceptable Toggle Buttons This toggle button controls whether or not SIMM should treat the motio
330. ormat supported by SIMM and norm is a binary format The information in the file is identical to that in the old SIMM ASCII format but the file is binary in order to reduce its size This format is identified with the bin file suffix Previous versions of SIMM required bones to be in this binary format so corresponding versions of norm would output binary bone files by default Note when a musculoskeletal model is loaded into SIMM all of the model s bones that are specified in the SIMM binary format are automatically processed with norm so that the vertex normal information is available For bones with many polygons this can add significantly to the time it takes to load a model Thus for large bone files it is recom mended that you convert them to the SIMM ASCII format before adding them to your model Chapter 3 Input Files 227 3 2 Bone Files 228 Chapter 3 Input Files 3 2 4 Wavefront OBJ SIMM also supports bone files in the Wavefront OBJ for mat identified with the obj file suffix This is an ASCII for mat developed by Wavefront Technologies that contains positions and normals of the vertices plus how they are connected into polygons Comments can be included in the file by beginning the line with a An example is shown in Figure3 3 OBJ files can also contain UV texture coordi nates for each vertex as well references to files with mate rial and texture information However these material and texture data ar
331. ormation from the heel strike and toe off events so you normally do not need to specify these values yourself Other Data Columns of motion data that do not correspond to general ized coordinates muscles or motion objects are called other data These columns must contain datarows ele ments like all data columns but they do not need to corre spond directly to anything in a model For example they can be used for plotting previously computed joint moments or accelerations during gait You can put columns of other data anywhere in the motion file just make sure that the data lines up with the column names When SIMM reads the motion file it will automatically figure out which columns correspond to model components e g generalized coordinates and which ones are other data It will print the other data column names to the message window so you can see which ones SIMM did not associate with a model component 3 5 5 3 5 6 3 5 Motion Files Standard Deviation Data For any of the columns of data in a motion file except mus cle activations and motion object components you can also specify standard deviations of the values for each time frame This is useful if you averaged recorded data from several motions and want to display the standard deviations along with the averages To specify them for a column of data add a second column of data containing the non nega tive values for one standard deviation and label the col
332. orso TY 0 296529 0 056601 unclamped unlocked gencoord lower torso TZ 0 978603 0 147046 unclamped unlocked gencoord lower torso RX 95 196316 34 665062 unclamped unlocked gencoord lower torso RY 7 692675 45 201578 unclamped unlocked gencoord lower torso RZ 165 942628 6 438312 unclamped unlocked gencoord lumbar roll 6 413519 51 289117 clamped unlocked gencoord lumbar yaw 6 227815 90 353578 clamped unlocked gencoord lumbar pitch 16 100601 13 478036 clamped unlocked gencoord hip add r 1 303244 25 054797 clamped unlocked gencoord hip rot _r 5 860699 38 671449 clamped unlocked gencoord hip flex r 20 731736 116 748438 clamped unlocked gencoord knee flex r 18 675811 53 727468 clamped unlocked gencoord ankle flex r 3 320019 23 947414 clamped unlocked gencoord subt_ angle r 29 011612 0 023848 clamped unlocked gencoord toe angle r 0 000000 0 000000 clamped unlocked gencoord hip add 1 8 522440 50 374307 clamped unlocked gencoord hip rot 1 9 505861 21 264489 clamped unlocked gencoord hip flex 1 29 704103 90 207294 clamped unlocked gencoord knee flex 1 56 643236 159 016982 clamped unlocked gencoord ankle flex 1 13 763388 84 145542 clamped unlocked gencoord subt_ angle 1 27 571145 6 870360 clamped unlocked gencoord toe angle 1 0 000000 0 000000 clamped unlocked muscle semimem r 0 088945 on muscle semiten r 0 088945 on muscle bi fem 1h r 0 000000 on muscle bi fem sh r 0 000000 off muscle rectus fem r 0 040599 on muscle semimem 1 0 350749 on
333. ota tion mode Also a circle is drawn over the model centered on the origin of the bone with the current XYZ rotation angles shown next to it Dragging the cursor moves a virtual trackball that controls the rotation of the bone Release the middle mouse button when you are done As you transform x 2 s 2 15 Bone Editor the bone with any of these editing commands a ghost bone is drawn showing its original position in the model You can also translate the bone along the X Y and Z axes of its body segment using the x y z and Shift keys Pressing x translates the bone in the negative X direction while pressing Shift and x translates it in the positive X direction similarly for Y and Z RIGHT CLICKING BONES You can right click on a bone to display a pop up menu with several display and editing options The options allow you to change the drawmode and material of the bone display its normal vectors display the body segment s reference frame center the viewing transformations on the segment and select the bone or its body segment for editing Note you can right click on any bone without holding down any keyboard keys and without first clicking on the Bone Editor icon in the HUD SELECTING POLYGONS PATCHES If bone 1 is a polyhedron you can use model window com mands to select and edit its polygons If the bone is a NURBS surface the same commands will select and edit the patches on the surface To se
334. otate fields then click the button below the text fields one or more times to apply the transform If the transform in local frame radiobutton is selected then the specified transform will be applied relative to the deform object s local XYZ axes Otherwise the transform will be applied relative to the deform object s parent segment s XYZ axes To apply the inverse transform click the but ton To clear all values from the translate and rotate fields click the clear button Current Transform Display The deform object s current transform is displayed in the lower right corner of the Deform Editor window as a sequence of XYZ rotations and an XYZ translation The order of the rotation sequence that is displayed is X fol lowed by Y followed by Z This order cannot be changed If the transform in local frame radiobutton is selected then the rotations displayed are about the deform object s local XYZ reset 2 11 6 2 11 Deform Editor axes a k a body fixed rotation If the transform in parent frame radiobutton is selected then the rotation sequence displayed is about the deform object s parent segment s XYZ axes a k a space fixed rotation Click the reset button to restore the current deform object s transform to identity In position mode this will realign the deform object s reference frame with its associated body segment s reference frame In deform start or deform end modes this will realign the deform object s inner box
335. otion was recorded These files thus contain a series of 2 12 Marker Editor p BM Marker Editor x Model Anteversion Model model gt marker gt name R Knee save selected segment femur_r Fi Sel sacks offset 0 00000 0 40400 0 05000 delete selected weight 1 00000 restore selected restore all visible fixed unselect all 1 marker is selected radius 0 00500 wisible Figure 2 18 Marker Editor window marker clouds each one representing the 3D coordinates of all the markers on the subject at a particular instant of time during the motion The Motion Module reads these marker data and fits the SIMM model within the marker cloud for each time frame By placing markers on the SIMM model that match the names and positions of the markers placed on the subject the Motion Module is able to adjust the model s gencoord values to determine a best fit of the model to the marker cloud The result is a SIMM motion that matches the TRC or TRB motion Chapter 2 Tools 109 2 12 Marker Editor 110 2 12 1 model gt help 2 12 2 marker gt save selected save all Chapter 2 Tools Selector Menu The model selector lets you select the current model If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Marker Editor
336. ou can enter your own title to an existing plot at any time This field contains the text string that will be used to name the next data curve that is generated If the field is empty when a curve is created a default name will be used The default name depends on what you are plotting and the set tings of the plotting options as follows When plotting computed muscle properties from your model the curve name depends on the setting of the sum option If sum is turned off the name of each curve gener ated defaults to the name of the muscle used to create it If the sum option is on then the curve name defaults to a con catenation of muscle names used to make the curve When plotting data from motion files the default curve name is the name of the motion followed by the label of the column of data as it appears in the motion file When plotting data from plot files the default curve name is the name of the file You can change this default either by entering the name of the curve directly into the plot file see Section 3 6 Plot Files for details or by editing the curve name field If you enter your own curve name and then try to generate multiple curves at once by selecting several muscles and turning off the sum option the curve name will be deleted and default names will be used for all the curves When this happens it usually indicates that you have forgotten to turn off the swm option or to select only one muscle for plo
337. ovies marker cloud defined 311 Marker Editor 108 115 command menu 110 information header region 110 model window commands 113 moving markers 115 selecting markers 114 markers Index 4 creating 110 deleting 111 fixed 112 moving 115 name 111 offset 112 radius 113 restoring from buffer 111 saving to buffer 110 segment of attachment 112 selecting 114 unselecting 111 visible 112 weight 112 mass specifying for body segments 129 mass center specifying for body segments 129 material properties ambient 256 diffuse 256 emission 256 specular 256 materials assigning to body segments 238 assigning to bones 238 assigning to world objects 254 default 256 258 defined 256 properties see material properties setting in Segment Editor 128 max positive moment defined 45 maximum isometric force defined 63 menu defined 7 mocap model 328 340 choosing 330 joint center calculations 335 marker set 338 scaling 336 static pose 331 model archive files 300 opening 14 saving 19 model display animating motions 30 33 moving joints 34 muscle attachment points 31 rotating 32 trackball method 31 zooming and panning 31 model poses restoring 22 saving 23 specifying in joint file 275 model selector defined 10 model view see camera Model Viewer 20 36 generalized coordinate form 28 information header region 20 model name form 29 model window viewing commands 31 moving joints 34 rotating the model 32 sli
338. owing all of the markers in the model The ones that have data in the motion are checked You can use this dialog to select which markers you want to display during playback This option toggles the display of marker trail lines which are white lines showing the trajectory of each marker during the entire motion If there is no marker data in the motion this option is grayed out You can right click on the check box to display a dialog box showing all of the markers in the model The ones that have data in the motion are checked You can use this dialog to select which marker trails you want to display during playback Chapter 2 Tools 167 2 17 Motion Editor 168 show marker trails points show foot prints show force plates show external forces Chapter 2 Tools This option toggles the display of marker trail points which are light blue spheres showing the positions of each marker at every time frame during the motion If there is no marker data in the motion this option is grayed out You can right click on the checkbox to display a dialog box showing all of the markers in the model The ones that have data in the motion are checked You can use this dialog to select which marker trails you want to display during playback This option toggles the display of foot prints which are dis played on the floor to represent the position of the foot dur ing stance Each foot print is calculated as follows First the positio
339. parameters form in the Muscle Editor it merely sets the activations for plotting purposes only to reset activations in the parameters Chapter 2 Tools 51 2 5 Plot Maker 52 Chapter 2 Tools isometric form to their defaults see reset activations in Section 2 7 2 Command Menu When act override is turned off the mus cles individual activations as listed in the parameters form will be used This toggle button is particularly useful when you have loaded a motion file which contains muscle acti vations see Section 3 5 Motion Files After animating the model according to the motion the muscle activations will be changed to match the values in the motion file so that their size and color will vary during the animation How ever if you want to plot the muscles maximum isometric forces during the motion you can simply set the Plot Maker s activation level to 1 0 and turn on act override rather than individually changing each muscle s activation in the Muscle Editor There is no way to override just a sub set of the muscle activations The current setting of act override has no effect if you are plotting data from plot data files or columns of data from motion files This toggle button gives you control over the use of the force velocity characteristics of the muscle fibers when cal culating muscle force during a motion When on fiber velocities are set to zero and isometric muscle forces are calculated When off
340. path as it attempts to wrap over the active quad rants of the wrap object If this occurs you should rotate or translate the wrap object until the muscle paths behave as desired Cloning a wrap object can be useful if you are having trou ble getting several muscles to wrap properly over a single wrap object For example if you already have a wrap object in place with two muscles wrapping over it but would need to translate or rotate it slightly to properly wrap a third mus cle you can instead clone the object adjust it as needed and apply it only to the third muscle To clone a wrap object right click on it in the model window and choose clone from the pop up menu Deform Editor The Deform Editor allows you to twist bend and warp por tions of a body segment that would normally be considered rigid When a segment is deformed all bone vertices distal joint centers muscle attachment points and muscle wrap ping objects in the deformed region are transformed accord ingly In this way the effect of a bone deformity can be examined and measured using SIMM s other tools Modeling Bone Deformities in SIMM Bone deformities are simulated in SIMM by assigning one or more deform objects to a body segment A deform object Chapter 2 Tools 93 2 11 Deform Editor 94 Chapter 2 Tools is defined by two regular six sided boxes an inner box and an outer box These two boxes are attached to a portion of the segment to determi
341. pen each one and create a new model from it How ever when selecting more than one joint file you cannot select more than one muscle file as well because SIMM has no way to determine which muscle file corresponds to which joint file If you want to load multiple joint files at once you should specify the corresponding muscle file names within each joint file A bone file defines a mesh of polygons representing the sur face of an object Bone files in SIMM are used to define not only anatomical bones but also world objects motion objects force mattes spring floors and contact objects You cannot open bone files using the File menu in SIMM though you can load them into a model using the Bone Edi motion files 2 2 Opening Files tor see Section 2 15 for details Instead bones are refer enced from within a joint file and loaded automatically when the joint file is loaded To locate bone files for bones referenced in a joint file SIMM searches the folders in the following list in the order shown If a particular folder does not exist or the bone file is not found in it SIMM proceeds to the next folder in the list 1 the folder specified by the bone path parameter in the joint file 2 the folder bones in the folder containing the joint file 3 the folder containing the joint file 4 the folder specified by the BONES FOLDER preference this preference if not defined by the user defaults to Simm Resources bones 5
342. plain 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 Non critical markers are all other markers in the set Note starting with SIMM 4 0 the critical marker set has been modified slightly For example instead of using the sacral marker V Sacral you may use the right and left PSIS markers R PSIS and L PSIS Consult the Guide to Mocap Model Markers for complete details on which combinations of marker sets are required for all of the mocap models Once the Motion Module has determined the locations of the joint centers and the orientations of the segment refer Chapter 5 Motion Module 339 5 4 Analog Configuration Files 5 4 340 Chapter 5 Motion Module ence frames from the static pose it calculates the proper off sets for all of the critical markers plus the static only medial markers For examp
343. pose for more accurate calcula tion of knee and ankle joint centers You can also supple ment 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 Choose which of the six OrthoTrak marker sets you would like to use for capturing motion Add the medial knee and ankle markers for better calcula tion of knee and ankle centers not required but highly rec ommended 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 as described in Section 5 3 5 The Marker Set 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 out from their body with their thumbs facing forward Remove the medial knee and ankle markers and any others that you do not want to use for capturing motion Note If you use a marker set with no upper extremity mark ers the Motion Module will remove the upper extremity from the mocap model and display only th
344. ppears then it must be followed by an integer number that SIMM uses as the voltage usually in millivolts for the maximum voluntary contraction when scaling that EMG channel If no MVC value is specified 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 Here are some example channel mappings Rt rectus muscles rectus fem_r mvc 500 Rt tibialis muscles tib_ant_r mvc 735 Rt gastroc muscles gas lat r gas med r Chapter 5 Motion Module 343 5 4 Analog Configuration Files marker other data 344 Chapter 5 Motion Module Rt hamstring muscles semimem_r semiten r This keyword specifies a critical marker SIMM uses criti cal markers to measure the lengths of the body segments in the static trial in order to scale the mocap model to fit the subject The critical markers must be given special names so that SIMM can recognize them and SIMM has several built in names for each marker For example the built in names for the right ASIS marker are R ASIS RASIS RAST and RILI If you use any one of these names for the right ASIS marker in your motion data then SIMM will automat ically recognize it as the appropriate critical marker If you do not want to use one of those names or you have numer ous motion trials that have already been captured and pro cessed using a different marker name you can define a mappin
345. pped onto a plot or plotkey window they will be Chapter 2 Tools 15 2 2 Opening Files 16 Chapter 2 Tools MOT ASC OBJ STL STLB DAE SSC TXT JPG TIF WMV AVI MPG MOV Mp4 added to that plot If they are dropped anywhere else a new plot will be created to hold the data One or more motion files can be dropped onto a SIMM model window or tool window set to a specific model They will be added to the model associated with that window One or more bone files can be dropped onto a SIMM model window They will be added as bones to the body segment on which they are dropped If they are dropped onto some thing in the model window that is not associated with a spe cific body segment they will be added to the ground segment A single script file can be dropped onto SIMM If the file is dropped onto a model window or any window if there is only one model loaded the model specific commands in the file are executed with respect to that model e g speci fying settings in the tool windows If there are multiple models loaded into SIMM and the script file is dropped onto a window not associated with a particular model e g back ground window plot SIMM will execute only the com mands in the file that are not specific to a model A single image file can be dropped onto a SIMM model window in order to change a texture The pixel on which it is dropped must be part of a bone or world object which already contai
346. preserved in the scaled model the alternative is to scale the mass of each body segment based on its geometric scaling For more information on scaling mass parameters see Section 5 3 4 Scaling the Mocap Model This preference is used to initialize the appropriate checkbox in the static import dialog box but you can change it as you load individ ual static trials For C3D import only This preference specifies whether the marker names for the static trial should be read from the POINT LABELS field or the POINT DESCRIPTIONS field in the C3D file This preference is used to initialize the appro priate field in the static import dialog box but you can change it as you load individual motion trials This preference specifies whether or not to save a joint file for the scaled model when importing a static trial This prefer Appendix B SIMM Resources B 11 B 1 Preferences MOCAP STATIC JOINT FILE MOCAP STATIC SAVE MUSCLE FILE MOCAP STATIC MUSCLE FILE TIE PM OPTIONS TO PLOT B 12 Appendix B SIMM Resources ence is used to initialize the appropriate checkbox in the static import dialog box but you can change it as you load individual static trials This preference specifies the name of the joint file to create when importing a static trial For most applications you do not want to explicitly set this preference because every time you import a static trial the saved joint file will have the same name unless you browse
347. press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Editing current constraint object Also a GUI box will be dis played around the constraint object This box lets you move rotate and scale the constraint object by left clicking on the box handles As you hover the cursor over a handle a tool tip describes the handle s function To move the constraint object click on any edge of the box and drag it to a new location To rotate the constraint object about its local X Y or Z axis click on one of the 6 circles on the box faces and spin it To scale the constraint object click on any of the GUI boxes at the corners of the box the midpoints of the edges or the centers of the faces and drag them Note not all GUI boxes will be displayed for all constraint object types For example spheres can only be scaled uniformly so there are no edge or face handles which would scale non uniformly RIGHT CLICKING CONSTRAINT OBJECTS You can right click on a constraint object to display a pop up menu with several editing options The options allow you to select the object for editing activate deactivate it hide its display hide all constraint objects other than this one and delete the object Note you can right click on any constraint object without holding down any keyboard keys and without first clicking on the Constraint Editor icon in the HUD 2 13 5 cl
348. ps of bones to one or multiple files There are three options you can choose from the pop up menu bone 1 gt operation gt 2 15 Bone Editor all bones as OBJ files same frames This option exports each bone in each body segment to its own OBJ file keeping it in the reference frame of its body segment This is an easy way to convert all of a model s bones to the OBJ format all bones to one file frame ground This option exports a single file ASC or OBJ containing every bone in the model Using the current model pose each bone is transformed into the ground reference frame and added to the file This is an easy way to create a single bone file containing the model s skeleton in a certain pose all bones in lt segment gt to one file frame ground This option is available if bone 1 is set to a valid bone It exports a single file ASC or OBJ containing every bone in the body segment of bone 1 Using the current model pose each bone in the segment is transformed into the ground ref erence frame and added to the file This is an easy way to merge all of a segment s bones into a single file This button lets you choose bone 1 Bone 1 is the current bone which can be transformed using the norm functions edited with the polygon and vertex editing functions and written to a file Bone 1 is also the first bone in the boolean operation as shown in the boolean equation below this but ton This button
349. ptive MVCs for EMGs IV use Bayes filter for EMGs live model update V load personal dat I output model markers Save Options I save HTR file save motion file Figure 5 1 Tracked Marker Import Dialog Box This checkbox is enabled when you select more than one tracked marker file for import If checked SIMM will use the current settings in the dialog for importing all remaining files instead of presenting the dialog when each file is opened If you keep the first and last frame fields see the next option below at their initial values SIMM will assume that you want to import all frames of all files If you set them to any other values SIMM will use those same values on all files For example if you set them to 100 and 200 SIMM will import only frames 100 to 200 of each file If this checkbox is checked and you also choose to save HTR Chapter 5 Motion Module 315 5 2 Opening Tracked Marker Files 316 import frames to increment quick solve crop ends Chapter 5 Motion Module or motion files SIMM will generate appropriate names for each output file and write it to the folder chosen in the dia log Note if this box is checked and you press the Cancel button the import of all remaining files will be cancelled Import Motion Trial Options 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 star
350. put motion If output is on only the reaction forces of the selected joints will be written to the output motion Joint_reaction_torques lt name gt lt on off gt joint_reaction_torques lt on off gt gencoord_moments lt name gt lt onl off gt gencoord_moments lt on off gt corrected_gencoord_moments lt on off gt gencoord_powers lt name gt lt on off gt gencoord_powers lt on off gt spring forces lt on off gt num_spring forces lt num gt 2 21 Scripting Tool adds or removes the specified joint to the list whose reac tion torques will be written to the output motion if output of joint reaction torques is turned on Name can also be the word all turns on off the writing of joint reaction torques to the out put motion If output is on only the reaction torques of the selected joints will be written to the output motion adds or removes the specified gencoord to the list whose moments will be written to the output motion if output of gencoord moments is turned on Name can also be the name of a gencoord group or the word all turns on off the writing of gencoord moments to the output motion If output is on only the moments of the selected gencoords will be written to the output motion specifies whether or not corrected gencoord moments should be written to the output motion See Section 2 16 Dynamics Tool for an explanation of the differences between gencoord moments and corrected genco
351. r your plots of muscle moment arms are not as smooth as you d like you should be able to achieve a smooth motion by experimenting with the midpoint or axial algorithms In rare cases you may need to change the position or orienta tion of your wrap object to achieve smooth wrapping motion 2 10 Wrap Editor THE HYBRID WRAPPING METHOD The hybrid method chooses a wrapping path by computing a weighted average of the results of the other two methods described below The accuracy of each result is used to determine its contribution to the overall path In most cases this results in a smooth transition between the two wrapping methods Occasionally you may experience an artificial change in slope in plots generated from muscles that use the hybrid wrapping method This is a side effect of the hybrid method that can occur as the weighting shifts from favoring the midpoint result to favoring the axial result or vice versa In this situation you can use the wrap method radiobuttons in the Wrap Editor or Muscle Editor tools to restrict the choice of wrapping algorithm to either the midpoint or axial methods thereby avoiding artifacts cre ated as the hybrid method blends between the midpoint and axial methods In most cases however the hybrid method will produce the best wrapping result THE MIDPOINT WRAPPING METHOD The midpoint method chooses a wrapping plane i e the plane the muscle path will occupy when wrapped around the ellipsoid b
352. r extrem ity model are shown to demonstrate the format of each file The input files that define this model are provided with SIMM It is often helpful to edit these files and then reload them into SIMM when you are learning to create your own models The files can also serve as templates when you make a new model This chapter also describes motion files Section 3 5 plot files Section 3 6 and model archive files Section 3 7 Chapter 3 Input Files 221 3 2 Bone Files 222 Chapter 3 Input Files 3 2 Motion files are used to specify the values of the general ized coordinates during a particular motion They are used to animate the model and to plot data versus a motion parameter For example if you define a motion file that specifies the generalized coordinate values during pedaling you can display the model as it moves through the pedaling cycle and plot independent variables vs the crank angle Plot data files are helpful for comparing data from outside sources to data computed with the model Model archive files are compressed archives that contain all of the files needed for a model Note SIMM does not impose specific units on your muscu loskeletal model nor do you need to define units explicitly It assumes that the numbers you enter into data files for bone vertices muscle parameters and joint kinematics are internally consistent and it uses them as is to calculate dependent variables such as muscle length
353. r range of motion at the same time Selector Menu The model selector lets you choose which model s deform objects you wish to edit When you select a new model with the model selector the Deform Editor window is redrawn with the new model s settings If the current model has no deform objects in it then the Deform Editor window will be blank except for the segment and deform object buttons which will let you add new deform objects to the model Clicking on the help button opens a window containing helpful text about the Deform Editor When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again Chapter 2 Tools 95 2 11 Deform Editor 96 G E Deform Editor xs Model Anteversion Model model gt mm a segment femur deform object gt object Mame anteversion min max min max E E MoRo e ao 0 0050 E 0 0800 0 0650 E 0 0900 inner box outer box delete Z 0 0800 fZ 0 0800 Z 0 0900 fZ 0 0900 l active position auto reset pA visible transform b deform start translate rotate y deform end body fixed rotation translation transform in bs 0 00 0 0000 N y 0 00 0 0000 gt local frame 0 00 0 0000 y parent frame reset anteversion_angle 40 000 ltroch_angle 0 000 neckshaft_angle 125 000 Figure 2 13 Deform Editor window 2 11 2 Command Menu Select this command to specify the current segm
354. rdinates 2 21 2 21 Scripting Tool This command makes a copy of the current function and switches the model component to use the copy This com mand is useful if a function is used by several model com ponents but you want to modify it only for the one you selected for editing This command creates a new function with two control points and switches the model component to use it The pre vious function is not deleted even if it is no longer used by any model component This item turns on or off the display of cross hairs when the cursor is in the function editing area In addition to the cross hairs the XY coordinates of their intersection are displayed as well This command resets the view of the function editing area so that all of the control points are visible in the window This command resets the view of the function editing area so that all of the function is visible in the window This item is enabled only if you right click on a control point or knot It displays a dialog box with fields for enter ing X and Y coordinates If you click on a knot all of the control points in the knot will be moved to the new coordi nates Scripting Tool The Scripting Tool Figure 2 28 lets you type SIMM com mands into a console window allowing you to perform sim ple batch processing The functions in SIMM that are currently accessible via the Scripting Tool are all file open close commands every function in the Model View
355. re considered to be identical The resulting event uses the time of the force event and the side left right of the marker event This tolerance can be relatively large e g 0 1 seconds to account for noise in the marker data without sacrificing the accuracy of the calculations This preference specifies the size of the moving window in seconds that is used to smooth raw EMG data The value is used to initialize the appropriate field in the motion import dialog box but you can change it as you load individual motion trials Appendix B SIMM Resources B 5 B 1 Preferences EMG SMOOTHING PASSES MOCAP_ INCREMENT MOCAP SHOW MARKERS MOCAP CROP ENDS MOCAP CALC GAIT EVENTS B 6 Appendix B SIMM Resources This preference specifies the number of smoothing passes performed on raw EMG data The value is used to initialize the appropriate field in the motion import dialog box but you can change it as you load individual motion trials This preference specifies the frame increment to use when importing motion trials A value of 1 means to import every frame a value of 2 means to import every other frame The value is used to initialize the appropriate field in the motion import dialog box but you can change it as you load individ ual motion trials This preference specifies whether or not to include the global XYZ marker positions in the motion created when importing a TRB TRC C3D file If they are included you can display
356. re still counted for the purposes of deter mining the range of muscle path segments to consider for wrapping If you do not specify a range of points for the wrap object association then the entire muscle path will be used Muscle Surfaces Muscle surfaces are objects designed to make the display of your musculoskeletal models more realistic They do not contain any biomechanical properties such as lines of action or optimal fiber lengths but rather are hollow shells that represent the surfaces of the muscles Like muscles each section of the muscle surface is attached to a body segment so the surface will change shape as you move the joints A muscle surface is a roughly cylindrical shape that is defined by a group of lines that run down the length of the cylinder Each line is defined much like the series of attach ment points of a normal muscle between the keywords beginpoints and endpoints you can even specify wrap ping points This group of lines is then put between the keywords beginmusclesurface and endmusclesurface to define the complete surface The points within each muscle line should be ordered in the same direction e g proximal to distal The sequence of muscle lines when viewed from the outside should be ordered left to right assuming the points within each line are ordered top to bottom If the points are ordered bottom to top then the sequence of lines should proceed right to left The last line of points in the
357. reasing It is recommended that all motion files you load into SIMM include a column of time data See Section 3 5 1 Motion File Header for more information about spec ifying time and the X column in a motion file Sliders Next to each field in the generalized coordinates form is a slider which can be used to change the value of the corre sponding generalized coordinate You can move the slider thumb to change the value quickly or press the left and right arrow buttons to decrease or increase respectively the value a little at a time The slider can not be used to set the gencoord value outside its range If the gencoord value is outside its range the slider thumb will display a red arrow to show this If the current model has any motions linked to it sliders for these motions are also located here Between each gencoord field and slider are two toggle but tons used to clamp labeled C and lock labeled L the gencoord Gencoords can be clamped or locked from either the Model Viewer window or the Gencoord Editor window If a gencoord is clamped its value can never go outside its range If for example a value outside the range is read in from a motion file the gencoord value will be set to the closest limiting value the range start or end If a gencoord is unclamped the value is allowed to go outside the range If a gencoord is locked its value cannot be changed by entering a new value in the form field or by moving
358. ritten to the output motion adds or removes the specified gencoord to the list whose muscle moments will be written to the output motion if out put of muscle moments is turned on Name can also be the name of a gencoord group or the word all turns on off the writing of muscle moments to the output motion If output is on only the muscle moments of the selected gencoords will be written to the output motion adds or removes the specified gencoord to the list whose total muscle moments will be written to the output motion if output of total muscle moments is turned on Name can also be the name of a gencoord group or the word all turns on off the writing of total muscle moments to the out put motion If output is on only the total muscle moments of the selected gencoords will be written to the output motion controls which muscles and which gencoords are used in static optimization of muscle activations Name can be the name of a gencoord gencoord group or all_gencoords It can also be the name of a muscle muscle group or all muscles optimized_muscle_activations lt on off gt 2 21 6 set model lt model gt set motion lt motion gt set event lt name gt set event lt time gt normalize normalize lt motion gt smooth smooth lt motion gt smooth lt motion gt lt frequency gt smooth lt motion gt lt tab gt lt frequency gt 2 21 Scripting Tool specifies whether or not the sim
359. rkers which is more than the number used in most appli cations 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 applications Then for a particular applica tion the mocap model will have all the necessary markers and the unused ones will automatically be removed when the model is loaded into SIMM To add or change markers in the mocap model use the Marker Editor which is described in Section 2 12 As dis cussed in Section 5 3 1 you should be careful not to over write the original GaitModel jnt file Instead after editing 5 3 Using the Mocap Model the marker set save the model to a new file name and copy the altered markers into GaitModel jnt All of the markers in the mocap model have X Y and Z offsets that put them in realistic locations given the dimen sions of the generic model Thus if you load the unscaled mocap model into SIMM by dragging it from a Windows file explorer and dropping it onto SIMM or using the File Open command in the menu bar 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 Moa ule to process any marker data To ex
360. roup of selected points If you click on an already selected point it will be unselected You can also box select spring points by pressing and holding down the left mouse button and drag ging the cursor to form a rectangle around the points you want to select or unselect As you select spring points the Segment Editor window is updated to show the new parameter values If more than one point is selected and they do not have identical parameter values those parameter fields in the tool window will be blank EDITING SPRING POINTS To edit the current segment first make sure the p button next to the Segment Editor icon in the HUD is highlighted then press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Moving spring points net move seg X Y Z where X Y and Z are the distances that the points have moved relative to the body segment seg If all of the selected spring points are attached to the same body seg ment then seg is that segment Otherwise seg is the current segment in the Segment Editor the one containing the con tact polyhedron To translate the selected points in the plane of the screen press and hold down the left mouse but ton anywhere in the model window and move it to drag the points in that direction A green arrow is also drawn in the model window starting at the original location of the first x Z 2 15 2 15 Bone Editor
361. s The dialog also contains a checkbox called Display as arrows This controls whether the joint reaction forces are displayed as arrows or as translucent spheres When dis played as arrows you can select which joints you want to display For each joint selected the XYZ components of the reaction force are shown as a single arrow When the forces are displayed as spheres each force component X Y and Z is displayed as its own sphere with red for X green for Chapter 2 Tools 169 2 17 Motion Editor show joint torques show contact forces show spring forces 170 Chapter 2 Tools Y and blue for Z Each sphere is centered on the joint cen ter and drawn partially transparent to help see overlapping spheres This option toggles the display of joint reaction torques in the motion data if there are none this option is grayed out You can right click on the checkbox to display a dialog box showing all of the joint reaction forces in the motion which you can use to turn on or off the display of individual forces The dialog also contains a checkbox called Display as arrows This controls whether the joint reaction torques are displayed as arrows or as translucent spheres When dis played as arrows you can select which joints you want to display For each joint selected the XYZ components of the reaction torque are shown as a single arrow When the torques are displayed as spheres each torque component X Y and Z is displ
362. s unclamped and the yellow vertical line shows the current value of the gencoord 2 20 Function Editor Bi Function Editor l Model Gait Model model gt Restraint Function for knee_flex_r IN 40 60 80 100 120 140 160 180 knee flex _t save restore control points Figure 2 29 Gencoord Restraint Editing This figure shows the Function Editor editing the restraint function for the knee_flex_r gencoord The Y axis is Newton meters of moment and the X axis is degrees The red regions on the ends indicate that the gencoord is clamped so its value in SIMM cannot leave the gray region During dynamic simula tions the gencoord can go outside this range but when it does the restraint function applies a moment to push it back Note If you create a function that has steep slopes or sharp corners the display of the function may look choppy That is you may be able to notice the series of line segments that is used to approximate the curve in the graph area This piece wise linear approximation is for display purposes Chapter 2 Tools 193 2 20 Function Editor add point add knot point 194 Chapter 2 Tools delete point change type switch to only When SIMM needs to evaluate the function for use in the model it finds an exact solution using the algebraic form of the function RIGHT CLICK MENU In addition to clicking on the function s control points and moving them you can also modify the fun
363. s Cutoff SIMM will generate this file when you press the initialize button When you choose a motion SIMM will also fill in the output file field with the name of a file in the working directory that will hold the results of the simulation Lastly when you choose a motion SIMM will fill in the three simu lation time fields with time values taken from the motion data Chapter 2 Tools 155 2 16 Dynamics Tool 156 2 16 5 kinematics forces EMG 2 16 6 muscles gt normalize gt Chapter 2 Tools Smoothing Low Pass Cutoff The following smoothing parameters are used only for smoothing data that is contained in the motion chosen with the motion button If you do not choose a motion but instead specify an input file that you created for the simula tion you can perform smoothing of that data only by enter ing the appropriate column labels in the file itself This specifies the low pass cutoff frequency for smoothing the gencoord data Enter a value of 1 for no smoothing This specifies the low pass cutoff frequency for smoothing the external force data e g ground reaction forces Enter a value of 1 for no smoothing This specifies the low pass cutoff frequency for smoothing the EMG data Enter a value of 1 for no smoothing Use the include buttons to specify whether or not to include the various columns of data e g if kinematics are not included any gencoord information in the input file w
364. s and endgroups keywords can be used to enclose the name s of one or more body segment groups to which the segment belongs Organizing your body segments into groups can make it easier to navigate and display your model with the SIMM Model Viewer The shadow parameter is used to specify the direction and location of the body segment s shadow In the example Chapter 3 Input Files 239 3 3 Joint Files 240 BODY SEGMENT right lower leg beginsegment right shank bone r_ tibia asc wireframe name of this body segment this bone uses the default material bone r_ fibula asc flat_shading my mat this bone overrides the default begingroups right leg lower body endgroups drawmode flat shading material my bone mat shadow Y 0 9 shadowcolor 0 1 0 1 0 1 axes 0 2 mass 3 25 masscenter 0 0 0 18 0 0 inertia 0 04 0 0 0 0 0 0 0 006 0 0 0 0 0 0 0 03 material and drawmode this segment belongs to two groups override default and use flat shading override default which is def bone draw the shadow directly below use a dark gray for the shadows show reference frame w axes 0 2 long mass in kg location of mass center inertia matrix relative to mass center and axes of segment reference frame marker R Ankle Lat 0 005 0 410 0 053 2 0 weight marker R Ankle Med 0 005 0 410 0 053 2 0 weight marker R Shank 0 02 0 25 0 0 1 0
365. s and joint torques The sample lower limb model uses units of meters for length and newtons for force Bone Files In SIMM a bone file is any file that contains a mesh of pla nar polygons Bone files are most frequently used to define anatomical bones that represent a musculoskeletal model s body segments but they are also used to define world objects motion objects force mattes spring floors and contact objects Each bone file can contain descriptions of any number of separate polygonal meshes or polyhedra but once loaded into SIMM these polyhedra are treated as a sin gle object Each polyhedron is usually a closed surface but it does not need to be closed for SIMM to be able to load and display it i e it can have holes in it Bone files list the 3 2 Bone Files 3D coordinates of the polygon vertices in a vertex list and define how the vertices are connected to form polygons in a polygon list The reference frame of the body segment to which the bone is attached serves as the local coordinate system for the polygon vertices Bone files used as part of a musculoskeletal model can be specified in any of five formats ASCH old ASCII binary Wavefront OBJ and STL To include a bone file in a model put the name of the file in the appropriate object definition in the joint file see Section 3 3 Joint Files for details SIMM will use the file suffix and the data in the first line of the file to automatically determin
366. s specified using the keyword restraint and a function name in the same format as that used for kinematic functions The keyword active is an optional parameter that can be used when a restraint function is associated with the genco ord If the function is active it will be used by the inverse kinematics solver when trying to close loops If the function is inactive it has no effect This is useful if you want to use the function in the Dynamics Pipeline but don t want to use it to solve loops If you define a restraint function for a gen coord it is active by default The keyword pd_stiffness can be used to specify a stiff ness value that is used by the Dynamics Pipeline when cal Chapter 3 Input Files 247 3 3 Joint Files 248 Chapter 3 Input Files culating joint torques w corrections while performing a dynamic simulation This calculation uses a PD propor tional derivative controller to determine the torques neces sary to drive a model to follow the input motion Consult the Dynamics Pipeline manual for more information about this feaure The keyword tolerance can be used to specify a tolerance value used when the gencoord is set to a new value If the difference between the new value and the current value is less than the tolerance the new value is ignored and the gencoord remains unchanged For most applications you do not need to specify a tolerance the default is 0 0 However it can be useful when you are i
367. scles wrapping over the current wrap object When checked the X Y Z coordinates of the tangent points will be displayed in the model window These radiobuttons and toggle buttons are used to specify that wrapping be constrained to a particular section of the current wrap object The x y and z radiobuttons let you specify the constraint axis and the positive and negative toggle buttons let you specify the constraint direction For example if the x radiobutton is selected with the positive toggle button then wrapping will be constrained to the half of the wrap object in which all X coordinates are greater than zero in the object s local reference frame When using these buttons you may need to rotate the wrap object within its local reference frame in order to properly orient the active section of the wrap object Chapter 2 Tools 87 2 10 Wrap Editor 88 Chapter 2 Tools 2 10 4 clear transform in reset Transforming Wrap Objects The current wrap object can be moved rotated and scaled using the model window commands described in the next section or by entering specific values into the numerical fields in the Wrap Editor window as described below NUMERICAL WRAP OBJECT TRANSFORMATION To apply precise transformations to the current wrap object enter the appropriate distances and angles into the translate and rotate fields then click the or buttons one or more times to apply the transform or its in
368. segments as well as the joint types match between the two models the simulation can proceed The simulation model is updated with the mass properties and joint kinematics from SIMM and an output motion is created to hold the data calculated by the simula tion This motion is added to the SIMM model and a slider for it is added to the Model Viewer As well the files con taining information about rigid body and NURBS contact dllcontactparams txt and dllnurbsparams txt are written out This button starts the dynamic simulation As it proceeds calculating each time step of data SIMM stores the frames of data in the motion that was created during the initialize step see above SIMM also updates the display of the model and the plots with the new data When the simulation has completed you can review the results using the motion s slider in the Model Viewer and by plotting motion curves with the Plot Maker This button pauses a running simulation or resumes a paused simulation When paused your only options for con trolling the simulation are to resume it or reset it which ends the simulation saving the partial results in the output motion This button ends a simulation and resets the dynamics to the uninitialized state If the simulation has been initialized but is not yet running when the reset button is pressed the motion created to hold the results is deleted from the model If the simulation is running when reset is press
369. ses is displayed Selecting one will restore the pose to the one saved in that buffer See the save pose com mand for directions on saving a model pose save pose gt muscles gt start gt 2 4 Model Viewer This command saves the current pose of the model to a buf fer A model pose contains the values and velocities of all of the gencoords as well as the activations and display state visible invisible of all of the muscles When you select this command a pop up menu of the current poses is displayed Selecting one will save the model pose to that buffer over writing the previous one You can also select make new pose from the menu to create a new pose See the restore pose command for directions on how to restore the pose once you have saved it This command lets you choose which muscles are displayed on the current model When you select this item a pop up menu of the muscle groups is displayed When you choose a muscle group from this menu it will appear at the bottom of the Model Viewer window If the chosen muscle group is already displayed at the bottom of the window then select ing it will turn it off so that it is no longer displayed As you select muscles from the menus at the bottom of the tool win dow the model window is redrawn to show the new muscle selections This command lets you automatically animate motions without having to press keys or mouse buttons When you select it a pop up menu is
370. sily compare the current state of the model to the original state The lookat command in the Model Viewer is a good way to focus the model display on a particular body segment or muscle By default the view is centered on the origin of the ground segment so when you rotate the scene it will rotate about this point This default setting can make it difficult to closely examine other areas of the model For example to look closely at the toes you might want to zoom in on that body segment then right click on a toe bone and select look at toe segment from the pop up menu Then when you rotate the view it will rotate about the origin of the toe segment You can reload the preferences file at any time by choosing Options gt Reload Preferences File from the menu bar You can also change preferences using the Scripting Tool and then save them back to the file by choosing Options gt Save Preferences File Motion Module If you load motion trials and the model does not seem to track the markers accurately or be scaled properly you might want to examine the static trial more closely After the mocap model has been scaled and loaded you can re load the static trial as if it were a motion trial e g using File gt Open instead of File Open Mocap Model This allows you to check the show markers box so you can replay the static trial and see how well or poorly the tracked markers match the model markers SIMM has a preferen
371. skin vertex is calculated by determining the position of each attachment in the ground frame mutiplying it by its weight and averaging all of the weighted attachments together With proper positioning of attachments and assign ing of weights the skin can be made to deform smoothly around the leg as the knee is flexed and extended Chapter 2 Tools 181 2 19 Skin Editor 2 19 1 model gt help 182 Chapter 2 Tools A skin can be used to represent the external skin of an ani mal but it can also be used to model muscle and ligament surfaces clothing or any other deformable surface Skins are typically stored as Collada DAE files but SIMM also supports a custom skin file format SKN that is similar to the Wavefront OBJ format Skins can be added to any mus culoskeletal model either by referencing them in JNT files or by making them in the Skin Editor SIMM can make a skin by taking one of the bones in a model and determining for each of its vertices which body segment s the vertex is closest to It then converts the bone vertex into a skin vertex with attachments on the one or two closest body segments and weights proportional to the dis tances to those segments This process is a good first step in making a skin but you will need to adjust the attachment weights manually to make the skin deform smoothly In addition to making skins the Skin Editor allows you to modify them by selecting one or more vertices an
372. soid s X Y and Z radii For planes there will be two fields to spec ify the size of the plane in the X and Y directions this is for display only the plane is infinite for the purpose of imple menting the constraint These radiobuttons let you choose the current constraint object s shape Typically you will choose the shape that most closely resembles the anatomical surface to which you want to constrain the points This toggle button lets you turn the current constraint object on and off When a constraint object is not active it is drawn in red and SIMM does not enforce its constraints This button toggles the visibility of the current constraint object in the 3D model window Typically once you are done editing a constraint object you will make it invisible so that it does not obscure the display of other features of your model A constraint object can be invisible but still active constrain to quadrant 2 13 4 2 13 Constraint Editor These radiobuttons and toggle buttons are used to specify that constraint points be constrained to a particular half of the constraint object The x y and z radiobuttons let you specify the constraint axis and the positive and negative toggle buttons let you specify the constraint direction For example if the x radiobutton is selected with the positive toggle button then the points would be constrained to the half of the constraint primitive in which all x coordinates are greater tha
373. specifies the starting X Y and Z scale factors of the motion object The default values are 1 0 1 0 1 0 This field specifies the starting X Y and Z rotations of the motion object in degrees The motion object s starting ori entation is achieved by first applying the X rotation around its local X axis then the Y rotation around its new local Y axis and finally applying the specified Z rotation around its Figure 3 17 Example motion object Chapter 3 Input Files 269 3 3 Joint Files material drawmode vectoraxis 270 Chapter 3 Input Files 3 3 13 new local Z axis this is known as an XYZ Euler rotation The default values are 0 0 0 0 0 0 This field specifies the name of the material used to deter mine the color and shading of the motion object s surface The material must be defined elsewhere in the joint file or be a default SIMM material The default material is arrow_mat See Section 3 3 7 Materials for information on defining materials and for a list of default materials This field specifies the drawing mode for the motion object The six drawmodes are solid fill wireframe flat shading gouraud_shading outlined and none The default drawmode is gouraud_shading This field specifies the axis of the world object that is used when animating with vx _vy _vz components in the motion file The motion object will be rotated so that the specified axis coincides with the vector formed by the _ vx
374. stinct function such as controlling the viewing of the models Model Viewer altering the muscles Muscle Editor and making plots for analysis Plot Maker Muscle Editor motion files l joint file R Ss new PAN muscle force iene new motion file new plot files new Figure 1 1 Structure of SIMM Input files describing the bone surfaces bone files joint kinematics joint file and muscle tendon parameters muscle file are read in to make a musculoskeletal model motion files can also be read in to animate the model A model can be altered using the Joint Editor Muscle Editor Gencoord Edi tor Wrap Editor Deform Editor Model Viewer Skin Editor and Function Editor Information is extracted from the model by making plots movies or by exporting edited joint muscle and motion files The Motion Reporter creates reports for gait analysis and study of other motions The Dynamics Tool and Motion Module not shown are optional modules that allow you to perform dynamic simulations and import motion capture data respectively Chapter 1 Introduction 1 5 1 5 About the Manual A musculoskeletal model is specified with three types of input files The bone files contain lists of the polygons rep resenting the bone surfaces The joint file specifies the kine matics of each joint Finally the muscle file contains a list of coordinates that describe the line of action of each mus cle tendon actuator a
375. t visible fixed This combo box lets you change the body segment to which a marker is fixed When you change a marker s segment the marker remains in the same position with respect to ground The link between the marker and the origin of the segment it is fixed to updates to show the change These three fields contain the X Y and Z offsets from the origin of the segment to the marker If more than one marker is selected and they do not have identical X Y or Z offsets the corresponding fields will be blank To change the offset simply type in new values If you enter an offset into a field that is blank because multiple markers are selected the off set will be assigned to all selected markers The units of the offsets are the implicit length units in your model usually meters This field contains the weight of the selected marker If more than one marker is selected and they do not have identical weights this field will be blank To change the weight simply type in a new value If you enter a weight into the field when it is blank because multiple markers are selected the weight will be assigned to all selected markers The weight of each marker determines how much emphasis is placed on it when the Motion Module fits the model to a frame of motion data The higher the weight the more the Motion Module tries to fit that marker to the data at the expense of the other markers If all the marker weights are the same regardl
376. t a time If some text is highlighted when you type in a character the highlighted text is deleted and the typed character is put in its place To delete the character just before the text cursor press the Backspace or Delete key You can copy the text from a text field to the Windows clipboard by selecting it and pressing Ctrl C You can also paste text from the clip board into a text field by pressing Ctrl V Some form fields can contain only numbers e g the genco ord form in the Model Viewer When editing a numerical field you can enter only numbers a decimal point and a minus sign You cannot enter exponents When you are done editing the text in a field press the Enter key or press the left mouse button while the cursor is outside the field and not over any other menu item or form Chapter 2 Tools 9 2 1 Introduction 10 slider toggle button selector menu Chapter 2 Tools field If the field is a numerical one SIMM will check to make sure that the number you have entered is valid If it is not SIMM will restore the previous value If the field is empty when you press return SIMM will restore the text that was in the field before you began editing it You can also press the Tab key when you are done editing a field This will move the text cursor to the next field in the form and select all of the text within it Sliders in SIMM are just like sliders or scroll bars in other programs Each has a thumb whi
377. t object it is colored orange to indicate this condition Segment Editor The Segment Editor allows you to edit the properties of the body segments in your SIMM model Many of these proper ties are used only for Dynamics Pipeline simulations If you will not be using your model for dynamic simulations then the only relevant items in the Segment Editor are the display parameters such as drawing mode and material If you will be performing dynamics then this tool gives you access to the mass properties mass mass center inertia force matte definitions and collision detection parameters contact objects and spring floors Consult the Dynamics Pipeline manual for more information on how to use these parame ters Selector Menu The model selector lets you select the current model If you never have more than one model at a time loaded into SIMM then you do not need to use the model selector Clicking on the help button opens a window containing helpful text about the Segment Editor When you are done reading it close the window using its close box You will be able to re open it at a later time by selecting help again 2 14 Segment Editor Model Full Body Model model gt aT name foot_r segment gt savecurrent _ inertial parameters rs mass 0 885000 restore current drawmode Mass center x 0 101865 material inertia xx 0 0009090000 ve 0 0000000000 Z 0 0000000000 force matte name right_foot
378. t segment first make sure the s button next to the Segment Editor icon in the HUD is highlighted then press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Editing segment The only function currently supported for editing body segments is scaling To scale the segment press and hold the middle mouse button with the cursor anywhere in the model window The HUD text box will update with scaling to confirm scaling mode Also a measurement bar is drawn over the model starting at the origin of the segment and ending at the cursor The current XYZ scale factors are shown at the end Drag the cursor to increase or decrease the scaling factors and release the mid dle mouse button when you are done SELECTING SPRING POINTS To select spring points first make sure the p button next to the Segment Editor icon in the HUD is highlighted then press and hold the S key While this key is pressed the Chapter 2 Tools 135 2 14 Segment Editor 136 one Chapter 2 Tools HUD text box in the lower left corner of the model window displays Selecting spring points As you move the cursor around the model window if it hovers over a spring point that is associated with the current body segment the point will be highlighted with a yellow wireframe sphere and the spring point name will be shown in a tool tip box If you then left click on the point it will be added to the g
379. t segment_name gt rename lt plot gt lt new_name gt plot_title lt title gt 204 Chapter 2 Tools muscle_orientation sets the Y variable linked to the specified gencoord The Y variable must be one of the following moment moment_arm moment_arm_numerical moment_max_force sets the X variable to the specified gencoord sets the X variable to the specified motion executes the make curves command deletes the current plot SIMM does not prompt you to con firm the action deletes the specified plot SIMM does not prompt you to confirm the action turns on off the specified muscle for plotting Name can also be the name of a muscle group turns on off the display of the specified muscle group menu in the Plot Maker window plots the specified curve of the specified motion adding it to the current plot sets the segment for the muscle orientation Y variable to the specified segment renames the plot specified by plot sets the name in the plot title field to the specified name This title will be used for the next new plot that is created curve_name lt name gt step_size lt number gt activation lt number gt x_min lt number gt x_max lt number gt y_min lt number gt y_max lt number gt scale lt number gt offset lt number gt sum lt on rectify lt on active lt on passive lt on act_override lt on isometric lt on off gt off gt off gt off gt off gt off
380. t 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 segment 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 Chapter 5 Motion Module 337 5 3 Using the Mocap Model 338 5 3 5 Chapter 5 Motion Module uniformly in X Y and Z The two exceptions are the TORSO and PELVIS which are scaled differently 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 The marker set in the full body mocap model that comes with SIMM includes every marker used in all six marker sets that OrthoTrak recognizes plus the medial knee and ankle markers In addition many other markers have been added such as medial elbow and wrist markers For a com plete 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 MotionModuleMarkers pdf located in SIMM Documentation The mocap model contains over 80 ma
381. tains spaces turns on or off the refreshing of the SIMM tool windows as script commands are executed Turning it off will speed up the execution of commands because the tool windows will not be updated and redrawn after each command Model based script files generated by SIMM use this feature so that the file can be processed quickly when a model is loaded Exits SIMM SIMM does not prompt you to confirm the action so make sure you have already saved any desired output files Model Viewer Commands The following commands are available in the Scripting Tool when the Model Viewer is the current tool enter the com mand tool mv to make the Model Viewer the current tool set model lt model gt restore_camera lt name gt Save_camera lt name gt restore_pose lt name gt Save_pose lt name gt muscles lt name gt lt on off gt muscle_menu lt name gt lt on off gt start lt motion_name gt start realtime look_at lt segment_name gt draw_mode lt name gt lt mode gt 2 21 Scripting Tool sets the Model Viewer to the specified model restores the camera view of the current model to the one specified by name saves the current view of the current model to the camera specified by name If name is not the name of an existing camera a new one will be created restores the pose of the current model to the one specified by name saves the current pose of the current model to the pose spec ified b
382. tate fields click the clear button CURRENT TRANSFORM DISPLAY The constraint object s current transform is displayed in the lower right corner of the Constraint Editor window as a Chapter 2 Tools 123 2 13 Constraint Editor reset 2 13 6 constraint point gt segment gt 124 Chapter 2 Tools sequence of XYZ rotations and an XYZ translation The order of the rotation sequence that is displayed is X fol lowed by Y followed by Z This order cannot be changed If the transform in local frame radiobutton is selected then the rotations displayed are about the constraint object s local XYZ axes a k a body fixed rotation If the transform in parent frame radiobutton is selected then the rotation sequence displayed is about the constraint object s parent segment s XYZ axes a k a space fixed rotation Click the reset button below the current transform display to return the current constraint object to the origin of its par ent segment s reference frame The constraint object s trans form is reset to the identity matrix Points Command Menu When you select this item a pop up menu of existing con straint points is displayed The first item in the pop up menu new constraint point creates a new constraint point adds it to the current model and makes it the current con straint point for editing The remaining items in the pop up menu allow you select existing constraint points for editing Select this com
383. tendon passive force length curve 18 passive force length curve for active force length curve 19 force velocity curve 20 max contraction velocity 10 0 muscle model 4 muscle model opt 10 activationl 7 667 activation2 1 46 mass 0 00286 damping 0 1 endmuscle active force length force velocity curve force model to use for dynamics force model for optimization of act coefficient used in activation dynamics coefficient used in activation dynamics normalized mass of muscle damping coefficient Figure 3 21 Example default muscle Chapter 3 Input Files 281 3 4 Muscle Files and tendon are not given in this example they would be inherited from the default muscle When defining a muscle you can optionally specify the activation level in addition to the other muscle specific parameters Put the keyword activation in the definition followed by a number between 0 0 no activation and 1 0 full activation The thickness and color of the muscles in the model window depend on their activations with the muscles getting thicker and brighter as activation increases If you do not specify the activation level when defining a muscle it will be initialized with a value of 1 0 regardless of the default muscle In most cases this is the value that you will want to start with because the Plot Maker uses the Rectus Femoris muscle beginmuscle RectusFemoris b
384. ter 2 Tools 2 12 3 muscle attachment points Each muscle point attached to the segment is deformed 4 muscle wrapping objects The origin of each wrap object associated with the segment is deformed However the surface of the wrap object is not deformed In other words wrap objects are moved and rotated to follow a deformation but the wrap object surface retains its shape i e sphere cylinder or ellipsoid Keep in mind that deform objects are always associated with a specific body segment A deform object will only affect elements that are also associated with that segment Deformity sliders on the other hand can control any combi nation of deform objects and thus are not tied to a particular body segment When moving muscle points be careful not to move muscle points that are currently being deformed Although the mus cle point may appear to follow the motion of the mouse cor rectly the next time you make a change to any deform object that is affecting the muscle point the point will jump to a new location Marker Editor The Marker Editor lets you edit the markers in your muscu loskeletal model Markers are used by the Motion Module to map motion capture data onto your model If you do not use the Motion Module to import TRC or TRB motion files into SIMM then you do not need to use markers or the Marker Editor TRC and TRB files contain 3D coordinates for the markers that were placed on the subject while a m
385. ter box By default an auto reset deform will apply both translation and rotation to restore the segment s origin to its original position and alignment However it is possible to specify that only translation be applied by including the transla tiononly keyword in the deform object s definition in the joint file In this case the segment s origin is moved back to its original position but the segment s reference frame may remain rotated from its original axes There is no way to change the translation only behavior of an auto reset deform interactively within SIMM See the Section 3 3 10 Deform Objects for more information about how to specify the translationonly keyword in the joint file Using Deformity Sliders Deformity sliders can be defined in a SIMM joint file as a way of coordinating the state of several deform objects with a single slider control Each deformity in the joint file will appear as a slider at the bottom of the Deform Editor win dow anteversion_angle 21 000 Chapter 2 Tools Figure 2 17 Deformity Slider Anteversion The range and default value for a deformity are completely arbitrary and may be specified in the deformity s definition in the model s joint file If the range is not specified it defaults to a minimum of 0 0 and a maximum of 100 0 If the default value is unspecified it defaults to 0 0 As you 2 11 7 2 11 Deform Editor drag a deformity slider side to side each of the deform obj
386. the box and drag it to a new location To rotate the wrap object Chapter 2 Tools 89 2 10 Wrap Editor 90 Chapter 2 Tools 2 10 6 about its local X Y or Z axis click on one of the 6 circles on the box faces and spin it To scale the wrap object click on any of the GUI boxes at the corners of the box the mid points of the edges or the centers of the faces and drag them Note not all GUI boxes will be displayed for all wrap object types For example spheres can only be scaled uni formly so there are no edge or face handles which would scale non uniformly RIGHT CLICKING WRAP OBJECTS You can right click on a wrap object to display a pop up menu with several editing options The options allow you to select the object for editing activate deactivate it hide its display hide all wrap objects other than this one clone the object and delete it Note you can right click on any wrap object without holding down any keyboard keys and with out first clicking on the Wrap Editor icon in the HUD Ellipsoid Wrapping Methods To overcome numerical instabilities involved with comput ing the optimal path over the surface of an ellipsoid SIMM allows you to choose between three different algorithms for calculating muscle paths over ellipsoidal wrap objects The default method hybrid works well for most muscles How ever if you notice erratic muscle motion e g skips or jumps when wrapping over an ellipsoidal wrap object o
387. the fiber length of a muscle SIMM finds the static equilibrium force in the muscle tendon actuator Thus the fiber length depends on the settings of the active and passive toggle buttons see Section 2 5 8 Toggle Buttons and also on the current acti vation level if the active component is turned on The isometric force of the selected muscles The force in a muscle depends on the settings of the active and passive toggle buttons see Section 2 5 8 Toggle Buttons and also on the current activation level if the active component is turned on The moment of the selected muscles calculated using the muscles peak isometric force at all muscle lengths Since this selection involves a moment calculation similar to the moment selection described above a generalized coordi nate must be chosen The generalized coordinate is chosen from the submenu that appears when you move the cursor off the right side of the moment max_force selection Since you cannot compute the moment of a muscle with respect to a motion variable the submenu lists only true generalized coordinates The tendon length of the selected muscles To compute ten don length SIMM finds the static equilibrium force in the muscle tendon actuator Thus the tendon length depends on the settings of the active and passive toggle buttons see tendon strain total positive moment total negative moment muscle orientation 2 5 Plot Maker Section 2 5 8 Toggle Buttons an
388. the folder Simm Resources mocap bones When you select a motion file in the file browser SIMM will link it to the current model If a model window is the topmost window that model is considered the current model If a tool window is the topmost window whatever model that tool is set to is considered the current model When the motion file is loaded SIMM matches the column names in the motion to the names of the gencoords mus cles markers and bodies in the model Any column that does not match one of these elements is labeled as other data Other data can be plotted in the Plot Maker but is not used to control the model when the motion is animated Once a motion has been linked to a model it behaves much like a true generalized coordinate That is you can animate the model display by pressing the keys specified in the motion file or moving the motion slider in the Model Viewer see Section 2 4 Model Viewer You can also use the motion variable as the independent variable when mak ing plots see Section 2 5 Plot Maker Chapter 2 Tools 13 2 2 Opening Files 14 plot files model archive files Chapter 2 Tools script files When you select a plot file in the file browser the way that SIMM processes it depends on which SIMM window was topmost when you selected File gt Open If a plot window was topmost SIMM will read the plot file and add the curves to the selected plot If some other window was top most SIMM
389. the model window To indicate that all keyboard and mouse com mands are being directed to the Segment Editor the icon will be highlighted with a yellow frame and the title bar of the Segment Editor will be highlighted in yellow When the Segment Editor is the active tool in the model window two buttons are displayed to the right of the Seg ment Editor icon in the HUD These buttons are labeled s and p When you click on the s button the Segment Editor activates segment mode meaning that you can select and edit body segments as described below When you click on the p button the Segment Editor activates spring point mode meaning that you can select and edit spring points as described below 6 B o8A 2 14 Segment Editor SELECTING SEGMENTS To select a body segment first make sure the s button next to the Segment Editor icon in the HUD is highlighted then press and hold the S key While this key is pressed the HUD text box in the lower left corner of the model window displays Selecting segment As you move the cursor around the model window if it hovers over a bone or any other model component that is fixed to one body segment the name of that segment will be shown in a tool tip box If you then left click on the object that body segment will be selected and the Segment Editor will update to show it as the current segment You cannot select more than one seg ment at a time EDITING SEGMENTS To edit the curren
390. the model window The active checkbox con trols whether or not the force matte will be used in a dynamic simulation Contact Object Contact objects are used by dynamic simulations to model rigid contact between polygonal surfaces For more infor mation on them consult the Dynamics Pipeline manual The interface in the Segment Editor does not let you define all of the properties necessary to set up rigid body contact detection for dynamic simulation but it does let you define and view the polygonal contact objects Once you have defined and positioned them appropriately in your model you will need to edit the joint file and enter the contact pairs Contact pairs specify which objects can contact which other objects To create a contact object for the current segment click on the contact object button and choose new from the pop up menu The name field specifies the name of the contact object which is used in the contact pair definitions The filename field specifies the name of the SIMM bone file which contains the polyhedron that comprises the object Type a name into this field or click on the browse button to browse for a file The visible checkbox controls whether or not the contact object is displayed in the model window 2 14 Segment Editor The active checkbox controls whether or not the contact object will be used in a dynamic simulation Spring Contact Spring contacts are used only by dynamic simulations and constit
391. the polygonal meshes then SIMM will post pro cess the Collada bone with norm in order to calculate them Texture maps within Collada files must be specified with JPG or TIF files IGES SIMM also supports bone files in the IGES format IGES Initial Graphics Exchange Specification is an open stan dard text format that is commonly used to transfer designs between CAD software packages SIMM will read NURBS surfaces from IGES files by importing NURBS patch defi nitions as well as trimming curves for the patches NURBS 3 3 3 3 Joint Files surfaces are required in SIMM to create NURBS contact and NURBS spring contact objects these cannot be created from polyhedra To display NURBS surfaces in the model window SIMM tesselates them into a set of triangles In some cases the tesselation may look rough or contain small gaps between the patches but the triangles are used for dis play only The original NURBS patch definitions are used when creating contact objects to be used in dynamic simula tions There is currently no way to output IGES files from SIMM but bones in SIMM that came from IGES files can be exported as polyhedra SIMM can output the tesselation triangles to ASC BIN OBJ or STL files Joint Files Joint files define the body segments joints generalized coordinates and kinematic functions used in musculoskele tal models They can also include optional components such as world objects muscle wrap objects deform o
392. the wrap objects are processed in the order in which they appear in this list The resulting path of the muscle may depend on the order of processing so care must be taken to define them in the appropriate order To see the ordered list of wrap objects assigned to a given muscle you must open the Muscle Editor tool and turn on the parameters for that muscle The only way to change the order of the list is to unassign the wrap objects and then re assign them in the desired order Wrap objects can take the form of spheres cylinders ellip soids or torii Additionally muscle wrapping can be con strained to a particular half of the wrapping primitive i e a hemisphere hemicylinder hemiellipsoid or hemitorus 2 10 1 model gt help 2 10 2 wrap object gt 2 10 Wrap Editor Figure 2 9 Cylindrical Muscle Wrap Example Selector Menu The model selector lets you choose which model s wrap objects you wish to edit When you select a new model with the model selector the Wrap Editor window is redrawn with the new model s settings If the current model has no wrap objects in it then the Wrap Editor window will be blank except for the wrap object button which will let you add new wrap objects to the model Clicking on the help button opens a window containing helpful text about the Wrap Editor When you are done read ing it close the window using its close box You will be able to re open it at a later tim
393. the wrap objects that are currently associated with the mus cle The order of the objects in the menu is the order in which they are processed when wrapping is calculated If you want to change this order you must use the Wrap Editor to unassign a wrap object from the muscle and then reas sign it to the end of the list You can use this pop up menu to choose which object s parameters you want to display and or change start pt endpt These two fields are used to specify the region of the muscle path that is allowed to wrap over the wrap object Start pt Chapter 2 Tools 65 2 7 Muscle Editor 66 hybrid midpoint axial Chapter 2 Tools 2 7 6 defines the first muscle attachment point and end pt defines the last attachment point in the region Only muscle path segments that are between start pt and end pt will be checked for intersection with the wrap object A value of 1 for start pt means to start at the first muscle point and a value of 1 for end pt corresponds to the last point in the muscle The muscle points are numbered starting at 1 and are in the order they are listed in the muscle definition including all via points points which are active only for certain gencoord ranges whether or not the via points are active at the time wrapping is calculated If the wrap object associated with the muscle is an ellipsoid then you will also see a set of radio buttons below the start pt and end pt fields for specifying th
394. them in either clockwise or counter clockwise fashion and can switch 3 2 Bone Files NORM ASCII 260 290 0 20459 0 45827 0 35921 0 27346 0 02846 0 68189 0 062448 0 071901 0 057002 0 195918 0 980604 0 005772 0 062417 0 062953 0 055540 0 010377 0 946434 0 322728 0 045919 0 070017 0 069408 0 203832 0 677009 0 707184 0 057682 0 053884 0 064535 0 232364 0 048436 0 971422 e Figure 3 1 Example bone file in ASCII format directions from polygon to polygon but you cannot list them randomly so that they criss cross through the polygon When you process the bone file with norm the polygons will be re ordered so that all of the vertices are specified in a counterclockwise fashion 3 2 2 Old SIMM ASCII There is a second version of the SIMM ASCII format that was originally developed for the first version of SIMM This format is shown in Figure 3 2 Like the first this for mat is identified with the asc file suffix SIMM examines the first line of text in the file to distinguish between the two formats It includes less information about the bone so it is easier to create if you are making a bone file from scratch Chapter 3 Input Files 225 3 2 Bone Files 226 Chapter 3 Input Files However if you are converting bone files from another soft ware package it is recommended that you not convert them to the old ASCII format but instead convert to OBJ STL or the new ASCII format The first line in an ol
395. ties of SIMM The tutori als are located in the Help menu accessible from the SIMM menu bar There are four tutorials Viewing a Musculoskel etal Model Plotting Muscle Properties Joint Editing and Gait Analysis There are also demos of the Motion Module and the Dynamics Pipeline A more complete version of the demo leg model is provided with the full version of SIMM You can use this model for a musculoskeletal analysis of the lower extremity or as a tem plate for building your own model For more details on the development and validation of the leg model consult the following publications Delp S L Loan J P A Computational Framework for Simulating and Analyzing Human and Animal Movement JEEE Computing in Science and Engineer ing vol 2 2000 pp 46 55 Delp S L Loan J P A Graphics Based Software System to Develop and Analyze Models of Musculosk eletal Structures Computers in Biology and Medicine vol 25 No 1 1995 pp 21 34 Delp S L Surgery Simulation A Computer Graphics System to Design and Analyze Musculoskeletal Recon structions of the Lower Limb Ph D Dissertation Stan ford University 1990 PDF versions of these publications as well as other articles describing research done with SIMM can be found here http www stanford edu group nmbl publications index htm 2 Tools 2 1 2 1 1 menu Introduction SIMM has 13 tools that enable you to create modify and
396. ting 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 increment of 2 The starting frame number field and the increment field are initialized to 1 The ending frame num ber is initialized to the number of frames in the marker file 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 begin ning and end of a motion that are missing some markers because the subject is outside the camera volume To auto matically 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 deleting each one until it encounters a frame containing all of the markers It will then ca
397. tion data this option is grayed out You can right click on the checkbox to display a dialog box showing all of the external forces in the motion which you can use to turn on or off the display of individual forces This option toggles the display of force trails which show the trajectories of the external forces during the motion A force trail consists of a white line representing the force at each time frame and a series of line segments connecting the tips of the white force vectors If there are no external forces in the motion data this option is grayed out You can right click on the checkbox to display a dialog box showing all of the external forces in the motion which you can use to turn on or off the display of individual force trails This option toggles the display of body forces in the motion data Body forces are forces that are applied to a specific body segment in the model If there are no body forces in the motion data this option is grayed out You can right click on the checkbox to display a dialog box showing all of the body forces in the motion which you can use to turn on or off the display of individual forces This option toggles the display of joint reaction forces in the motion data if there are none this option is grayed out You can right click on the checkbox to display a dialog box showing all of the joint reaction forces in the motion which you can use to turn on or off the display of individual force
398. tions 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 Chapter 5 Motion Module 313 5 2 Opening Tracked Marker Files 5 2 1 5 2 2 314 Chapter 5 Motion Module Selecting Tracked Marker Files To import a tracked marker file into SIMM you can simply drag the file from a Windows file explorer and drop it onto the model window you want to import it to You can drag and drop several files at once and SIMM will import them sequentially You can also load tracked marker files using File Open in the menu bar after first making sure that the model you want to import them to is the current model After dropping the files or selecting Open in the file browser SIMM will display a dialog box with several options for importing each data file into SIMM After dis missing the dialog you can cancel the import of a tracked marker file while its frames are being IK solved by pressing the Esc key at any time Note If your analog
399. tive When the restraint function is active it can be edited and it will be used by the inverse kinematics solver if the gencoord is not clamped If the restraint function is inactive it is displayed in gray in the function plot area and is not used to restrain gencoord val ues when using the inverse kinematics solver When the function is inactive it cannot be edited and points cannot be moved added or deleted This toggle button allows you to clamp or unclamp the cur rent gencoord If the gencoord is clamped it is forced to remain within its specified range and cannot be set to values outside its range This toggle button has the same effect as the toggle button in the Model Viewer and is updated if the button in the Model Viewer is used If the gencoord is unclamped its value can go beyond its range and it will be displayed in pink if it does so If the gencoord is unclamped and has an active restraint function this function will be used by the inverse kinematics solver If a gencoord is out side its range when clamping is turned on its value will be set to the closest range limit This toggle button allows you to lock and unlock the current gencoord When a gencoord is locked its value cannot be changed by moving its slider typing in a new value playing back a motion or by the inverse kinematics loop solver Its value can be changed only by restoring the gencoord using the restore current command or by applying a pose to th
400. to use when smooth ing the gencoord data in the input motion Enter a value of 1 for no smoothing specifies the low pass cutoff frequency to use when smooth ing the external force data in the input motion Enter a value of 1 for no smoothing EMG cutoff lt frequency gt include_kinematics lt yes no gt include_forces lt yes no gt include EMG lt yes no gt muscles lt name gt lt on off gt muscles lt group_name gt lt on off gt muscles all lt on off gt normalize lt none 1 0 100 0 gt gravity lt X X Y Y Z Z gt use_groups lt yes no gt baumgarte lt number gt initialize run pause resume reset 2 21 Scripting Tool specifies the low pass cutoff frequency to use when smooth ing the EMG data in the input motion Enter a value of 1 for no smoothing specifies whether or not to use the gencoord data from the input motion in the simulation specifies whether or not to use the external force data from the input motion in the simulation specifies whether or not to use the EMG data from the input motion in the simulation specifies the muscles to include in the simulation specifies whether to normalize the output motion to 101 time frames with the final time being 1 0 or 100 0 seconds specifies the direction of gravity in the simulation specifies whether or not to use optimization groups when performing static optimization of muscle activations specifies the value
401. tolerance 0 25 clamped yes locked no visible no pd stiffness 0 5 endgencoord is shown in Figure 3 5 A range of motion is defined that limits the values of the generalized coordinate and serves as the independent variable when making plots If the general ized coordinate represents a rotational degree of freedom the range should be specified in degrees If the gencoord is translational the units should match the units of the other lengths and translations that you specify in your model Also specified is the keyboard key k_key that controls the value of the generalized coordinate when animating the model in the model window You can specify either one or two keys to control the generalized coordinate and they must be on the same line as the word keys in the joint file The keyword wrap is an optional parameter that affects the control of the generalized coordinate in the Model Viewer When you include wrap in the definition you can repeat edly sweep through the range of motion for the generalized coordinate by resetting to the beginning of the range when you reach one end This is described in more detail in Sec knee angle name of gencoord this gencoord is a member of two groups range of motion for this gencoord degrees press this key to change gencoord value default and initial value of gencoord lets you loop through range of motion function used to keep gencoord in range
402. tor s current body segment Any new deform objects will be added to this segment You can use the segment button to the left of this field to change the current segment This field contains the current deform object s name Click and type in this field to rename the deform object Chapter 2 Tools 97 2 11 Deform Editor inner box outer box position deform start deform end 98 Chapter 2 Tools segment femur o en set E inner box outer box min max min max X 0 0600 f 0 0600 Be O0 0700 fee 0 0700 1 0 0050 E 0 0800 ER fenelsiele Z 0 0800 EZ 0 0800 Z 0 0900 E 0 0900 l active osition auto reset De Ee visible n deform start deformend Figure 2 14 Deform Object Attributes Panel These six fields contain the minimum and maximum X Y and Z dimensions of the deform object s inner box Change these values to modify the size and shape of the current deform s inner box These six fields contain the minimum and maximum X Y and Z dimensions of the deform object s outer box Change these values to modify the size and shape of the current deform s outer box These radio buttons specify the Deform Editor s current mode In position mode you can move and rotate both the inner and outer deform boxes together to specify how they are attached to the current body segment In deform start mode you can specify the inner box s starting transforma tion In deform end mode you can specify the inner box s
403. tting To change the name of a plot curve after the curve has been created right click on the name in the plot key and choose rename from the pop up menu step size activation x min x max 2 5 Plot Maker This field contains the step size used to generate data points for the plot curves It affects how many data points make up a curve and thus affects its resolution For example if you are making a plot curve for a generalized coordinate that ranges from 0 to 90 degrees a step size of 30 will mean that the curve will have data points at 0 30 60 and 90 degrees If you enter a step size greater than the range of the general ized coordinate e g 100 in the above example the step size will be changed to the magnitude of the generalized coordinate range 90 in this case When this happens any curves generated will contain only two data points This field contains a number between 0 0 and 1 0 represent ing the activation level of all of the muscles as used for plotting purposes For example if this number is set to 1 0 then when you make a plot curve all of the selected muscles will be assumed to be fully activated regardless of their individual activation levels as listed in the muscle parameter menu see Section 2 7 Muscle Editor This universal activation level will be used only when act override is turned on see Section 2 5 8 Toggle Buttons Otherwise the muscles individual activation levels will be used
404. ttom of the browser to limit the display to files of a single type to make it easier to locate a specific file It is possible to select and open multi ple files at once using the file browser This can be useful Chapter 2 Tools 11 2 2 Opening Files 12 joint and muscle files Chapter 2 Tools bone files when working with multiple models motions or plots or when applying different muscle files to a single model To define a musculoskeletal model all of the model compo nents except the muscles e g segments joints gencoords wrap objects kinematic functions materials must be defined in a joint file If muscles are to be part of the model they must be defined in a separate muscle file see Chapter 3 Input Files for a description of the format of each type of file If you select a single joint file to open SIMM will create a new model based on that file If a muscle file name is speci fied within the joint file using the muscle_file parameter that muscle file will be loaded as well If no muscle file name is specified the model will be loaded without any muscles unless a muscle file is also selected in the file browser If a muscle file is selected in addition to a joint file in the browser SIMM will load the model from the joint file and add to it the muscles from the muscle file thus overrid ing the muscle_file parameter if specified If you select multiple joint files in the file browser SIMM will o
405. turns on off the display of all body forces in the current motion turns on off the display of all joint reaction forces in the cur rent motion turns on off the display of all joint reaction torques in the current motion Chapter 2 Tools 217 2 21 Scripting Tool show contact_forces lt on show spring forces lt on show force_trails lt on show foot_prints lt on show moments lt on show other_objects lt on loop_motion lt on enforce_constraints lt on enforce_loops lt on 2 21 7 off gt off gt off gt off gt off gt off gt off gt off gt off gt set model lt model gt set muscle lt muscle gt save all save current 218 Chapter 2 Tools turns on off the display of all contact forces in the current motion turns on off the display of all spring forces in the current motion turns on off the display of all force trails for external forces in the current motion turns on off the display of foot prints in the current motion turns on off the display of gencoord moments in the current motion turns on off the display of other motion objects in the cur rent motion turns on off the loop motion checkbox for the current motion turns on off the enforce constraints checkbox for the current motion turns on off the enforce loops checkbox for the current motion Muscle Editor Commands The following commands are available in the Scripting Tool when t
406. u plan to load this curve into an existing plot to com pare to other curves it is important to give the X and Y vari 3 6 Plot Files Figure 3 26 Example plot file ables names that exactly match the names used in the other curves Next comes the text describing each plot curve Each curve s text should be preceeded by a tab The format for this text is curve name followed by a vertical bar followed by the name of the Y variable You can also include standard deviation data for the Y variable by enter ing a second vertical bar followed by the keyword std The name of the first curve in the example is Sale ave 90 and Chapter 3 Input Files 299 3 7 Model Archive Files 300 Chapter 3 Input Files 3 7 its Y variable is ankle_angle moment The name of the sec ond curve is Sale knee 90 and its Y variable is ankle angle moment Standard deviation data is supplied for the second curve After specifying all of the curve names and Y variables for the first set of curves you then enter the columns of plot data The first column contains the val ues of the X variable The second column contains the data for the first curve and the third and fourth columns contain the data and standard deviations respectively for the sec ond curve The second set of plot curves in the example file contains just one curve This curve has the same X and Y variables as the other two curves but it is defined separately because it uses a d
407. uence by selecting the motion variable field and entering a value The gencoord command can be used to toggle the visibility of generalized coordinate fields For models with more than 50 gencoords all gencoord fields with be hidden by default to avoid filling the Model Viewer window with too much information Model Name Form This field contains the name of the current model This name appears in the title bar of the model window and on the model icon when the model window is iconified The model name can be changed by editing this field These fields contain the width and height of the current model s window If you need to create snapshot images of a particular resolution you can enter the dimensions into these fields to set the model window to the same size as the desired snapshot image This field controls the speed at which motions are animated when using the start or movie buttons The value is the per centage of the actual speed of the motion as represented by the time column in the motion data You can enter any value between 1000 0 and 1000 0 into this field Note If there is no column labeled time in the motion SIMM will use the X column as time and will assume that the data in this column represents time stamps in seconds This may cause problems when animating the motion espe Chapter 2 Tools 29 2 4 Model Viewer 30 Chapter 2 Tools 2 4 4 cially if the data in the X column is not monotonically inc
408. ulation should calculate the muscle activations needed to generate the inverse dynamics moments and write them to the output motion If this option is turned on the activations of every muscle are optimized but only the moments for the selected gencoords are consid ered in the optimization Motion Editor Commands The following commands are available in the Scripting Tool when the Motion Editor is the current tool enter the com mand tool mt to make the Motion Editor the current tool sets the Motion Editor to the specified model sets the Motion Editor to the specified motion in the current model sets the Motion Editor to the event with the specified name in the current motion sets the Motion Editor to the event with the specified time in the current motion normalizes the current motion normalizes the specified motion smooths the current motion with the default low pass cut off frequency smooths the specified motion with the default low pass cut off frequency smooths the specified motion with the specified low pass cut off frequency smooths all of the curves in specified tab of the specified motion with the specified low pass cut off frequency Chapter 2 Tools 215 2 21 Scripting Tool smooth lt tab gt lt frequency gt smooth lt motion gt lt curve gt lt frequency gt smooth lt curve gt lt frequency gt crop crop lt start_time gt lt end_time gt crop lt motion gt lt start_ti
409. umn with the original data label appended by _std When you plot the data using the motion curves command in the Plot Maker the standard deviations are displayed underneath the data in the same color Auxiliary Data Auxiliary data is a column of data in a motion file that is linked to another column It has many uses but the most common is for storing onset offset data for muscles and linking them to the corresponding column of muscle EMG or activation data For example when the SIMM Motion Module imports a motion trial with EMG data it rectifies smooths and scales the raw EMG data and stores the result as a column of muscle activation using the muscle name as the column label The Motion Module also uses a threshold ing algorithm on the processed EMG to calculate onset times offset times and amplitudes The resulting step func tion is stored in an auxiliary data column linked to the acti vation column The label for an auxiliary data column is always the label of the primary column appended by _aux When you plot the data using the motion curves command in the Plot Maker the auxiliary data are displayed on top of the primary data in a lighter shade of the same color Chapter 3 Input Files 297 3 6 Plot Files 298 Chapter 3 Input Files 3 6 Plot Files Plot files contain sets of coordinates describing plot curves They can be loaded into SIMM and added to plots in order to compare with other curves They are desig
410. urrent model to the mode specified by mode changes the drawing mode of all of the world objects in the current model to the mode specified by mode changes the drawing mode of all of the skins in the current model to the mode specified by mode changes the drawing mode of all of the muscle surfaces in the current model to the mode specified by mode changes the drawing mode of all body segments world objects skins and muscle surfaces in the current model to the mode specified by mode turns on or off the slider for the specified gencoord in the Model Viewer tool window Name can also be the name of a gencoord group turns on or off the sliders for all of the gencoords sets the name of the file to be used when creating a movie of the model window If default is specified as the filename SIMM will generate an appropriate filename when the movie is created turns on or off auto movie mode When auto movie mode is on each time the model window is refreshed the image is appended onto the end of the movie creates a movie of the current model animated by the speci fied motion The animation starts at the current time value of the motion and proceeds at the rate specified in the motion speed field in the Model Viewer renames the current model to the specified name motion_speed lt percent gt trackball lt on off gt muscle_points lt on off gt shadows lt on off gt crosshairs lt on off gt 2 2
411. us movie if any If more than one motion is in the model SIMM will display a dialog box showing all of the motions and any movies linked to them You can use the check boxes to select one or more motions to which to link the movie To see a movie during motion playback there must be a bone named moviescreen obj in the model there can be more than one A bone with this name is in the SIMM Resources bones folder You can drag and drop it onto a model window to add a screen to that model This can be done before or after loading a motion with a movie To reposition the screen right click on it and choose edit moviescreen obj bone You can then use the Bone Editor commands to translate rotate scale the screen Note When a movie is linked to a motion SIMM assumes that the entire movie is time synched with the entire motion e g the first video frame is displayed with the first motion frame and last video frame is displayed with the last motion frame When a motion is cropped in the Motion Editor the linked movie is cropped as well Note When a movie is loaded into SIMM its frames are stored in an uncompressed format for faster playback If your computer does not have a lot of memory you should probably not load more than 1 or 2 short movies at a time 4 Norm Norm is a utility program that you can use to preprocess your bone and world object files collectively called object files before you can load them int
412. ut 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 parameter field in the C3D file to read the names of the tracked markers Because the POINT LABELS field in a C3D file is limited to four characters some soft ware 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 These options allows you to specify if SIMM will write out joint and muscle files containing the musculoskeletal model 5 3 3 5 3 Using the Mocap Model that is scaled to fit the subject 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 corresponding joint and muscle files depending on the states of these check boxes You may want 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 Calculation of Joint Centers Once the static pose has been loaded the Motion Module recreates the OrthoTrak skeletal model from the marker cloud The first step is determining the
413. ute a form of penalty based contact detection A spring contact consists of a contact polyhedron attached to one body segment and one or more spring points attached to other body segments When a point goes inside the poly hedron a non linear spring force is applied to the point s body segment to push it back out of the object This tech nique is commonly used to model contact between the feet and the floor during a forward dynamic simulation In this case the contact polyhedron is a single polygon represent ing the floor with a normal vector pointing upwards Spring points are positioned on the bottoms of both feet when they go below the floor spring forces push them back up Each body segment can contain only one contact polyhe dron To create a spring contact for the current segment click on the new spring contact button The name field specifies the name of the spring contact The filename field specifies the name of the SIMM bone file which containing the polyhedral object Type a name into this field or click on the browse button to browse for a file The visible checkbox controls whether or not the polyhedron and spring points are displayed in the model window The active checkbox con trols whether or not the spring contact will be used in a dynamic simulation The floor checkbox when checked means that the contact polyhedron should be interpreted as a floor with the first polygon in the file being used to define the plane of
414. utes This field contains the current constraint point s name Click and type in this field to rename the constraint point This field displays the name of the body segment to which the constraint point is attached To change the current con straint point s segment click the segment button to the right of the field This field let you specify the location of the constraint point as an offset from the origin of its body segment The weight of a point is a non negative floating point value which controls how much emphasis is placed on it when enforcing the constraints The higher the weight the more SIMM tries to position that point onto the object surface at the expense of the other points If the weights of all of the points are the same regardless of the actual weight value SIMM will treat them all equally e g you cannot try to enforce a constraint better by increasing all the weights from 1 0 to 2 0 Chapter 2 Tools 125 2 14 Segment Editor 126 tolerance 2 14 2 14 1 model gt help Chapter 2 Tools The tolerance of a point is the distance in model units that it is allowed to be from its correpsonding object and still be an acceptable solution It does not affect SIMM s calcula tion of the solution as does the weight of a point Rather it is a threshold value which is checked after the best con straint solution has been calculated If the point is not within tolerance of its constrain
415. uttons 2 hicusisinniaics medion 73 2 8 4 Gencoord Form 23 ci secshead drseao en aienetd ase 74 2 8 5 Inverse Kineniatiess a cias sian aseasinaieen 76 29 POL Viewer ss cccots nn a a ek E E 78 2 OAs Pop up Men s Yent n ER 78 2 9 2 Plot Window Commands ccccceceseeeeenees 80 2 9 3 Liye PIot CURVES 35 niinn 81 Z LO Wrap Editor amnion ten eia E E E 82 2 10 1 Selector Menu soooeeeeeesesssssssssessssrersrerereresee 83 2 11 2 12 213 2 14 2 10 2 Command Menu 00 ccccee cece eeeececececccecccceeecesceceee 83 2 10 3 Wrap Object Attributes sxcateatatwonstiiiede 86 2 10 4 Transforming Wrap Objects eeeeeeeereeeee 88 2 10 5 Model Window Commands ccsccecsseeeeees 89 2 10 6 Ellipsoid Wrapping Methods cece 90 2 10 7 Wrapping Tips amp Techniques cceeeceeseee 92 Deform Editor scree ica heer aaa Coes Gos ae eS 93 2 Lhd Selector Menu senese n Sake 05 2 11 2 Command Menu oi 5 068 4 tietcsce tends etecavieaeieeae 96 2 11 3 Deform Object Attributes 0 eee eeeseereeees 97 2 11 4 Model Window Commands cccceceseeeetees 99 2 11 5 Transforming Deform Objects c cece 101 2 11 6 Combining Multiple Deform Objects 103 2 11 7 Deform Tips Techniques and Caveats 107 WA ETRCIT GOV ice tid aes dees cus hence ogni eee AAEE 108 2 12 1 Selector Menu 5 Sa 2 sansa sc ease avatarah tales ee aante 110 2 12 2 Command Menu s c 0cec
416. values and positive moment for oth ers its moment will be included in the sum only when it is negative This variable does not generate a plot curve but rather writes out an ASCII data file with muscle orientation infor mation For each selected muscle with an attachment point Chapter 2 Tools 45 2 5 Plot Maker 46 motion curve Chapter 2 Tools 2 5 6 on the chosen body segment the one selected using the seg ment command the vector describing the muscle line as it attaches to that body segment is written to the data file The point pt is the attachment point on the segment the point pt2 is the next point on the muscle path and vec is the nor malized vector pt2 ptl This information is written to the file for each value of the corresponding X variable The name of the file is created using the names of the muscle s the name of the X variable and the suffix mo The folder that the file is created in is the current value of the OUTPUT_FILE_FOLDER preference This option lets you plot one column of motion data versus another The submenu contains a list of the motions linked to the current model and each of those has submenus giving you access to all of the columns of motion data To use this option you must select a motion curve as both the Y vari able and the X variable The selected curves do not have to be from the same motion but they must contain the same number of data points Once you have selected both c
417. verse If the transform in local frame radiobutton is selected then the specified transform will be applied relative to the wrap object s local XYZ axes Otherwise the transform will be applied relative to the wrap object s parent segment s XYZ axes The values you enter into these fields remain there after they are applied To clear all values from the translate and rotate fields click the clear button CURRENT TRANSFORM DISPLAY The wrap object s current transform is displayed in the Wrap Editor window as a sequence of XYZ rotations and an XYZ translation The order of the rotation sequence that is dis played is X followed by Y followed by Z This order can not be changed If the transform in local frame radiobutton is selected then the rotations displayed are about the wrap object s local XYZ axes a k a body fixed rotation If the transform in parent frame radiobutton is selected then the rotation sequence displayed is about the wrap object s par ent segment s XYZ axes a k a space fixed rotation Click the reset button below the current transform display to return the current wrap object to the origin of its parent segment s reference frame The wrap object s transform is reset to the identity matrix 2 10 5 2 10 Wrap Editor Model Window Commands Wrap objects can be selected and edited using keyboard and mouse commands in the model window To use these com mands you must first set the tool mode to the Wrap Editor by
418. weight the name of the body segment it is attached to and its tolerance value The weight of the point is a non negative floating point value which controls how much emphasis is placed on it when enforcing the constraints The higher the weight the more SIMM tries to position that point onto the object surface at the expense of the other points The tolerance of a point is the distance in model units that it is allowed to be from its correpsonding object and still be an acceptable solution It does not affect SIMM s calculation of the solution as does the weight of a point Rather it is a threshold value which is checked after the best constraint solution has been calcu lated If the point is not within tolerance of its constraint object it is colored red to indicate this condition 3 3 14 3 3 Joint Files Model Poses A model pose is information about the position and orienta tion of the model see Example in Figure 3 19 It can con tain the values velocities clamped states and locked states of the gencoords as well as the activations and display states visible invisible of the muscles You can define any number of poses for a model and switch between them in SIMM using the restore pose button in the Model Viewer If you do not define a pose named default in your JNT file SIMM will create one when you load the model When defining a pose you can choose to include any subset of the gencoords and muscles However for
419. will be used at the X axis when plotting data from the motion smooth divide into strides delete motion delete event gt edit motion 2 17 Motion Editor This command smooths the data in the current motion It fits a GCV spline to each column of data and evaluates it at the existing time frames The low pass cut off frequency used for the smoothing has a default value of 6 0 but can be specified with the MOTION _ SMOOTHING FREQUENCY prefer ence This command divides the motion into a set of smaller motions one for each complete left and right gait cycle A gait cycle is defined as the motion frames between two heel strike events of the same foot The original motion is pre served and a new motion is created for each gait cycle If there are no heelstrike events in the motion this command does nothing This command deletes the current motion The motion is unlinked from the model and it will no longer be able to be viewed or plotted Any existing plots using the deleted motion will remain unchanged This command lets you delete the events in the current motion From the pop up menu you can choose any one event or delete all at the bottom to delete all of the events This command allows you to edit the columns of data in the current motion When you select it SIMM displays a dialog box showing all of the columns If you select one and click OK SIMM fits a GCV spline to the data for that colum
420. will create a new plot window and add the curves to it In this way multiple plots from separate files can be combined into a single plot if desired A model archive is a compressed file containing all of the files associated with a model including joint file muscle file bone files and even motion files that are linked to the model If you select multiple model archives in the file browser SIMM will open each one and create a new model from it A script file is a text file containing SIMM scripting com mands These commands described in Section 2 19 Script ing Tool can be used to load and save models process motion data and specify settings in the tools You can create your own script file with a text editor by typing commands into a file SIMM can also automatically generate script files as described in Section 3 8 Script Files Script files that SIMM creates have the ssc suffix If you make your own script file you can use the ssc or txt suffix When you load a script file using the File menu SIMM executes the commands in it using the Scripting Tool Any commands in the file that are model specific e g specifying settings in the tools are executed with respect to the model that was current when you selected File gt Open If there is no cur rent model model specific commands in the script file are ignored 2 2 1 JNT MSL SMM TRB TRC C3D PLT 2 2 Opening Files Drag and Drop All of the types of i
421. will rotate the model about an axis perpendicular to that direction The second method of changing the model view is active when the trackball toggle button in the Model Viewer win dow is turned off In this case the Ctrl key and mouse but tons function as follows To rotate the model around the X axis of the world frame which always points horizontally to the right press the Ctr1 key and the left mouse button The direction and speed of rotation are determined by the posi tion of the cursor in the model window If the cursor is at the far right edge of the window the model will rotate quickly in the positive direction around the X axis As you move the cursor left towards the center of the window the rate of rotation slows down If the cursor is in the middle of the window the rotation rate is zero As you move the cursor further left towards the left edge of the window the rotation rate increases but in the negative direction In a similar fashion pressing the Ctrl key and the middle mouse but animating motions changing display properties 2 4 Model Viewer ton rotates the entire model around the Y axis which always points straight up Pressing the Ctrl key and the right mouse button rotates the model around the Z axis which points out of the screen towards you If you have loaded a motion file see Section 3 5 Motion Files into SIMM you can move the model according to the motion sequence as if the motion parameter e
422. word name followed by the desired name SIMM assumes that all text following the keyword on the same line comprises the name so you can put spaces in your model name If you do not name your model in this way SIMM will assign a default name to it consisting of the word model followed by a number Here is an example name Lower Extremity This parameter specifies the name of the muscle file that will be loaded with the joint file This is a convenient fea ture if you often load the same muscle file with a certain joint file To specify the muscle file use the keyword muscle file followed by the name of the file Then when you load a model by selecting the joint file with the file browser SIMM will also open the specified muscle file This parameter can be changed within SIMM by right click ing on the background in the model window and choosing edit model preferences from the pop up menu muscle file leg _model msl This parameter specifies the name of the motion file s that will be loaded with the joint file To specify a motion file use the keyword motion_file followed by the name of the bone_path read_script_file 3 3 Joint Files file Then when you load a model by selecting the joint file with the file browser SIMM will also open the specified motion file s and link them to the model You can specify up to 100 motion files in each joint file motion file walk mot motion file run mot This parameter specifies th
423. written norm infile outfile Norm will process infile and save the output object in outfile norm infilel outfilel infile2 outfile2 overwrite outdir dirname files filter sep tol num fill Norm will process infile1 infile2 and save the out put objects in outfilel outfile2 respectively norm files asc All files in the current directory ending with asc will be passed to norm as input files For each file norm will pro cess it and then prompt you to make sure you want to over write the file with norm s output Use of the files option may be combined with the use of input output file name pairs on the command line Norm has several options that allow you to perform simple geometric transformations on your object files They can be helpful when creating a musculoskeletal model from raw bone surface data Below is a complete list of norm s options automatically overwrite existing files without prompting put all output files in the specified directory If the directory doesn t already exist norm will create it process all files in the current directory that match the spec ified filter These files will be overwritten with the output write out each polyhedron that is in the input file to a sepa rate output file The name of each output file will be based on the single output file name you specify for each input file this option sets the tolerance that norm uses when checking for
424. x in the motion import dialog box but you can change it as you load individual motion tri als For most applications you can set this preference to off This preference specifies whether or not to calculate deriva tives of the imported data when loading a TRB TRC C3D file If the preference is on SIMM will calculate first deriva tives of the gencoords forces and EMG data and make them available for plotting in the Plot Maker The value is used to initialize the appropriate checkbox in the motion import dia log box but you can change it as you load individual motion trials Unless you want to create plots of these derivatives you should set this preference to off If you use the motion as input to an inverse dynamic simulation for which derivatives are needed the simulation will calculate its own derivatives so you do not need to calculate them when importing the motion This preference specifies the units of the X axis when import ing a TRB TRC C3D file For most applications you should set it to TIME so that event calculation and real time playback give better results But you can also set it to FRAME NUMBER allowing you to plot motion data as a function of frame num ber This preference is used to initialize the appropriate field in the motion import dialog box but you can change it as you load individual motion trials This preference specifies whether or not the imported motion should start at time 0 0 or frame number
425. x lies somewhere inside the triangle depending on the weights Note if you cannot see the attachments for a skin vertex they may either be coincident with each other and or the vertex or hidden underneath the skin itself You can usually reveal them by changing a gencoord value to move the attachments apart Figure 2 27 shows a typical view of a skin vertex with two attachments and a vertex with three attachments To change the attachment weights of a skin vertex put the cursor over the vertex the yellow sphere and press and hold the left mouse button As you drag the vertex along the line two attachments or triangle three attachments the Skin Editor window will update to show the new weights Release the left mouse button when you are done Note if the skin vertex has more than three attachments you cannot interactively change the weights this way you can only type in values in the Skin Editor window To change the location of a skin vertex attachment put the cursor over the desired attachment the greenish blue sphere and press and hold the left mouse button Drag the sphere to the desired location and release the left mouse but ton Function Editor The Function Editor allows you to modify any function in a model as well as create new functions To edit a function you must select it for editing in another SIMM tool such as the Muscle Editor for muscle functions or the Joint Editor for joint functions The function
426. ximum isometric force defined 63 maximum thickness defined 283 minimum material defined 283 minimum thickness defined 283 optimal fiber length defined 63 pennation angle defined 63 tendon slack length defined 63 muscle wrapping see wrap objects muscles adding attachment points 59 deleting 60 deleting attachment points 60 displaying attachment points 31 Index 6 displaying in model window 23 editing groups 60 including in dynamics 156 making groups 60 moving attachment points 70 parameters see muscle parameters restoring from buffer 59 saving to buffer 59 selecting attachment points 69 surfaces 284 musculotendon length defined 42 musculotendon velocity defined 43 N natural cubic spline defined 250 norm 305 310 options in Bone Editor 142 norm fiber length defined 44 norm musculotendon length defined 42 numerical moment arm defined 43 NURBS objects adding to body segments 132 NURBS spring objects adding to body segments 132 O offsetting plot curves 50 opening bone files 12 model archive files 14 motion files 13 muscle files 12 plot files 14 script files 14 tracked marker files 312 opening files 11 optimal fiber length defined 63 other data in motion files 296 outlined drawmode defined 239 output strides 181 output strides normalized 181 P passive toggle button 51 password txt file 16 patches selecting 147 pennation angle defined 63 plot curves clipping 49 creating see P
427. xt This preference specifies whether or not to set all of the SIMM tools to a given model when that model is first loaded DISPLAY PREFERENCES This preference specifies whether or not SIMM utilizes mul tiple screens monitors on your computer If this preference is on the SIMM tool windows are created as separate top level windows They can be moved outside of the main SIMM window and they will have their own icons in the Windows task bar The model and plot windows are still con strained to the main SIMM window This option works best if you keep the main SIMM window on one screen and the tool windows on another screen because when you click any where in the main SIMM window or cause a new model or plot window to open the main SIMM window is popped above all of the tool windows This preference cannot be changed while SIMM is running it is checked only when SIMM is first launched This option causes SIMM to display the muscles without their attachment points and with a coarser cylinder repre senting their lines of action SIMM performs this faster muscle drawing only when animating a motion continu Appendix B SIMM Resources B 3 B 1 Preferences DISPLAY ANIMATION HZ DISPLAY POLYGONS PER SECOND DISPLAY MOTION INFO MOCAP MODEL MARKER HEEL STRIKE OFFSET B 4 Appendix B SIMM Resources ously using the start button in the Model Viewer If you have many muscles in your model this option can signifi cantly
428. xt time the program is launched The file contains commands to open close and position tool windows so that the set up of the windows is preserved from one use of SIMM to the next You can customize this file by adding any commands you want but if you do so be sure to turn WRITE_STARTUP_SCRIPT off so that your modifications are not overwritten when you exit SIMM In addition to the session based script file SIMM can also use model based scripts to save and restore settings for indi vidual models If the write_script_file parameter is set to on in a joint file SIMM will write a script file each time the model is saved or closed The file is created in the same folder as the joint file and has the same base name with the suffix ssc The file contains commands to restore the set tings in the Model Viewer Plot Maker Motion Reporter Motion Editor and Dynamics Tool to the same values as when the file was created If the read_script_file parameter is set to on in the joint file SIMM will read this script file each time it loads the model and use it to restore the set tings in those tools You can customize this file by adding any commands you want but if you do so be sure to turn off the write_script_file parameter so that your modification are not overwritten when you save or close the model Note model archives contain their corresponding script files within the archive If there is a separate script file in the 3 9 auto load
429. y While this key is pressed the HUD text box in the lower left corner of the model window displays Selecting vertices As you move the cursor around the model window if it hovers over a vertex on bone 1 the vertex will be highlighted with a light blue wireframe sphere and the vertex index will be shown in a tool tip box If you then left click on the vertex it will be highlighted with a red sphere and added to the group of selected verti ces If you click on an already selected vertex it will be unselected You can also box select vertices by pressing and holding down the left mouse button and dragging the cursor to form a rectangle around the vertices you want to select or unselect You cannot select the control points of a NURBS surface BBA x Z 2 16 2 16 Dynamics Tool EDITING VERTICES To edit the selected polygon vertices first make sure the v button next to the Bone Editor icon in the HUD is high lighted then press and hold the E key While this key is pressed the HUD text box in the lower left corner of the model window displays Moving vertices net move X Y Z where X Y and Z are the distances that the points have moved To translate the vertices in the plane of the screen press and hold down the left mouse button anywhere in the model window and move it to drag the vertices in that direc tion A green arrow is also drawn in the model window starting at the original location of the first sele
430. y lt on off gt joint_reaction_forces lt name gt lt on off gt joint_reaction_forces lt on off gt 212 Chapter 2 Tools turns on off the output of muscle fiber velocities If output is on only the selected muscle fiber velocities will be written to the output motion turns on off the writing of contact forces to the output motion adds or removes the specified body segment to the list whose mass center positions will be written to the output motion if output of mass center positions is turned on Name can also be the word all turns on off the writing of mass center positions to the out put motion If output is on only the mass center positions of the selected segments will be written to the output motion adds or removes the specified body segment to the list whose mass center velocities will be written to the output motion if output of mass center velocities is turned on Name can also be the word all turns on off the writing of mass center velocities to the out put motion If output is on only the mass center velocities of the selected segments will be written to the output motion turns on off the writing of total system energy to the output motion adds or removes the specified joint to the list whose reac tion forces will be written to the output motion if output of joint reaction forces is turned on Name can also be the word all turns on off the writing of joint reaction forces to the out
431. y a message at the bottom of the window indi cating that a recording is in progress This message will not appear in the output movie file Note SIMM uses a separate CPU thread to write model images to the movie file Thus if your computer has at least two CPUs the animation of the motion will not be slowed by the writing of the movie file to disk However this also means that it may take up to a minute after the SIMM dis play has stopped before the movie file is completely written to disk During this time the movie file will be unavailable for viewing and SIMM will not be able to start creating a another movie for the same model Forms Generalized Coordinates Form This form contains a numerical field for each generalized coordinate in the current model You can use it to position the model accurately by typing in exact values for the gen eralized coordinates Just click the left mouse button in the field of the generalized coordinate you want to change then enter a new value If the gencoord is clamped you will not be allowed to input a value outside its range If the gencoord name w h width height motion speed 2 4 Model Viewer is not clamped any values outside its range will be dis played in pink When you load a motion file the motion variable e g of gait cycle appears in this form as if it were a generalized coordinate Thus you can also position the model at a spe cific time step in a motion seq
432. y finding the point on the surface of the ellip soid closest to the midpoint of the imaginary muscle line passing straight through the ellipsoid This method produces smooth changes in the wrapping path unless the muscle line through the ellipsoid passes close to the center of the ellip soid In this situation the midpoint method becomes numeri cally unstable creating erratic jumps in the wrapping path that it computes If you are able to orient your wrap objects such that muscles do not pass near the ellipsoid s center then the midpoint method will produce well behaved wrap ping paths Chapter 2 Tools 91 2 10 Wrap Editor 92 Chapter 2 Tools 2 10 7 THE AXIAL WRAPPING METHOD The axial method chooses one of the ellipsoid s principal axes X Y or Z then computes a wrapping path based on the point where the imaginary muscle line passing straight through the ellipsoid intersects the plane perpendicular to that axis i e the X 0 Y 0 or Z 0 planes For example if the X axis is chosen then the intersection of the muscle line with the x 0 plane is used to find a point on the surface of the ellipsoid The surface point is then used to determine the wrapping plane The axial method works best when the muscle line is nearly parallel to the chosen axis The accu racy of the axial method decreases as the angle between the muscle line and the chosen axis increases Therefore the axial method automatically chooses the princip
433. y in the dynamics code the total energy potential plus kinetic of the model during the simulation If there are no muscle external or friction forces applied system energy will be conserved during the simulation the reaction forces at the joints These forces are those applied by the proximal segment to the distal segment They are applied at the origin of the distal segment and are expressed in the distal segment s reference frame the joint reaction torques at the joints These are the torques applied by the proximal segment to the distal segment expressed in the distal segment s reference frame They include user applied torques such as joint restraint torques the moments applied to the gencoords by the simulation to generate the prescribed motion These moments are calcu gencoord moments corr gencoord powers spring forces muscle moment arms 2 16 Dynamics Tool lated after all system forces e g gravity and user applied forces e g muscle ground reaction forces are applied In a typical inverse dynamics analysis the gencoord motion is fully prescribed and no muscles are included The gencoord moments are thus equal to the net moments required e g by the subject s muscles to produce the prescribed motion If you include muscles in your inverse dynamics analysis your gencoord moments will be different If you include exactly the right set of muscles and excitations as was used by the subject in the
434. y name If name is not the name of an existing pose a new one will be created turns on or off the display of the specified muscle in the cur rent model Name can also be the name of a muscle group turns on or off the display of the specified muscle menu in the Model Viewer tool Name must be the name of a muscle group animates the current model with the specified motion The animation begins at the current time value of the motion and proceeds at the rate specified in the motion speed field connects the current model to the Cortex or EVaRT program running on the computer specified by the CORTEX MACHINE preference fixes the origin of the specified body segment in the current model to the ground for display purposes only changes the drawing mode of the object specified by name in the current model to the mode specified by mode Name can be the name of a body segment segment group world object skin or muscle surface Chapter 2 Tools 201 2 21 Scripting Tool draw_mode all_segments lt mode gt draw_mode all_world_objects lt mode gt draw_mode all_skins lt mode gt draw_mode all_muscle_surfaces lt mode gt draw_mode all lt mode gt gencoords lt name gt lt on off gt gencoords all lt on off gt movie_file lt filename gt auto_movie lt on off gt movie lt motion_name gt model_name lt name gt 202 Chapter 2 Tools changes the drawing mode of all of the body segments in the c
435. you to specify the name and location of the movie file to be created by SIMM If you do not use this option to specify a file name SIMM will use a default name based on the name of the model as described below This menu item instructs SIMM to use a default name when creating a movie file The default name is based on the name of the model and if appropriate the name of the motion If you create a movie using the auto movie option the file name will be lt model name gt avi If you create a movie of a motion the file name will be lt model name gt _ lt motion name gt avi This menu item puts SIMM in auto movie mode In this mode SIMM will add a frame to the movie each time the current model window is refreshed To exit this mode select auto movie again to disable it Chapter 2 Tools 27 2 4 Model Viewer 28 2 4 3 generalized coordinates Chapter 2 Tools In addition to these menu items if the current model has any motions linked to it then these motions will be listed at the bottom of the movie pop up menu Selecting one of these motions will cause the motion to be played back starting at the current motion value and using the current motion speed Each image of the model showed on the screen will be written to the movie file To stop this process you can click the stop button or select the motion s menu item in the movie pop up menu again Note While SIMM is creating a movie of the model win dow it displa

SIMM 7.0 User Guide - MusculoGraphics, Inc.

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