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SIMM User`s Guide - Stanford University

1. 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 con taining the motion that SIMM calculates from the marker data This file contains exactly the same data that is in the motion that SIMM loads onto the model You can load this motion file into SIMM at a later time rather than re importing the marker file If this box is checked a browse button is enabled that 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 sync 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 cor respond to the chosen TRB TRC files If the analog file Chapter 5 Motion Module 217 5 2 Opening Tracked Marker Files 218 forceplate data Chapter 5 Motion Module has the same base name as the TRB TRC file then the Motion Module will load it automatically when you select the marker file Otherwise you should select the analog file as well in the file browser
2. 2 15 Bone Editor 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 per formed 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 field specifies the name of the bone file to use when reading a bone file with the read bone command or when writing a bone file with the write bone 1 com mand The folder that this file is read from or written to is the folder containing the joint file for the current model This command reads the bone file specified in the r w file name field and adds the bone to the body segment speci fied in the add to segment field This command writes bone 1 to the bone file specified in the r w filename Chapter 2 Tools 123 2 15 Bone Editor 124 Chapter 2 Tools 2 15 4 Norm Options Norm is used to process a bone when you
3. 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 by finding the point on the surface of the ellipsoid 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 ellipsoid In this situation the midpoint method becomes numerically unstable creating erratic jumps in the wrapping path 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 wrapping paths 2 10 6 2 10 Wrap Editor 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 sur face 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 accuracy of the axial method decreases as the angle between the mu
4. 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 cyl Chapter 3 Input Files 181 3 3 Joint Files active visible 182 Chapter 3 Input Files inder 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 enforcing the constraint The constraint points are required to remain on the section of the plane defined by these two values 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 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 parameter s value is no or false then the constrai
5. 88 2 11 2 segment gt deform object gt save restore delete Chapter 2 Tools 2 11 3 Command Menu Select this command to specify the current segment for the Deform Editor Any newly created deform objects will be added to this segment The name of the current seg ment is displayed to the right of the button 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 edit ing The remaining items in the pop up menu allow you select existing 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 combination 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 attribute
6. Motion Editor The Motion Editor 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 according to certain events such as heel strike and toe off Chapter 2 Tools 137 2 17 Motion Editor 138 2 17 1 model gt help 2 17 2 motion gt save to file delete Chapter 2 Tools 2 17 3 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 close 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 This command allows
7. 0 0743 x 9 12 y 16 21 10 42 reset 0 1800 0 0520 106 Chapter 2 Tools Figure 2 18 Constraint Editor window delete 2 13 3 object name segment radius height plane sphere cylinder ellipsoid active 2 13 Constraint Editor This command deletes the current constraint object from the model 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 attributes 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 con straint object For spherical constraint objects there will be only one field to specify the sphere s radius For cylin ders there will be two fields for the cylinder s radius and height For ellipsoids there will be three fields to specify the ellipsoid s X Y and Z radii For planes there will be two fields to specify the size of the plane in the X and Y directions this is for display only the plane is infinite for the purpose of implementing the constraint These radiobuttons let you choose the current constraint object s shape Typically you will
8. 2 cif tf ey a ay S ci 2 a same as line 1 191 3 4 Muscle Files 192 Chapter 3 Input Files 3 4 3 with muscles use the name of the muscle surface as a col umn label and enter activations from 0 0 to 1 0 The materials muscle_mat0 through muscle_mat20 specified in the joint file are used to color the muscle surfaces For example muscle_mat0 is used when the activation is 0 0 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 mus cle surface so as you create them you should make each line an ordinary muscle so you can move the points using the Muscle 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 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
9. It must be followed by three values 1 The forceplate number 1 2 3 etc then 2 The keywords force or moment then 3 The channel component x y or z for AMTI or Bertec forceplates or x12 x34 y14 y23 z1 Z2 z3 z4 for Kistler forceplates muscles other data 5 4 2 5 4 Analog Configuration Files 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 appears then it must be followed by an integer num ber that SIMM uses as the voltage for the maximum vol untary 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 resa mpled to the motion s frequency This keyword specifies a data channel that exists simply to be included in SIMM plots This keyword may be optionally followed by a single word that will be used to label this channel in SIMM plots If no name follows the other data keyword then the name of the imported vari able will be used forcepla cal When importing analog data from ANB ANC files SIMM uses the same calibration file as EVaRT and OrthoTrak for processing forceplate data Therefore you can simply copy the forcepla cal file from your EVaRT folder into the Resources mocap misc folder For users who need to create a forcep
10. The same holds for XLS files which are not actually analog files but are treated similarly XLS files can contain other data corresponding to the recorded motion such as kinetic data 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 analog 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 EVa EVaRT and OrthoTrak To use it with SIMM you should put a copy of it in the same folder as your motion data or in the folder SIMM Resources mocap misc If you have only one forceplate configuration for your motion capture system it is preferable to put for cepla cal in SIMM Resources mocap misc rather than copying 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 importVa
11. This command is not available if the function is already defined This command lets you add a control point to the muscle function displayed in the plot area After selecting this item it remains highlighted until you click the left mouse button in the function plot area at the location where you want to add the new control point SIMM figures out which two points the new point should go between and adds it to the function The point is added to the function as soon as you press the left mouse button and if you keep the button pressed you can move the point around within the plot area before releasing the button If you selected an existing control point SIMM will add a node to the spline A new points will be added slightly offset from the chosen point Keeping the mouse pressed will not allow you to move this new point around You will have to select and edit it individually This command is not available if the function is not defined This command lets you delete a control point from the currently displayed muscle function After selecting it this item remains highlighted until you select the point you want to delete by clicking the left mouse button on the point You can cancel this command by clicking the left mouse button while the cursor is not on any point This command does nothing if no function is currently dis played if the current function has only two points or if the function is iherited This command is not available i
12. Toggle Buttons When you turn shadows on only those body segments for which you have specified shadow properties will cast a shadow The axes parameter is used to display the coordinate sys tem of the body segment in the model window The num ber after the keyword axes is the length of each vector forming the reference frame Fixed Segment The fixed segment is the body segment that does not move when you move the joints in your musculoskeletal model That is the origin of this segment 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 seg ment Note that segment names are used in joint defini tions as well as segment definitions so the order in which you enter joints may also matter For example in the sam ple 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 characteri
13. expressed in the distal segment s reference frame They include user applied torques such as joint restraint torques the torques applied to the gencoords by the simulation to generate the prescribed motion These torques are calcu 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 genco spring forces muscle moment arms muscle joint torques total muscle torques 2 17 2 17 Motion Editor ord motion is fully prescribed and no muscles are included The joint torques are thus equal to the net torques required by the subject s muscles to produce the prescribed motion If you include muscles in your inverse dynamics analysis your joint torques will be different If you include exactly the right set of muscles and excita tions as was used by the subject in the recorded motion no additional torques will be needed to produce the pre scribed motion and the joint torques will be zero In a simulation that has no prescribed motion e g forward dynamics the joint torques will be zero the forces applied by the spring floor objects Each force is expressed in the reference frame of the corresponding spring point s body segment the moment arms of all of the muscles in the simulation the moment that each muscle applies to each gencoord the total net moment applied to each gencoord by all of the muscles
14. gles 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 normals assuming that all of the polygons are counter clockwise tells norm that all polygons are ordered in a clockwise direction i e the vertices within each polygon are speci fied 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 nor mals Norm will attempt to determine the inside and out side of a polyhedron without using a reference normal If the polyhedron is not a closed object however it may oldascii binary tx num ty num tz num rX num ry num rz num SX num sy num have difficulty finding the outside If norm does have dif ficulty and you do not know if the polygons are all clock wise or all counter clockwise you should specify a reference normal This vector 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
15. object will rotate about its parent segment s XYZ axes 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 trans form If the transform in local frame radiobutton is selected then the specified transform will be applied rela tive 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 button The values you enter into these fields remain there even after they are applied To clear all values from the translate and rotate fields click the clear button Chapter 2 Tools 109 2 13 Constraint Editor transform in reset 2 13 5 constraint point gt segment gt 110 Chapter 2 Tools CURRENT TRANSFORM DISPLAY The constraint object s current transform is displayed in the lower right corner of the Constraint 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 constraint object s local XYZ axes a k a body fixed rotation If the tra
16. 0 innermax 0 05 outermin 0 07 outermax 0 07 3 3 Joint Files 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 05 0 080 0 05 0 025 0 07 0 100 0 07 0 005 xyz_ body rotation POSITION 33 6900 25 6600 16 1100 translation POSITION 0 0153 0 0279 0 0287 xyz_ body rotation _DEFORM START 80 0 0 translation DEFORM START 0 0 0 xyz_ body rotation _DEFORM_END 80 0 0 translation DEFORM END 0 0 0 enddeform innermin innermax 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 transforma tions since they will be computed automatically Also remember that auto reset deform objects should be the last deform object within a segment Figure 3 15 shows a typ ical 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 Chapter 3 Input Files 173 3 3 Joint Files outermin outermax xyz body rotation POSITION 17
17. 23 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 23 three curves are spec ified 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 3 6 Plot Files Figure 3 23 Example plot file ankle angle If you plan to load this curve into an existing plot to compare to other curves it is important to give the X and Y variables 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 Chapter 3 Input Files 201 3 6 Plot Files 202 Chapter 3 Input Files Y variable The name of the first curve is Sale ave 90 and its Y variable is ankle angle moment The name of the second curve is Sale knee 90 and its Y variable is ankle angle moment 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 firs
18. For more infor mation on how this process works and the various options for importing 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 created 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 EVa and EVaRT manuals contain X Y and Z coordinates for each identified marker for each time 5 2 Opening Tracked Marker Files frame You can also import analog data files containing forceplate and EMG data recorded during the motion These analog data files can be in either the ANB or ANC formats The Motion Module can also read XLS files con taining 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
19. Full Body Model model gt help A wrap object gt object name pect_min_wrap_r segment gt segment ribcage method muscles gt radius x 0 0700 O cylinder midpoint save all y 0 1550 ore ws p lt p ellipsoid axial restore all z 0 0690 torus delete constrain to quadrant H active 7v X E positive transform __ visible ey negative translate rotate show pts x A body fixed rotation translation transform in x 8 08 0 0081 z ao cle 0 1653 EBA clear local frame 9 74 0 0916 E trackball eae reset Bj pecmaj_cl_r Bj pecmaj_c2_r _ pecmaj_c3_r _ pecmaj_c4_r Bj pecmaj_sl_r D pecmaj_s2_r _ pecmaj_s3_r _ pecmaj_s4_r EJ pecminl_r Bj pecmin2_r Bj pecmin3_r lt lt done gt gt Figure 2 8 Wrap Editor window 76 Chapter 2 Tools save all restore all delete 2 10 3 object name segment radius height 2 10 Wrap Editor individual muscles from these group menus will cause the muscles to wrap over the current wrap object The mus cles 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 combination with
20. If the dof is a function you can change the function in the plot area of the tool window When you click the left mouse button in the dof s field the function is displayed in the function plot area See Section 3 3 3 Joints for a description of the six dofs Chapter 2 Tools 47 2 6 Joint Editor 48 Chapter 2 Tools 2 6 4 Function Plot Area Once a function is displayed in the plot area you can add delete and move its control points To move a control point press the left mouse button while the cursor is on the point The region behind the point you select is shaded to indicate where you can move the point You cannot move a control point so that it overlaps one of its neigh bors As you move a control point its coordinates are shown just above the plot area to help you position the point When you release the left mouse button the point remains at its new location and the joint will now move according to this new function To help you edit a joint function you can press the i o 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 Note If you create a kinematic 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
21. 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 format 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 pro vided so that you can create polyhedron files in the format which early versions of SIMM required but it is recom mended that you create ASCII files 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 Chapter 4 Norm 207 208 Chapter 4 Norm SZ num tx min tx max tx mid 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 translate the origin of the object along the X axis so that the smallest X coordinate is 0 0 i e find the s
22. This command deletes all of the cross hair points from the current plot window See Section 2 9 3 for directions on how to display cross hair points Toggle Buttons This command toggles the display of the cursor in the cur rent plot The cursor is the vertical bar in the plot that shows 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 contains 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 contains one or more event parameters see Section 3 5 Motion Files for details on specifying a motion events Plot Window Commands These keys allow you to zoom and pan within the plot windows 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 move them left and right left mouse button 2 10 2 10 Wrap Editor 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 pressing t
23. Tools 79 2 10 Wrap Editor 80 Chapter 2 Tools trackball clear If the trackball toggle button is checked then the left mouse button will move the current wrap object left right up and down in the plane of the computer screen The middle mouse button will move the wrap object in and out perpendicular to the screen Finally the right mouse button will rotate the wrap object as if it were attached to a virtual trackball If the trackball toggle button is not checked then the left mouse button will rotate the current wrap object about the X axis the middle mouse button will rotate it about the Y axis and the right mouse button will rotate it about the Z axis Furthermore if the transform in local frame radiobutton is selected then the wrap object will rotate about its local XYZ axes If the transform in parent frame radiobutton is selected then the wrap object will rotate about its parent segment s XYZ axes NUMERICAL WRAP OBJECT TRANSFORMATION To apply precise transformations to the current wrap 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 trans form If the transform in local frame radiobutton is selected then the specified transform will be applied rela tive to the wrap object s local XYZ axes Otherwise the transform will be applied relative to the wrap object s parent segment s XYZ
24. You can select the current plot in a similar fashion using the plot selector labeled plot If a tool does not operate on spe cific models e g Plot Viewer the model selector is not displayed in the header 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 com mands However three of the tools Model Viewer Mus cle Editor and Plot Viewer can recognize key and mouse button presses when they occur in the model or plot win dows 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 win dow See the relevant tool section in this chapter for more details Chapter 2 Tools 11 2 2 Opening Files 12 2 2 joint and muscle files Chapter 2 Tools Opening Files To locate joint muscle motion and plot files and load them int
25. 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 which 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 selector menu 2 1 Introduction All tools have a selector menu at the top of the tool win dow 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 button 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
26. a real time SIMM motion import you should either specify MVC levels or have the subject perform MVCs just after connect ing SIMM to EVaRT 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 loca tions in the model must exactly match those for the sub ject whose motion is being recorded Because it is time consuming to measure and scale the body segments and measure and record the offsets of all of the markers the Motion Module has the ability to automatically scale a pre made model the mocap model to fit the subject To use the mocap model select Open Mocap Model from the File menu SIMM will display a Windows file browser and ask you to select the name of a static pose file This static pose described in more detail in Section 5 3 2 is used to calculate joint center locations and seg ment 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 Chapter 5 Motion Module 223 5 3 Using the Mocap Model 5 3 1 224 Chapter 5 Motion Module use the same motion capture protocol as you would for OrthoTrak You can use either
27. an undesirable muscle path as it attempts to wrap over the active quadrants of the wrap object If this occurs you should rotate or translate the wrap object until the muscle paths behave as desired The radiobuttons labeled local frame and parent frame serve multiple purposes 1 For transforms that are applied by numerical entry they determine which reference frame the transform is relative to 2 For transforms that are applied interactively when the trackball toggle button is unchecked they determine which reference frame s major axes will be rotated about 3 They control whether the wrap object s current transform is displayed as a sequence of body fixed or space fixed rotations Deform Editor The Deform Editor allows you to twist bend and warp portions of a body segment that would normally be con sidered rigid When a segment is deformed all bone verti ces distal joint centers muscle attachment points and muscle wrapping objects in the deformed region are trans formed accordingly In this way the effect of a bone defor mity can be examined and measured using SIMM s other tools 2 11 Deform Editor 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 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 determine which region of the
28. and on the model icon when the model window is iconified The model name can be changed by editing this field w h width height gear 2 4 4 2 4 Model Viewer 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 contains the current gear which affects the speed of movement for the model viewing commands i o 1 r u and d see Section 2 4 6 Model Window View ing Commands and the speed of the model animation controlled by the start stop command The gear can have a value between 10 0 and 20 0 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 buttons used to clamp labeled C and lock labeled L th
29. 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 Chapter 2 Tools 35 2 5 Plot Maker 36 fiber length force moment max_force gt tendon strain Chapter 2 Tools attachment points and the current configuration of the model s joints The fiber length of the selected muscles To compute the fiber length of a muscle SIMM finds the static equilib rium 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 activation 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 coordinate 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
30. averaged together to determine the static pose These fields are ini tialized 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 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 out If it is checked and you do not want to load personal dat click the box to turn it off For C3D import only This option allows you to choose from which 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 EVaRT 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 DESCRIPTI
31. can also be changed with this tool 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 interactively 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 Chapter 2 Tools 49 2 7 Muscle Editor jr Muscle Editor Model Dynamic Mocap Model model gt help muscle gt name vas_int_r force wrapping save all TF L AF L PF L F EXC 7 0 1360 object distal_femur 1 restore all P U En 1365 00 delete muscle peel startpt 1 curve editing 08 at endpt 1 1 0000 dynamic timescale mass global parameters damping g reset activations activation1 show coordinates activation2 length D muscle_model r fact Acti amp color factor Active Force Length Curve muscle point editing segment patella_r add muscle point polygon none delete muscle point selected pts net move t ament gt vas_int_r4 0 0001 0 0017 0 0050 Figure 2 4 Muscle Editor window reading it close the window using its close box You will be able to re open it at a later time by selecting h
32. 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 con straints Chapter 2 Tools 107 2 13 Constraint Editor 108 visible constrain to quadrant Chapter 2 Tools 2 13 4 This button lets you toggle 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 invisi ble but still active 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 than zero in the constraint object s local refer ence frame Transforming Constraint Objects The collection of controls labeled transform can be used to move and rotate the current constraint object within its parent segment s frame of refe
33. 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 spec ify the material 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 body segment the default material def bone is used See Section 3 3 7 Materials for infor mation on defining a material If no drawmode is defined the default is gouraud_shading There are six draw modes 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 collec tion 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 3 3 Joint Files 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 may be the slowest drawmode 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
34. easier to manipulate the camera interac tively within SIMM use the save camera command see Section 2 4 2 Command Menu to save the transforma Chapter 3 Input Files 167 3 3 Joint Files 168 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 OZ Or Se Orla endcamera Chapter 3 Input Files 3 3 10 posterior is the name of this pose Figure 3 11 Example camera tion matrix to a buffer then write the model to a file so that you have the precise 4x4 matrix saved to a file You can 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 usu ally want 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 cre ate and modify wrap objects with the Wrap Editor rather than editing the joint file directly See Section 2 9 Wrap Editor for more information Wrap objects are specified in the model s joint file How ever before a muscle can wrap over a wrap object the muscle must
35. in your model you will need to edit the joint file and enter 2 14 Segment Editor 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 Spring Contact Spring contacts are used only by dynamic simulations and constitute a form of penalty based contact detection A spring floor is attached to one body segment and one or more spring points are attached to other body segments When a point passes below the floor a non linear spring force is applied to the point s body segment to push it back above the floor This technique is commonly used to model contact between the feet and the floor during a for ward dynamic simulation Each body segment contain only one spring floor To cre ate a spring floor for the current segment click on the new spring floor button If the segment already has one defined the button will be grayed out and the spring floor s parameters will be displayed T
36. 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 overwritten norm infile outfile Norm will process infile and save the output object in outfile overwrite outdir dirname files filter sep tol num norm infilel outfilel infile2 outfile2 Norm will process infilel 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 overwrite 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 sim ple 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 exi
37. is calculated If the wrap object associated with the muscle is an ellip soid then you will also see a set of radio buttons below the start pt and end pt fields for specifying the desired ellipsoidal wrapping technique The three techniques hybird midpoint and axial are described in detail in Sec tion 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 Dynamic Parameters Form If the muscle has dynamic parameters defined for use with the muscle models in Dynamics Pipeline simula tions SIMM will display them in a form 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 parameters in the Muscle Editor but you can change their values for the selected muscle Chapter 2 Tools 57 2 7 Muscle Editor 58 Chapter 2 Tools 2 7 6 via this form To add or delete parameters edit the muscle file as described in the Dynamics 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 i
38. 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 sliders by default to avoid filling the Model Viewer win dow with too much information The snapshot command allows you to easily capture still images and animations from the SIMM model window in TIFF image format When you select the snapshot com mand a pop up menu is displayed The menu contains the following items 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 cre ate snapshots starting with the filename snapshot_0001 tif Each subsequent snapshot file will have the numeric portion of the filename incremented by Chapter 2 Tools 21 2 4 Model Viewer 22 include alpha channel take snapshot F12 auto snapshot Chapter 2 Tools 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 number If so SIMM uses that number as its snapshot counter Finally SIMM will make sure that the name of each snapshot file it creates ends with tif This identifies the file to other programs as a TIFF image file This menu item allows you to specify whether SIMM should include an alpha channel in the snapshot images it creates By d
39. joint torques The sample lower limb model uses units of meters for length and newtons for force Bone Files A bone is a mesh of planar polygons It 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 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 that is associated with each body segment serves as the local coordinate system for the polygon vertices Each bone file can contain descriptions of any number of sepa rate bone surfaces e g tibia and fibula but all the bones in one file will move as a single object An example bone file is shown in Figure 3 1 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 Figure 3 1 Example bone file in ASCII format Note Bone files are not necessary for developing and ana lyzing musculoskeletal models in SIMM Even without bones you can define segments joints and muscles and display the muscles in the model window Bones are merely visual aids for moving the joints and positioning muscle attachment points Bo
40. lation dofs tx ty tz are translations along the X Y and Z axes respectively of the first body segment listed after the 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 transforma tions To make any of the dofs a constant put the key word constant after the name of the dof then enter a value This value should be in degrees for the rotations Chapter 3 Input Files 155 3 3 Joint Files 156 FEMORAL TIBIAL JOINT beginjoint femoral tibial segments femur tibia order t rl r2 r3 axis1 0 axis2 1 axis3 0 0 loopjoint show axis1 0 2 tx function f1 knee_angle ty function f2 knee_angle tz constant 0 0 rl function f3 knee_angle r2 constant 0 0 r3 constant 0 0 endjoint 00 0 1 0 o 0 0 0 0 1 0 0 0 name of this joint joint from FEMUR frame to TIBIA frame translate then rotate about axisl axis2 and axis3 rotation axis definitions display rotation axis1l length 0 2 The kinematic functions f1 and f2 specify the relations between the generalized coordinate knee_angle and tx and ty the translations in the x and y directions respectively 3 specifies the relation between knee_angle and the rotation around axisl Figure 3 4 Example joint definition Chapter 3 Input Files For translations you can use any units you
41. 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 attachment points of a normal muscle between the key words beginpoints and endpoints you can even spec ify wrapping points This group of lines is then put between the keywords beginmusclesurface and end musclesurface 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 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 0 SOF oooo o oooo oooo
42. make it easy to visualize vectors and points in SIMM animations The ball object is repre sented by a sphere defined in the SIMM bone file unit_sphere asc The other five objects are each repre sented by an arrow defined in the file arrow asc You can override the parameters of these shapes or define addi tional shapes by defining motion object in your joint file Chapter 3 Input Files 177 3 3 Joint Files 178 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 filename position scale xyzrotation material Chapter 3 Input Files Figure 3 17 Example motion object 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 value for this field is 0 0 0 0 0 0 This field specifies the starting X Y and Z scale factors of the motion object The default value for this field is 1 0 O05 120 This field specifies the starting X Y and Z rotations of the motion object in degrees The motion object s starting orientation 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 it
43. 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 sys tem 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 those of the markers placed on the Chapter 5 Motion Module 209 5 2 Opening Tracked Marker Files 5 2 210 Chapter 5 Motion Module subject the Motion Module can adjust the model s genco ord values to determine a best fit of the model to the marker cloud The quality of a fit is determined by how closely each of the model s markers is to its corresponding marker in the marker cloud It then uses this best fit as the starting position for solving the next frame of data The result is a SIMM motion that matches the tracked marker data The model that is used to fit the data can either be one that you create or the pre made model the mocap model that comes with the Motion Module 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
44. o 0 0 0 0 rf_surface 0877 0059 0072 0090 0930 0139 0060 0016 0930 0139 0060 0016 0931 0139 0060 0016 0877 0059 0072 0090 3 4 Muscle Files to top then the sequence of lines should proceed right to left The last line of points in the surface definition should be the same as the first so that the surface is a complete cylinder Figure 3 20 To make the muscle surfaces change color with activation you can specify their activation levels in a motion file As segment segment segment segment pelvis femur femur patella segment segment segment segment pelvis femur femur patella segment segment segment segment pelvis femur femur patella segment segment segment segment pelvis femur femur patella segment segment segment segment pelvis femur femur patella Surface desc of Rectus Femoris line 1 defines the anterior contour of the muscle surface proximal to distal 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 line 4 defines the lateral contour of the muscle surface proximal to distal line 5 needed to close the muscle surface Figure 3 20 Example muscle surface Chapter 3 Input Files i oo te ef cy
45. 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 window 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 kinematic functions select File gt Save Joints To save the model s muscles select File gt Save Muscles Use the Windows file browser to specify the name and location of the joint or muscle file to be written If you do not spec ify a jnt or ms file name extension for the file SIMM will add the appropriate one to the file name you specify motion files plot files 2 3 Saving Files To create a motion file for a model either the model s window 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 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 fr
46. parameters set to no for this reason Gencoords and Muscles The most common types of data found in motion files are generalized coordinate values and muscle activation lev els You can also specify velocities of one or more gener alized 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 gen coord the column name must be the name of the gencoord appended by vel 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 informa tive animations As the body segments are animated through the motion sequence the muscles will change their appearance to reflect their relative levels of 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 col umn name must be the name of the muscle If you want to put other muscle parameters in a motion file such as their force e g as calculated by a dynamic simulation to compare to SIMM s force calculations the column name should be the name of the muscle appended 3 5 3 3 5 Motion Files by a suffix e g semimem force The actual suffix you choose does not matter in SIMM Columns of muscle data that are labeled in this way are not used to set any muscle parameter values in the model They on
47. points 46 L ligaments 192 look at command 20 M marker cloud defined 209 Marker Editor 99 103 command menu 100 information header region 99 markers creating 100 deleting 101 fixed 102 name 101 offset 101 radius 102 restoring from buffer 101 saving to buffer 101 segment of attachment 101 visible 102 weight 102 mass specifying for body segments 115 mass center specifying for body segments 115 material properties ambient 165 Index 4 diffuse 165 emission 165 specular 165 materials assigning to body segments 151 assigning to bones 151 assigning to world objects 164 default 165 166 defined 165 properties see material properties setting in Segment Editor 115 maximum isometric force defined 56 menu defined 7 mocap model 223 235 choosing 225 joint center calculations 230 marker set 232 scaling 231 static pose 226 model display animating motions 25 29 moving joints 29 muscle attachment points 26 rotating 27 trackball method 26 zooming and panning 27 model selector defined 11 model view see camera Model Viewer 16 29 generalized coordinate form 24 information header region 18 model name form 24 model window viewing commands 27 moving joints 29 rotating the model 27 sliders 25 moment arm defined 35 moment defined 35 moment maxforce defined 36 Motion Editor 137 140 command menu 138 creating events 140 cropping motions 138 information header region 138 motion events creatin
48. points on the scapula can be constrained to remain in con tact with the ribcage which is represented as an ellipsoid Once this constraint is activated when you change the value of one of the generalized coordinates in the shoul der SIMM will adjust 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 informa Chapter 3 Input Files 179 3 3 Joint Files tion 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 weight segment tolerance cl 0 0900 0 1800 0 0520 1 0000 xr scapula 0 001 c2 0 0950 0 1400 0 0700 2 0000 xr scapula 0 001 c3 0 0550 0 0900 0 0550 1 0000 xr 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 con strained to remain on the surface o
49. 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 would be constrained to the half of the wrapping primitive in which all x coordinates are greater than zero in the wrap 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 Transforming Wrap Objects The collection of controls labeled transform can be used to move and rotate the current wrap object within its par ent segment s frame of reference The current wrap 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 Wrap Editor window INTERACTIVE WRAP OBJECT TRANSFORMATION To interactively transform the current wrap object hold down the w key then click and drag in the model window The behavior of the left middle and right mouse buttons depends on the setting of the trackball toggle button at the bottom left corner of the Wrap Editor window Chapter 2
50. radii respectively The outer radius is the distance from the cen ter of the torus to the axis of the curved cylindrical sec tion 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 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 coordi nates 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 model window The display of these points can be helpful when creating the wrap object or adjusting muscle attachment 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 ellipsoi dal wrap objects The valid wrap methods
51. reset the crop limits to their original values Motion Events You can create and edit events in a motion using this fea ture You can edit the event s name and the time at which it occurs in the motion New events created using this fea ture 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_xX adds it to the current motion at time 0 0 and makes it the current event for editing 140 Chapter 2 Tools 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 loa
52. s X variable If you change a dof from a constant to a func tion SIMM creates a new function to use for the dof This restore 2 6 3 rlr2r3 tx ty tz 2 6 Joint Editor 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 Inverse 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 configu ration that closes all the loops If no solution is found an error message is displayed and the model is displayed with broken loops This command restores a previously saved joint descrip tion Selecting it restores the joint from a buffer that was saved last time you used the save command When you first 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 in the lower left corner of the Joint Editor window gives you access to each of the six degrees of freedom dofs in the current joint 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
53. 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 seg ment that lie within the inner box follow its movement exactly Elements of the body segment 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 multi ple deform objects to a body segment Each deform object is responsible for deforming the particular region of the segment 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 Inter active transformation 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 defor mity 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 their range of motion at the same time Chapter 2 Tools 85 2 11 Deform Editor 86 2 11 1 model gt Chapter 2 Tools Selector Menu Th
54. 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 abort this process you can click the start stop command or select the motion s menu item in the snapshot pop up menu again Combining Multiple Snapshot Images Into An Animation SIMM does not automatically create digital movie files such as AVI QuickTime or MPEG However there are several third party software packages capable of combin ing multiple image files into a single animation Inexpen sive examples include QuickTime Pro from Apple Inc available for MS Windows and Macintosh and makemovie which comes free with all SGI computers running the IRIX operating system Specifying Snapshot Image Dimensions The height and width of snapshot images will match the dimensions of the model window exactly Therefore if you need to create an animation with a specific pixel reso lution you must first set the model window to the appro priate size You can do this by entering values into the height and width text fields in the bottom right corner of the Model Viewer A Nifty Trick SIMM does not include the ability to take snapshot images of plot windows However on some computers it is possible to simply place a plot window on top of the model window to have the plot window included in the snapshot image In this way it is possible to create snap Chapter 2 Tools 23 2 4 Model Vie
55. the model selector Clicking on the help button opens a window containing helpful text about the Bone 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 119 2 15 Bone Editor 2 15 2 do boolean norm bone split polygon delete polygons scroll edges 120 Chapter 2 Tools 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 seg ment The boolean operations work on two bones speci fied by the bone 1 and bone 2 buttons This command executes the specified boolean operation between bone 1 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 command splits the selected polygon displayed in green by adding a vertex at the center of it and forming triangles using that vertex and each edge of the original polygon This command works only if there is one selecte
56. the save button to help you undo changes made while editing wrap objects This command deletes the current wrap object from the model 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 seg ments The controls described in this section allow you to edit the other parameters 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 Chapter 2 Tools 717 2 10 Wrap Editor sphere cylinder ellipsoid torus 78 hybrid midpoint axial Chapter 2 Tools active visible 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 Typically you will choose the shape that best resembles the surfa
57. the scaling factor for the isometric force as a function of the normalized fiber velocity optimal fiber lengths per second divided by max contraction velocity Thus the range of the function s abscissa should be 1 0 to 1 0 and its ordinate should be 1 0 for a velocity of 0 0 When a muscle con tracts it is defined to have a negative velocity Note Case is significant when entering text into muscle files All SIMM keywords e g beginmuscle endmuscle must be in lower case letters You are free however to use upper as well as lower case letters for naming the muscles 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 sam ple default muscle is shown in Figure 3 18 A sample lower limb muscle rectus femoris is shown in Figure 3 19 The muscle path is defined by three points one in each of the pelvis femur and patella body seg ments The point in the femur frame is included in the path only when the knee angle is between 120 and 80 degrees This is done so that the muscle path wraps over the femur whe
58. 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 negative torque will be applied to decrease its value 3 3 Joint Files 50 25 40 10 70 10 80 25 30 deg 60 deg genci Figure 3 7 Example restraint function The gencoord and function definitions in this example would look like this begingencoord gencl range 30 60 restraint f31 endgencoord beginfunction f31 50 0 25 0 40 0 10 0 25 0 0 0 pe AO 2 03 80 0 25 0 endfuntion Note the coincident control points at 25 and 55 degrees This is very important so that the restraint function has a value of exactly zero between 25 and 55 degrees Chapter 3 Input Files 163 3 3 Joint Files 3 3 7 WORLD OBJECT floor beginworldobject floor filename floor asc origin 0 0 0 9 0 0 material floor material drawmode flat shading endworldobject 164 Chapter 3 Input Files World Objects World objects are polygonal surfaces that are fixed to the world reference frame They can be used to enhance the display of a model by providing a setting for the muscu loskeletal structure Typical examples include a floor walls stairs and a bottom bracket and seat for a cycling model A sample world object is shown in Figure 3 8 The fi
59. to the gencoords when finding model configurations to satisfy the loop constraints The restraint functions are specified using the keyword restraint and a function name in the same format as that used for kinematic functions Chapter 3 Input Files 159 3 3 Joint Files 160 Chapter 3 Input Files 3 3 5 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 Kinematic Functions Kinematic functions define translations and rotations between body segments as functions of the generalized coordinates For example the anterior posterior transla tion tx between the femur and the tibia as a function of knee angle is specified by the kinematic function f1 shown in Figure 3 6 The knee angle tx pairs are interpolated by a natural cubic spline When SIMM needs the value of tx to calculate a joint transformation it evalu ates the cubic spline function using the current value of knee angle 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 perform a linear extrapolation of the function to obtain any Y values that it needs The X coor dinates like the
60. try to generate multiple curves at once by selecting several muscles and turning off the sum option the curve name will be Chapter 2 Tools 39 2 5 Plot Maker 40 Chapter 2 Tools step size activation x min x max deleted and default names will be used for all the curves When this happens it usually indicates that you have for gotten to turn off the sum option or to select only one mus cle for plotting 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 the resolution of and time to create a curve 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 generalized coordinate e g 100 in the above example the step size will be changed to the magnitude of the generalized coor dinate 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 repre senting 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 t
61. two keys and moving the cursor will trans late the selected vertex of the current bone The vertex can be moved within the plane of the screen and will track the cursor s movement Pressing these keys will translate the selected vertex along the negative X Y and or Z axes as appropriate Press the Shift key as well to translate along the positive axes 2 16 2 16 Dynamics Tool 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 dynamics and the desired output variables e g joint torques 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 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 cap ture data then the dynamics code calculates and applies the necessary constraint torques in order to ensure that the joints move as prescribed In a typical forward dynamics simulation muscle and external fo
62. vz for the force vector The names of 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 information 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 vectors 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 displayed 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 defini tion to your joint file like this Figure 3 22 Overriding built in motion object parameters The scale factors shown here are the SIMM defaults for the built in f
63. 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 window Chapter 2 Tools 113 2 14 Segment Editor E Segment Editor model gt segment gt name foot_r save segment restore segment drawmode material inertial parameters mass 0 885000 mass center x 0 101865 inertia xx 0 0009090000 yx 0 0000000000 zx 0 0000000000 force matte name right_foot filename r_shoe asc E visible contact object gt spring contact name floor filename spring point heell spring point gt segment gt segment foot_r x 0 13402000 friction 0 00 a 600000 0 d 0 80000000 E visible y 0 0226500 b 2 20000000 e 1 50000000 total mass of model 75 000000 y 0 015600 xy 0 0000000000 yy 0 0023140000 zy 0 0000000000 Simm Models bones floor1 asc z 0 000000 xz 0 0000000000 yz 0 0000000000 zz 0 0026830000 display parameters E show mass center E show inertia show segment axes show normals global parameters show mass center show inertia browse z 0 00000000 16000 0 f 0 068400 Figure 2 19 Segment Editor window 114 Chapter 2 Tools material 2 14 3 Mass mass center inertia 2 14 Segment Editor This command lets you change the material that is used to display the bones in the current segment The pop up menu shows th
64. wrist markers For a complete list of the markers in the model as well as infor mation on when they should be used and where they should be placed on the subject read the Guide to Mocap Model Markers document The mocap model contains over 80 markers which is more than the number used in most applications When the static trial is loaded any marker in the mocap model which is not in the static trial is removed from the model Thus it is not a problem to 5 3 Using the Mocap Model 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 application the mocap model will have all the necessary markers and the unused ones will automati cally 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 mocap jnt file Instead after editing the marker set save the model to a new file name and copy the altered markers into mocap jnt All of the markers in the mocap model have X Y and Z offsets that put them in realistic locations given the dimensions of the generic model Thus if you load the unscaled mocap model into SIMM using the File Open command not the File Open Mocap Model command which will scale it the markers will appear i
65. 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 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 Cropping a Motion You can change the range of an existing motion using this feature Start and end frames can be entered into the form boxes 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 2 17 Motion Editor Model Dynamic Mocap Model model gt j motion gt name gait_cycle Ee cropping 9 09184 ZAPE lt i aAa reset events event gt name rhs x coord 0 14000 Figure 2 22 Motion Editor window accordingly Use the crop button to crop the motion when you are satisfied with the new range SE 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 Chapter 2 Tools 139 2 17 Motion Editor reset 2 17 4 events gt Before you have cropped the motion you can use this command to
66. your own custom motion objects as well and animate their position scale orientation and color See Section 3 5 3 Motion Objects for more information about adding motion objects to an animation Columns of data in a motion file can correspond to a gen eralized coordinate possibly with a suffix a muscle possibly with a suffix a motion object component or other data Chapter 3 Input Files 193 3 5 Motion Files 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 One legged walking motion name gait cycle datacolumns 6 datarows 100 range 0 0 100 0 keys g_key wrap cursor 1 0 1 0 0 0 event 40 0 heelstrike event color 1 0 0 0 1 0 enforce loops no enforce constraints no calc derivatives 0 01 endheader hip flexion 17 3492 13 8255 12 3931 8606 3476 0183 6743 194 Chapter 3 Input File knee_angle z2 ele 20 SEO TL97 STOS 18 S 7508 2797 5520 2399 0344 0093 2846 name of this motion 6 columns of data 100 rows of data 1 for each motion time step 0 to 100 of gait cycle press this key to make the model walk so you can walk the model continuou
67. 0000 arent frame VP reset E trackball Figure 2 13 Deform Object Transform Panel 2 11 4 Transforming Deform Objects When adding deform objects to a model most of your time will be spent choosing the proper size and placement for each object The inner box and outer box fields described in the preceding section 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 trans form them again to actually apply a deformation to the model 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 The current deform object s transformation can be modified interac tively in the model window or it can be modified pre cisely by entering values in the translate or rotate fields of the Deform Editor window Chapter 2 Tools 91 2 11 Deform Editor 92 Chapter 2 Tools trackball clear Interactive Deform Object Transformation To interactively transform the current deform object hold down the e key then click and drag in the model window The behavior of the left middle and right mouse buttons depends on the setting of the trackball toggle button at the bottom lef
68. 0000 0 050000 1 482000 0 100000 1 600000 0 300000 1 720700 0 500000 1 700000 1 000000 1 775000 endforcevelocitycurve max contraction velocity 10 0 endmuscle Figure 3 18 Example default muscle Chapter 3 Input Files 187 3 4 Muscle Files 188 Rectus Femoris muscle beginmuscle RectusFemoris beginpoints 0 029 0 031 0 096 segment pelvis 0 033 0 403 0 001 segment femur ranges 1 knee angle 120 80 0 012 0 043 0 001 segment patella endpoints begingroups hip flexion knee extension endgroups wrapobject distal femur_ell midpoint range 1 1 max force 780 0 Newtons optimal fiber length 0 0840 meters tendon_slack_ length 0 3460 meters pennation_ angle 5 0 degrees min_thickness 0 004 max thickness 0 008 min_material muscle min max material muscle max endmuscle Figure 3 19 Example muscle definition Chapter 3 Input Files the muscle 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 required muscle specific parameters Just put the keyword activation in the definition followed by a number between 0 0 no acti vation and 1 0 full activation The thickness and color of the muscles in the model window depend on their acti vations with the muscles getting thicker and brighter as activation increases If you do not specify
69. 2 Tools objects When SIMM wraps a muscle over its assigned objects 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 ellipsoids or torii Additionally muscle wrapping can be constrained to a particular half of the wrapping primitive i e a hemisphere hemicylinder hemiellipsoid or hemi torus 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 win dow 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 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 Select this command to
70. 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 functions will not be used in SIMM If your model does have loops you may want to define restraint functions to Chapter 3 Input Files 161 3 3 Joint Files 162 Chapter 3 Input Files 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 As with kinematic functions natural cubic splines are fit to the control points that define restraint functions 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 coin cident 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 sup pose 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
71. 4 translation POSITION deform my auto reset deform autoreset yes translationonly yes innermin 0 05 0 44 0 08 innermax 0 05 0 05 0 08 outermin 0 07 0 45 0 1 outermax 0 07 0 1 0 1 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 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 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 xyz body rotation _DEFORM START translation DEFORM START xyz body r
72. Appendix A Tips and Caveats 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 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 When a body segment or world object is di
73. 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 Chapter 4 Norm 203 204 Chapter 4 Norm the specified output file The polyhedra in an object file do not have to be closed surfaces they can have holes in them However norm may have difficulty computing surface normals for such polyhedra If norm reports that it was unable to compute normals for one or more polyhe dra it will still create an output file but some of the sur face 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 poly gons in the object file norm may have difficulty comput ing surface normals for the object However norm has an option described below to subdivide polygons as it pro cesses 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 fol lowed by one or more file names and the desired options if any Norm can read any of the three file formats described
74. By default this option is set to snapshot To use a different file name delete the default and type in a new name When this option is on SIMM will display the frequency of the model display in the lower left corner of the model window but only when animating a model using the start button 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 To turn it on change its value to on DISPLAY POLYGONS PE R_ S ECOND B 2 B 2 Colors 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 To turn it on change its value to on Colors You can change any of the colors in SIMM by editing the color file called simmcolors in the SIMM Resources directory You may want to make a backup of the file before you change it To change colors in SIMM find the name of the item whose color you want to change in the simmcolors file After the name are listed the red green and blue com ponents respectively of the color The numbers can range from 0 0 to 1 0 The simmcolors file is loaded by SIMM each time it s
75. Input Files 169 3 3 Joint Files translation object dimensions 170 Chapter 3 Input Files 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 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 cyl inder is specified by the keyword height followed by a single value radius 0 10 height 0 25 Note The cylinder s height is used when calculating mus cle wrapping If both of the tangent points the points of contact between the muscle and the wrap object are beyond the visible 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 active visible show_wrap pts quadrant wrapmethod 3 3 Joint Files torus The inner and outer radii of the torus are specified by the keyword radius followed by the inner and outer
76. MM and then save the new model to a file do not replace mocap jnt with the new file Instead copy the rele vant portions of the new file into mocap jnt using a text editor 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 ankle markers in the static pose for more accurate calculation of knee and ankle joint centers You can also supplement the OrthoTrak marker set with your 5 3 Using the Mocap Model 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 kne
77. Module reads these offsets from personal dat as written by OrthoTrak The default values for these offsets are taken from Bell et al Journal of Biomechanics 23 6 1990 pp 617 21 posterior displacement 22 lateral displacement 32 inferior displacement 34 To change these values edit the file personal dat as described in 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 centers If you choose not to use them you should enter knee and ankle diameter measurements into personal dat The Motion Module will use them to locate the knee and ankle centers if no medial markers are used The default method for determining shoulder elbow and wrist joint 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 represen tation of arm motion 5 3 4 5 3 Using the Mocap Model Scaling the Mocap Model Once the locations of the OrthoTrak joint centers have been calculated from the static pose the Motion Module determines the orientations of the OrthoTrak segment ref erence frames It then can measure
78. ONS 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 save JNT file save MSL file 5 3 Using the Mocap Model init _c3d Options fi tohame ne POINT DESCRIPTIONS F Sia TEs Wee Niet FA eta BIGWSe E Meine AEA EA ms Figure 5 3 Static Trial Import Dialog Box These options allows you to specify if SIMM will write out joint and muscle files containing the musculoskeletal 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 pro cess again Chapter 5 Motion Module 229 5 3 Using the Mocap Model 230 5 3 3 Chapter 5 Motion Module 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 locations of the joint centers for all of the joints in the OrthoTrak model The pelvis hip knee and ankle centers are all found using the same procedure used by OrthoTrak The hip center is determined using percentage offsets from the pelvis markers The Motion
79. SIMM 4 0 for Windows Software for Interactive Musculoskeletal Modeling User s Manual SIMM 4 0 for Windows User s Manual June 2004 Part SPC 40001 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 2004 MusculoGraphics Inc a divison of Motion Analysis Corporation All rights reserved This manual may not be repro duced in whole or in part without the expressed per mission of MusculoGraphics Inc MusculoGraphics Inc A division of Motion Analysis Corporation 3617 Westwind Blvd Santa Rosa CA 95403 Phone 1 707 579 6500 Fax 1 707 526 0629 E mail info musculographics com http www musculographics com and http www motionanalysis 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 Credits Program Creation amp Documentation Peter Loan Scott Delp Kenny Smith Krystyne Blaikie Cover Illustration Idd Delp Technical Support 1 773 769 6152 support musculographics com Acknowledgements Development of the initial version of SIMM was fun
80. a polygon you should order them so that they walk around the perimeter of the polygon You can specify them in either clockwise or counter clockwise fashion and can switch 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 coun terclockwise fashion The second bone file format that is supported is an older ASCII format that is used on the SGI versions of SIMM and norm This format is shown is Figure 3 2 It includes less information about the bone so it is easier to create if you are making a bone file from scratch or converting a file from another software package It is recommended that when creating new bone files you create them in the old ASCII format and then process them with norm to out put them in the newer ASCII format The old ASCII for mat is described below 3 2 Bone Files 260 290 0 062448 0 071901 0 057002 0 062417 0 062953 0 055540 0 045919 0 070017 0 069408 0 057682 0 053884 0 064535 Figure 3 2 Example bone file in older ASCII format The first line in the file must contain the number of verti ces 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 t
81. adding to motions 140 F fiber length defined 36 fixed segment changing interactively 20 fixed segment defined 154 flat_shading defined 153 force mattes adding to body segment 116 force defined 36 form defined 9 editing 9 forward dynamics 127 G Gencoord Editor 61 70 command menu 63 dof form 66 information header region 62 generalized coordinate groups defining in joint file 160 slider display 21 generalized coordinate values restoring 18 saving 19 generalized coordinates 158 160 calculating velocites of 195 clamping 25 65 default value 67 159 defining restraint functions 159 locking 25 65 restoring from buffer 63 saving to buffer 63 slider display 21 specifying velocities 196 tolerances for 66 typing in values 66 gouraud_ shading defined 153 gravity in dynamic simulations 134 specifying in joint file 149 I image capture see snapshots inertia matrix specifying for body segments 115 inertial parameters setting 115 Inverse Dynamics spedifying motion for 132 inverse dynamics 127 inverse kinematics defined 67 specifying in joint file 147 turning on off 67 isometric toggle button 43 J Joint Editor 44 49 command menu 45 dof form 47 function plot area 48 69 information header region 44 joint files 146 177 opening 12 saving 14 joints 155 157 restoring from buffer 47 saving to buffer 46 Index 3 K kinematic functions 160 adding control points 46 deleting control
82. allowable values of the deformity slider The default values for range are 0 0 to 100 0 This field specifies the default value of the deformity slider The default value is 0 0 deform 3 3 13 3 3 Joint Files 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 con trolled by the deformity s slider in the Deform Editor win dow 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 external 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 orienta tion 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 pro vides six built in motion objects named force ball contact joint force joint torque and spring force that
83. an be either time in sec onds or frame number The starting X value of the motion will be 0 0 if the units are time and if the units are frame number unless frames of data are cropped because of missing markers 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 Chapter 5 Motion Module 215 5 2 Opening Tracked Marker Files 216 auto load analog data calibrate forces remove old forceplates read marker names from Chapter 5 Motion Module of time and 13 for units of frame number If you want the X values to start at 0 0 or 1 for frame number even if frames are cropped turn on the start at zero option When this box is checked SIMM will look for and auto matically load any analog ANB ANC or XLS data files with the same base name as the TRB TRC file If SIMM did not detect the presence of any analog files when the TRB TRC file was selected this option is grayed out If you selected a C3D file with the file browser then this box controls whether or not the analog data will be read from the C3D file If an analog file is present and the auto load analog data box is checked see above then this box is active and gives you control over the calibration of the forceplate data When this box is checked SIMM determines the baseline of each forceplate channel and automa
84. approximate the curve in the plot area This piece wise linear approximation is for display purposes only When SIMM calculates joint kine matics and needs a Y value for the function given an X value which is a generalized coordinate it finds an exact solution using the algebraic form of the cubic spline The gencoord range limits are displayed in the plot area using red vertical lines If the model has closed loops and the Inverse Kinematics solver is on changing the kine matic function will change the model configuration SIMM will try to find a configuration that closes all the 2 6 5 2 7 2 7 1 model gt help 2 7 Muscle Editor loops If a solution cannot be found an error message will appear and the model will be displayed with broken loops Joint Axis Toggle Buttons You can turn on and off the display of the axes of rotation for each joint using these toggle buttons The three but tons below the DOF form control the display of axis axis2 and axis3 for the current joint Muscle Editor The Muscle Editor gives you access to all of the parame ters 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 mus cle point toward a specific vertex on a bone surface The muscle tendon parameters
85. are hybrid Chapter 3 Input Files 171 3 3 Joint Files 172 3 3 11 beginsegment begindeform my simple deform enddeform endsegment midpoint and axial For more information see Section 2 9 5 Ellipsoid Wrapping Methods Deform Objects Deform objects allow you to twist bend and warp por tions of a body segment that would normally be consid ered rigid When a segment is deformed all bone vertices distal joint centers muscle attachment points and muscle wrapping objects in the deformed region 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 situations to create or modify deform objects manually by editing the model s joint file Deform objects are defined within a segment definition in the model s joint file within a begindeform endde form pair All deform object fields have reasonable default values so it is possible to specify a simple deform with just two lines as shown in Figure 3 13 Figure 3 13 Minimal deform object specification located within a segment definition Chapter 3 Input Files In most cases however you will also define the dimen sions of the deform object s inner and outer boxes the transformation necessary to position the deform within the deform neck_angle innermin 0 05
86. 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 automatically detect and ignore these frames as the file is read turn on this option it is on by default When the option is on SIMM will start at the first frame and delete it if it is missing one or more markers It will then con tinue to scan forward through the frames deleting each one until it encounters a frame containing all of the mark ers It will then do the same procedure starting at the last frame and working backwards SIMM will not remove walk1 c3d Options OK markers 23 frames 477 data rate 120 0 Hz Cancel r Import Options import frames fi to 477 increment fi X axis T quick solve units time sec x T start at 0 0 M crop ends Analog Data T calculate derivatives IV auto load analog data T show markers I calibrate forces IV remove old forceplates read marker names from POINT DESCRIPTIONS 7 Save Options I save HTR file Alene CTEM REWIRI HT I save motion file moton Ae EATERS AKIT Figure 5 2 Tracked Marker Import Dialog Box calculate derivatives show markers X axis units start at zero 5 2 Op
87. axes To apply the inverse transform click the button The values you enter into these fields remain there even after they are applied To clear all values from the translate and rotate fields click the clear button transform in reset 2 10 5 2 10 Wrap Editor CURRENT TRANSFORM DISPLAY The wrap object s current transform is displayed in the lower right corner of the Wrap 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 wrap object s local XYZ axes a k a body fixed rotation If the trans form in parent frame radiobutton is selected then the rota tion sequence displayed is about the wrap 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 wrap object to the origin of its parent segment s reference frame The wrap object s transform is reset to the identity matrix Ellipsoid Wrapping Methods To overcome numerical instabilities involved with com puting the optimal path over the surface of an ellipsoid SIMM allows you to choose between three different algo rithms for calculating muscle paths over ellipsoidal wrap objects The default method hybrid works well for most muscles However if y
88. be associated with that wrap object Associa tions between muscles and wrap objects are specified in the muscle s definition in the muscle file see Section 3 3 Joint Files 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 3 4 1 Muscles 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 position and orientation of the geometric primi tive 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 cylinder ellipsoid and torus If no wrap type is specified the default type sphere is used segment This parameter specifies the body segment to which the wrap object is attached xyz body rotation 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 values are 0 0 0 0 0 0 Chapter 3
89. ble 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 been created you cannot use the default plot title generator to automatically re title it As described above however you 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 settings 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 concatenation 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
90. 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 without having to change the drawmode of each individual segment in the limb Note There is another method for changing the draw modes of bones and world objects If you right click on a bone or world object in the model window SIMM will gencoords gt snapshot gt choose snapshot file 2 4 Model Viewer 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 display of the segment axes and object s normal vectors You can also set the camera to look at that seg ment 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 visibility of several gencoord sliders at a time Note when a model
91. both be assigned to the same segment so the parent segment of the associated constraint object will be grayed out 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 combination 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 constraint point s attributes 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 Chapter 2 Tools 111 2 14 Segment Editor 112 Chapter 2 Tools weight tolerance 2 14 The weight of a point is a non negative floating point value which controls how much emphasis is placed on it when enforcing th
92. ce you intend to wrap muscles over Spheres and cylinders are simpler to define and more straightforward for SIMM to wrap muscles over Ellipsoids are more complicated are there are three tech niques 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 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 edit ing 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 show pts constrain to quadrant 2 10 4 2 10 Wrap Editor This button toggles the visibility of muscle tangent points for muscles wrapping over the current wrap object When checked the X Y Z coordinates of the tangent
93. command reverses the directions of the normal vec tors for the selected polygons It then recomputes the ver tex normals for the bone This command deletes bone This operation cannot be undone This command moves bone 1 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 parameter values in the norm options region 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 bool ean operation as shown in the boolean equation below this button This button 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 bone The boolean operation is performed when you press the do boolean button bone 2 gt 2 15 3 change segment gt new bone name r w filename read bone write bone 1
94. create a new wrap object or to select an existing wrap object for editing When you select segment gt muscles gt 2 10 Wrap Editor Figure 2 7 Cylindrical Muscle Wrap Example this item a pop up menu of existing wrap objects is dis played 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 remaining items in the pop up menu allow you select existing 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 However when the model is animated the wrap object will follow 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 bottom of the Wrap Editor window If the chosen muscle group is already displayed at the bottom of the window then selecting it again will hide it Selecting Chapter 2 Tools 75 2 10 Wrap Editor Model
95. d constraint objects at the same time In some cases having loops and constraint objects that involve the same gencoords may make finding a solu tion more difficult 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 adjust ing 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 con straint objects loop_tolerance 2 8 6 2 8 Gencoord Editor This parameter specifies the acceptance level for the solutions that the solver module reaches when implement ing 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 acceptable 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 dis tance is zero When the loop is not properly enforced the loop joint disarticulates and the two poi
96. d described in Section 2 4 2 Chapter 2 Tools 29 2 5 Plot Maker 30 2 5 2 5 1 model gt plot gt Chapter 2 Tools Plot Maker The Plot Maker allows you to plot various computed properties of the muscle tendon actuators including mus cle force moment moment arm and length You can cre ate these plot curves for any set of muscles as a function of any generalized coordinate or motion variable In addi tion to generating data curves that are calculated from the musculoskeletal 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 win dow 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 win dow 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 selector The plot selector lets you choose the plot to which you will add curves Before you have made any plots the pop up menu c
97. d polygon 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 2 15 Bone Editor i zj Bone Editor model gt do boolean bone 1 gt operation gt bone 2 norm bone 1 Bone editing pelvis_rv asc pelvis pelvis_lv asc pelvis bone asc ground Boolean and read write options split polygon GEAAIPOZRONS add to segment ground change segment gt scroll edges split edge new bone name bone asc flip normals riw filename filename asc read bone write bone 1 delete bone 1 move bone 1 to gt Norm options vertex tolerance 0 00050 show normals convexify polygons tx 0 00000 rx 0 27 triangulate separate bones ty 0 00580 ry 23 07 fill holes tz 0 01592 rz 11 65 1 00000 1 00000 1 00000 Figure 2 20 Bone Editor window Chapter 2 Tools 2 15 Bone Editor split edge flip normals delete bone move bonel to gt bone 1 gt operation gt 122 Chapter 2 Tools This command splits the selected edge in half causing each of the two polygons which use it to be split into two pieces This
98. d 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 current plot If the cur rent 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 genera tor 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 contain ing 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 curve name 2 5 Plot Maker 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 varia
99. 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 the absolute 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 nega tive 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 ten don 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 act override isometric 2 5 Plot Maker if you are plotting data from plot data files or columns of data from motion files This toggle but
100. ded by the Rehabilitation Research amp Develop ment Center Veterans Affairs Medical Center Palo Alto CA We would also like to thank Frans C T van der Helm Ph D of the Delft University of Technology for his contribution of muscle wrapping algorithms 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 graphics based models of the musculoskeletal system In SIMM a musculoskeletal model consists of a set of bones that are connected by joints Muscle tendon actuators and ligaments span the joints The muscles and 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
101. ded into SIMM This chapter describes how to create a musculoskeletal model using input files Examples from the lower 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 and plot files Section 3 6 Motion files are used to specify Chapter 3 Input Files 141 3 2 Bone Files 142 Chapter 3 Input Files 3 2 the values of the generalized coordinates during a particu lar 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 coordi nate 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 Note SIMM does not impose specific units on your mus culoskeletal model nor do you need to define units explic itly 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 calcu late dependent variables such as muscle lengths and
102. 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 window 2 11 Deform Editor anteversion 31 724 lt f Figure 2 15 Deformity Slider Anteversion The range and default value for a deformity are com pletely arbitrary and may be specified in the deformity s definition in the model s joint file If the range is not spec ified 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 drag a deformity slider side to side each of the deform objects associated with the deformity will be adjusted such that their individual deform percentages match the deformity 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 val
103. deform start mode you can specify the inner box s starting transforma tion In deform end mode you can specify the inner box s ending transformation 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 Editor is in position mode both the inner and outer boxes are displayed for all visible deforms in the current seg ment 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 2 11 Deform Editor transform translate rotate body fixed rotation translation transform in x 29 38 0 0000 y 0 00 0 0000 z E clear gt local frame 0 00 0
104. del SIMM saves copies of all of the muscles so you can restore them back to their original form without sav ing them first There is no way to restore a single muscle or subset of muscles This command deletes the currently selected muscle The default muscle cannot be deleted Global Parameter Commands These commands control parameters that not specific to a particular muscle Chapter 2 Tools 51 2 7 Muscle Editor 52 reset activations show coordinates Chapter 2 Tools sensitivity color factor This command resets the activation levels for all of the muscles in the current model to their default values If you specified activations in the muscle file these values are used as the defaults If you did not specify activations for some or all muscles a value of 1 0 is used as the default for those muscles This toggle button turns on and off the display of the coor dinates of selected muscle attachment points The coordi nates of each point are expressed in that point s reference frame and are displayed next to the point in the model window This field contains the sensitivity factor or gear which affects the speed of movement for the commands x y z and 1 2 3 4 5 6 7 8 9 See Section 2 7 5 Model Window Keyboard Commands for more details on these commands for moving selected muscle points This field contains the color factor which is used to color all of the muscles according to their l
105. directory are in the newer ASCII format If you want to use them in another model that you are developing you should copy them to a bones directory located in the directory containing your joint and muscle files see Section 3 2 Opening Files for more details Appendix B SIMM Resources B 5 B 5 Bones B 6 Appendix B SIMM Resources Index A act override toggle button 43 activation muscle defined 56 resetting 52 specifying in file 188 active toggle button 42 analog data files opening 217 animations see snapshots B body segment groups changing drawmode 20 defining in joint file 153 body segments 151 154 changing display parameters 118 restoring 113 saving to buffer 113 setting inertial parameters 115 Bone Editor 119 126 boolean operations 120 command menu 120 deleting polygons 120 flipping normals 122 information header region 119 running norm on bone 120 splitting polygons 120 bone files 142 146 opening 13 bones deleting 122 moving to different body segment 122 reading from files 123 specifying in body segments 151 writing to files 123 C C3D files see tracked marker files cameras restoring position of 18 saving position of 18 specifying in joints file 167 capturing images see snapshots color factor using to display muscles 52 colors setting in simmcolors file B 3 Constraint Editor 103 112 information header region 104 objects command menu 105 points command menu 110 co
106. don The active force length curve of mus cle 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 inter polated by natural 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 calcu lated by differentiating the generalized coordinate posi tion data See Section 3 5 Motion Files for details Then muscle tendon velocity is calculated and this value is dis tributed to the fibers and tendon based on their relative stiffnesses The more compliant element is assigned more of the velocity Chapter 3 Input Files 185 3 4 Muscle Files 186 Chapter 3 Input Files To use these force velocity features you need to specify two additional parameters in the definition of each mus cle 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
107. dow put the keyword show in the joint defini tion followed by the name of the axis i e axis1 axis2 or axis3 and the desired length of the axis This can be helpful when verifying a new joint definition or when visualizing 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 satisfy the loop constraints and keep the loops closed If you turn the IK solver off or if it cannot find a configura tion 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 plot ting purposes so you won t be able to animate the joint or plot muscle properties as a function of the joint s genco ords To specify which joint should act as the loop joint put the keyword loopjoint in the joint definition In most cases however it is recommended that you do not specify loop joints and instead allow the IK solver to con trol the loops in your model Chapter 3 Input Files 157 3 3 Joint Files 158 3 3 4 Generalized Coordinate begingencoord knee _angle begingroups right_leg lower body endgroups range 0 0 120 0 keys k_key default value wrap endgencoord 30 0 Generalized Coordinates Generalized coordinates are degrees of f
108. e 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 Appendix B SIMM Resources B 1 B 1 Preferences FASTER MUSCLE DRAWING SNAPSHOT FILE NAME DISPLAY ANIMATION HZ B 2 Appendix B SIMM Resources the Plot Maker to a particular one the x and y variable set tings will change to the ones used in the plot you are choos ing Thus you can add additional curves of the same type to the plot without resetting these variables This option is enabled by default To disable it comment it out by putting a at the beginning of the line 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 ously using the start button in the Model Viewer If you have many muscles in your model this option can signifi cantly increase the display of your model making the ani mation playback much smoother This option is on by default To turn it off change its value to off 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
109. e and then selecting it but you cannot change the generalized coordinate values for which the point is active Appendix A Tips and Caveats A 5 A 2 Caveats and Limitations A 6 Appendix A Tips and Caveats B 1 Preferences Appendix B SIMM Resources SET TOOLS TO N B 1 EW MODEL SET TOOLS TO N EW MODEL The SIMM installation procedure creates a directory named Resources within the directory where SIMM is in stalled For SIMM to execute properly the SIMM Resourc es directory must not be moved or renamed SIMM needs to access several 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 preferences file is read by SIMM when it starts up This file can be edited by the user to change SIMM s behav ior To change one of the options in the file you either change its on off state or comment it out as described below Whenever you change the preferences file you must restart SIMM for the changes to take effect This option when present causes all of the tools in SIMM to set themselves via the model selector to a new model as soon as you load it into SIMM Thus you can use the tools to edit a new model without having to use each tool s model selector This option is enabled by default To disable it comment it out by putting a at the beginning of the lin
110. e The Joint Editor will remain in this mode until you add the desired point by clicking the left mouse button in the appropriate location The method of cancelling this type of command can vary depending on the particular com mand Some menu items display pop up submenus when they are selected Menu items that do this can be differentiated from other menu items by an angle bracket greater than sign on the right side of the item box For example the model selector which displays a pop up menu of the mod els is labeled model 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 high lighted When you click the left mouse button on that item again the muscle is unselected Several of the tools dis play 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 muscle in the Model Viewer it changes the model view but does not select the muscle form 2 1 Introduction within the Plot Maker If you want to generate a plot curve for that muscle you must also select it from the musc
111. e use the keyword event followed by the time of occurrence within the range that you specified and the name of the event The color of events can be specified with the event color keyword and an RGB color value If you want SIMM to calculate the velocities of the genco ords put the keyword calc derivatives in the header of the file followed by the time in seconds between rows of data SIMM will differentiate each column of data in the file and use these data to obtain the gencoord velocities that you did not specify explicitly in the file To differentiate the data SIMM assumes that the rows of motion data are equally spaced in time with the spacing equal to the value entered after the calc derivatives keyword Natural cubic splines are then fit to the data and derivatives are evaluated at each data point Chapter 3 Input Files 195 3 5 Motion Files 196 enforce_loops enforce_constraints Chapter 3 Input Files 3 5 2 These two parameters control whether or not loops and constraints are enforced when playing back the motion in SIMM i e whether the solver module attempts to adjust the gencoords to satisfy the constraints If the loops and constraints were enforced when the motion was created you will usually want to set both of these parameters to no so that the solver module does not run unnecessarily thus slowing down the animation Motion files created by the Motion Module and the Dynamics Pipeline have these
112. e Hz mass center velocities total muscle joint torques xv system energy system parameters joint reaction forces muscles gt none normalize gt 0 0 gt 0 99 simulation execution gravity gt rh initialize Figure 2 21 Dynamics Tool window Chapter 2 Tools 129 2 16 Dynamics Tool 130 2 16 1 model gt help Chapter 2 Tools 2 16 2 working dir DLL input 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 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 simulation 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 accordingly 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 sur
113. e and ankle markers for better calcu lation of knee and ankle centers not required but highly recommended 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 oth ers that you do not want to use for capturing motion Note If you use a marker set with no upper extremity markers the Motion Module will remove the upper extremity from the mocap model and display only the pel vis 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 pose In many cases you will want to use the default set Chapter 5 Motion Module 227 5 3 Using the Mocap Model 228 average frame from to load personal dat read marker names from Chapter 5 Motion Module tings 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 These fields allow you to specify the starting and ending numbers for the sequence of frames that are
114. e constraints The higher the weight the more SIMM tries to position that point onto the object sur face 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 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 calculated If the point is not within tolerance of its constraint 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 properties are used only for Dynamics Pipeline simula tions 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 informa tion on ho
115. e 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 out side the range If a gencoord is locked its value cannot be changed by entering a new value in the form field or by Chapter 2 Tools 25 2 4 Model Viewer 26 2 4 5 trackball muscle points Chapter 2 Tools shadows crosshairs moving the slider The value can only be changed if the gencoord is restored using the restore gencoord com mand in the Gencoord Editor or the model s gencoord values are restored using the restore gc values command in the 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 naviga tion This button toggles the display of unselected muscle points on the current model Initially muscle points are displayed only when you select them with most points you can tell where they are and be able to select them without having SIMM explicitly draw them If you wish to display all of the points on all of the muscles how
116. e is added to a plot each of the data points is com pared 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 max 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 com mand 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 Chapter 2 Tools 41 2 5 Plot Maker 42 Chapter 2 Tools 2 5 8 SUM rectify active passive Toggle Buttons This toggle button lets you choose whether or not you want to sum the curves of the selected muscles to generate a single curve If sum is off then each selected muscle cre ates a curve that is added to the plot If sum is on then the individual curves are summed and only one curve is added to the plot The current setting of sum has no effect if you are plotting data from plot
117. e 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 win dow Segment Parameters Inertial Parameters This panel can be used to modify the mass and inertia properties 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 seg ment You can specify the mass in whatever units you want but they should match the units you use to specify inertias muscle 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 The coordinates are expressed in the body segment s reference frame These fields let you specify the inertia matrix of the cur rent 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 kilograms meters meters Chapter 2 Tools 115 2 14 Segment Editor 116 Chapter 2 Tools Force Matte Force mattes are used only by dynamic si
118. e 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 Figure 2 9 Attaching Figure 2 10 Applying Deform Boxes Deformation 2 11 Deform Editor Model Lower Extremity model gt help 7 segment gt segment femur deform object gt object name neckangle inner box outer box save min max min max restore x 0 0500 x 0 0500 lt Er Rao y 0 0500 fy 0 0500 y 0 0700 fy 0 0700 delete 2 0 0800 2 0 0250 2 0 1000 2 0 0050 Bl active AET ee z visible transform deform start Ej translate rotate for n deformend lt f gt x x y position auto reset y Y n s body fixed rotation translation z transform in a A 7 no A clear local frame 0 00 0 0000 Bj a y parent frame reset anteversion 31 724 at gt Figure 2 11 Deform Editor window object buttons which will let you add new deform objects to the model heap 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 87 2 11 Deform Editor
119. e 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 Chapter 2 Tools 125 2 15 Bone Editor 126 2 15 5 B key left mouse button B key right mouse button C key V key left mouse button V key X Y and or Z keys Chapter 2 Tools Keyboard Commands There are several keyboard commands that you can use to transform bone 1 or to move individual vertices on bone 1 To use them click on the model window to make it the active window and then press the appropriate key s described below Pressing these two keys and moving the cursor will trans late the current bone within the reference frame of its body segment The translation is stored in a matrix the actual bone vertex coordinates are transformed only when you run norm on the translated bone Pressing these two keys and moving the cursor will rotate the current bone within the reference frame of its body segment The rotation is stored in a matrix the actual bone vertex coordinates are transformed only when you run norm on the rotated bone Pressing this key will select the vertex on the current bone that is closest to the cursor Pressing these
120. e 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 simu lation 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 automatically fill in the input file field with the output file 2 16 3 Start end step 2 16 Dynamics Tool name of a new file SIMM will create this file with all the appropriate data columns 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 output 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 output motion For most inverse dynamics applications you do not need to set these parameters they will be set automatically when you choose a motion see Section 2 16 4 Motion for Inverse Dynamics This spec
121. e use of the force velocity characteristics of the muscle fibers when calculating muscle force during a motion When on fiber velocities are set to zero and isometric muscle forces are calculated When off fiber velocity is used to scale the muscle force according to the muscle s force velocity curve See Section 3 4 Muscle Files for details on how Chapter 2 Tools 43 2 6 Joint Editor 44 2 6 2 6 1 model gt help Chapter 2 Tools fiber velocities are estimated and used to scale isometric muscle force Note fiber velocities affect only force and moment calcu lations and only when plotting against motion variables which contain gencoord velocity information For all other plotting scenarios this toggle button has no effect 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 com prise the joint are displayed If the rotations and transla tions are constants you can change them by clicking in their fields and typing in new values If they are functions of the generalized 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 function or c
122. e window moves a selected muscle point towards a vertex in the selected polygon If the selected polygon has n vertices then the keys 1 through n move the selected point For example if the polygon has 2 8 2 8 Gencoord Editor three vertices pressing 3 moves the point toward the third vertex Pressing 1 and 3 at the same time moves the mus cle point toward the midpoint of the line connecting the first and third vertices If you want to move the point directly onto the surface of the polygon keep the appro priate number keys pressed until the net move coordi nates displayed in the Muscle Editor window stop changing These keys do nothing if more than one muscle point is selected or if no polygon has been selected The left and right arrow keys change the selected polygon If there is no selected polygon these keys do nothing If there is one then the right arrow key changes the selected polygon to the next polygon in the bone file Similarly the left arrow key changes the selected polygon to the previ ous polygon The number of the selected polygon is dis played in the tool window The up and down arrow keys change the selected muscle point within a muscle For example if the second point in a muscle is selected then pressing the up arrow key would select the third point and unselect the second Similarly pressing the down arrow key would select the first point The muscle points are numbered according to their order
123. eady set to new so you don t have to set it Chapter 2 Tools 33 2 5 Plot Maker 34 Chapter 2 Tools 2 5 4 3 4 5 6 7 Note Select the Y variable you want to plot e g force moment using the pop up menu that is displayed when you click on the y variable box 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 the x variable box 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 Set any other options like sum active passive and curve name Click on make curves When plotting musculotendon properties that depend on activation e g moment force make sure that the muscle activations are set correctly they might have been changed by a motion variable See the descriptions of act override in Section 2 5 8 Toggle Buttons and reset activations in Section 2 7 2 Command Menu for details Plotting Data from Motion Files Use the following technique to plot columns of data from motion files See Section 3 5 Motion Files for informa tion on creating these files 1 2 3 Use the model selector to choose which model s motion curves you want to plot Use the plot selector to choose which plot the curve will be added to Click on the command labeled motio
124. ecifies how large a distance 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 only their display it does not affect any marker 3 3 1 3 3 Joint Files offset calculations that the Motion Module performs when loading the model Marker visibility controls the visi bility 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 their visibility Even if the markers are not visi ble 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 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 components e g names of joints and segments and SIMM will display these names exactly as you type them into the joint file Body Segments A body s
125. ect 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 Com bining Multiple Deform Objects for more information about auto reset deforms The default value is no Chapter 3 Input Files 175 3 3 Joint Files translationonly 3 3 12 begindeformity anteversion range 20 0 60 0 value 0 0 deform anteversion twist deform neck angle deform auto reset enddeformity range value 176 Chapter 3 Input Files 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 seg ment s origin back to its original undeformed position but it will not apply a rotation to realign the segment s refer ence frame with its original axes The default value is no Deformities Deformity sliders are specified in the model s joint file after all of the segment definitions There is no way to cre ate 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 Figure 3 16 Example deformity Deformity Fields This field specifies the minimum and maximum
126. ect s transform in reset 2 11 5 2 11 Deform Editor parent segment s XYZ axes To apply the inverse trans form click the button To clear all values from the trans late 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 axes a k a body fixed rotation If the trans form in parent frame radiobutton is selected then the rota tion 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 associ ated body segment s reference frame In deform start or deform end modes this will realign the deform object s inner box with its outer box Note If you hold down the Alt or Ctrl key while click ing 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
127. ect the accuracy or step size of the numerical integration during the simulation 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 vector In general you should specify the gravity vector in your joint file in which case that value is used to initialize the parameter in this tool However if you want to change it from the default you can do so with this button 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 number and connectivity of the body segments as well as the joint types match between the two models the simu lation 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 simulation This motion is added to the SIMM model and a slider for it is added to the Model Viewer 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 pause resume reset 2 16 8 muscle activations muscle lengths 2 16 Dynamics Tool simulation has compl
128. ed the IK solver does not use the restraint function to calculate residuals for the gencoord Instead it uses a different function that guarantees that the gencoord will not go outside its range of motion When a function is displayed in the plot area you can add delete and move its control points To move a control point press the left mouse button while the cursor is on the point The region behind the point you select is shaded to indicate where you can move it You cannot move a control point so that it overlaps one of its neighbors As you move a control point its coordinates are shown just above the plot area to help you position the point When you release the left mouse button the point remains at its new location To help you edit a restraint function you can press the i o 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 Note If you create a restraint 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 plot area This piece wise linear approximation is for display purposes only When SIMM needs a Y value for the function given an X value which is a generalized coordinate it finds an exact
129. edit it If you want to modify the func tion for this muscle only then you must first right click in the editing window and choose make unique from the pop up menu This will give the muscle its own copy of the function from the default muscle which you can now edit by clicking on control points with the left mouse but ton and moving them to the desired locations To remove the muscle s own copy of the function 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 function you must first select the default muscle using the muscle button The buttons to the left of the editing window can also be used to edit the selected muscle function These buttons are described below This command creates a new muscle function for the cur rent muscle Active force length curves passive force length curves tendon force length curves and force veloc ity curves are defined as natural cubic splines If an exci tation curve is created it will be created using the default Chapter 2 Tools 53 2 7 Muscle Editor 54 add fcn point delete fcn point change spline type Chapter 2 Tools excitation format If no default excitation format is speci fied a pop up menu lets you choose what type of function step or spline to create New step functions are created with 2 control points spline functions with 3 control points
130. efault SIMM creates a 24 bit RGB image without an alpha channel If this menu item is selected SIMM will create a 32 bit RGBA image that includes z depth values 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 This menu 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 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 One way to create an animation of a model spinning 360 degrees would be to enable auto snapshot mode disable trackball mode select the model window then press the Control key and click and hold the middle mouse button in the model window until the model has rotated a full 360 degrees Once you are finished be sure to select auto snapshot again to dis able auto snapshot mode SIMM helps you to remember by playing a snapshot sound each time a snapshot file is created 2 4 Model Viewer 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 starting at
131. egment consists of one or more bones fixed in a reference frame The only required component of a seg ment definition is a name You will usually want to spec ify one or more bone files as well however so that you can see the body segment in the model window Other optional components include the segment s material prop erties drawmode shadow shadow color associated deform objects and display 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 Chapter 3 Input Files 151 3 3 Joint Files 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 40 40 40 axes 0 2 endsegment 152 Chapter 3 Input Files 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 Figure 3 3 Example body segment drawmode for displaying the bone The material is used to set the color and lighting of the bone The
132. elp again 2 7 2 Command Menu muscle gt aA This command lets you create a new muscle or choose an existing muscle for editing When you select this item a 50 Chapter 2 Tools save all restore all delete muscle 2 7 3 2 7 Muscle Editor pop up menu of existing muscles is displayed The first item new muscle creates a new muscle named 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 positioned attachment points The muscle properties are inherited from the default muscle if there one If there is not then selecting 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 the paths and muscle tendon param eters of 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 first load a model SIMM saves copies of all of the muscles so you can restore them back to their original form without hav ing to save them first There is no way to save a single muscle or subset of muscles This command restores the paths and muscle tendon parameters of all the muscles in the current model The muscles are restored from the buffer that was saved last time you used the save command When you first load a mo
133. en muscle motion curve gt segment gt 2 5 3 2 5 Plot Maker group is already displayed at the bottom of the window then selecting it again will turn it off 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 move the cursor to the right to display a menu of the data columns from that motion file When you select one of these columns the data curve is added to the current plot see Section 2 5 5 Y variables for more details This command lets you choose the body segment to be used with the muscle orientation Y variable See the description of this Y variable in Section 2 5 5 Y vari ables 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 musculotendon properties that you can plot 1 If you have more than one model loaded into 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 windows yet the plot selector is alr
134. engths When the factor is 0 0 this technique is not used and the muscles are colored 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 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 2 7 4 create new fcn 2 7 Muscle Editor Editing Force Generating Functions The spline functions which control the generation of force in the muscles can be edited using the function editing area At the top of this region are thumbnails for the five functions that you can edit 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 click on one of the thumbnails the function is displayed in the larger editing window below If the selected function is inherited from the default muscle its display in the editing window will be grayed out indicat ing that you cannot
135. ening Tracked Marker Files 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 cal culating 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 val ues i e joint velocities during the motion It will also calculate derivatives of any force or EMG data in the analog file if present These derivatives can then be plot ted using the motion curves command in the Plot Maker see Section 2 5 2 for more details 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 are the marker locations that the Motion Module is trying to fit the model to for each frame It can be helpful to display them in the model window in order to visualize how good the fit is and to help debug problems with the data These options give you control over the specification of the X axis of the motion that is created from the marker data The units along the X axis c
136. er 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 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 sum 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 unse lected 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 for which you want 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 chos
137. era positions 18 generalized coordinate values 19 generalized coordinates 63 joint files 14 joints 46 markers 101 motion files 15 muscle files 14 muscles 51 plot files 15 saving files 14 scaling plot curves 41 Segment Editor 112 119 command menu 113 information header region 113 setting inertial parameters 115 selector menu 11 shadows defining 153 displaying 26 specifying color of 153 slider defined 10 snapshots 21 24 auto snapshot mode 22 choosing snapshot file 21 combining multiple 23 including an alpha channel 22 motion snapshots 23 specifying dimensions 23 taking 22 solid fill defined 152 spring floors adding to body segments 117 spring points adding to body segments 117 static pose see Motion Module sum toggle button 42 surface normals 203 systemInfo txt file B 4 T tendon slack length defined 56 tendon strain defined 36 TIFF images see snapshots toggle button defined 10 tracked marker files cropping ends 214 opening 210 TRB TRC files see tracked marker files Index 7 U units specifying in input files 142 Vv velocities of generalized coordinates 195 of muscle fibers 43 185 specifying in motion file 196 W wireframe defined 152 world objects 164 Wrap Editor 73 84 command menu 74 information header region 74 tips amp techniques 83 wrap objects creating 74 defined 73 specifying in joint file 168 transforming 79 wrapping methods see ellipsoid wrapping methods Ind
138. ers and the orientations of the segment refer ence frames from the static pose it calculates the proper offsets for all of the critical markers plus the static only medial markers For example once the right thigh 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 whatever offsets were in the model input file After the offsets of all the critical markers have been determined in this fashion the mocap model is fit to the static pose marker cloud 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 mea sured 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 pro cess 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 definitively locate without knowing anything about the mocap model Then these critical markers are placed on the mocap model and the model is fit to the static pose 5 4 forceplate data EMG data other data 5 4 Analog Configurati
139. eted 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 controlling 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 initial ized 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 pressed the results calculated so far are stored in the motion 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 Below is a list of the available output variables 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 all of the muscles in the simulatio
140. ever use this command 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 for locating the center of the model window which is also the center of the perspec tive transformation that is applied to the model view 2 4 6 2 4 Model Viewer 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 There are two methods of changing the view of the model within the model window The first method which oper ates when the trackball toggle button in the Model Viewer window is turned on works as follows Pressing the Control 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 Control key and the middle mouse button lets you zoom in on and out of the model Moving the cursor to the right will zoom in and moving it left will zoom out T
141. ex 8
142. f the function is not defined This command lets you change the spline type of excita tion functions The type can be a step function a natural change abscissa 2 7 5 2 7 Muscle Editor cubic or you can choose to inherit the type from the default muscle This command is only available when excitation function is the currently selected function This command lets you change the abscissa of the excita tion function When selected a pop up menu will appear The abscissa can be time or any gencoord defined in the model This command is only available when excitation function is the currently selected function Editing Force Generating Parameters When you choose a muscle using the parameters com mand a form containing that muscle tendon actuator s force generating parameters is displayed This form has five fields described below 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 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 mu
143. f the geometric primi tive at all times The fields in a constraint object definition shown below specify the size position and orientation of the geometric primitive as well as the loca tions of the points 180 Chapter 3 Input Files constrainttype segment xyz body rotation translation object dimensions 3 3 Joint Files 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 not specified in the constraint object defi nition 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 If no translation is specified 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
144. fiber parameters of existing muscles You can also add degrees of freedom to the model in order to more accurately represent a particu lar motion e g adding toe joints and gencoords to exam ine toe motion in greater detail If you modify the mocap model however you should keep in mind two things First the model has been set up to correspond to the skel etal model that OrthoTrak uses when processing gait data The lower extremity body segments and orientations of Chapter 5 Motion Module 225 5 3 Using the Mocap Model 226 5 3 2 Chapter 5 Motion Module the reference frames closely match those in the OrthoTrak model Also each body segment in the mocap model is scaled to fit the subject by relating its length to the length of an OrthoTrak segment These relations are specified in the mocap model by defining scale segments and scale factors for each body segment If you add delete or mod ify joints or body segments in the mocap model you should make sure that each segment still properly relates to an OrthoTrak segment Second mocap jnt contains several macros that are used to properly define the orientation of the floor and to auto matically remove the upper body segments if there are no upper body markers When SIMM reads a joint file it per forms 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 SI
145. 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 associated analog files SIMM attempts to map the data onto the current musculoskeletal model thus creating a SIMM motion that is linked to the model 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 locations in the SIMM model match where they were placed on the subject The marker names should match exactly except that they are case insensitive If the file contains markers that are not in the model their data will be ignored by the Motion Module Similarly if the model contains markers that are not in the file they will not be used to help fit the model to the motion data If you need to add rename or move markers in your SIMM model before loading a tracked marker file you can use the Marker Editor to do so See Section 2 12 Marker Editor for more details Chapter 5 Motion Module 211 5 2 Opening Tracked Marker Files 5 2 1 212 Chapter 5 Motion Module SIMM 3 2 3 File Model Plot Help Look in E Simmaz3 7 c ml Documentation Resources EVaRT Extras Models Motions PipelineDemo File name Files of type SIMM File
146. file will override a muscle file selected in the file browser bone files motion files 2 2 Opening Files If you select multiple joint files in the browser SIMM will open each one and create a new model from it However when selecting more than one joint file you cannot select muscle files as well because SIMM cannot determine which muscle files correspond to which joint files If you want to load multiple joint files at once you must specify the corresponding muscle file names within each joint file You cannot open bone files directly in SIMM Instead bones are referenced 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 for a directory named bones in the same directory as the joint file If a bones directory exists SIMM first looks in it for each of the model s bone files If the bones directory does not exist or a bone file cannot be found in the bones directory then SIMM searches in the bones directory in the SIMM resources directory see Appendix B SIMM Resources for more details Whenever you select a motion file in the file browser SIMM will load the motion and attempt to apply it to every open model in SIMM including any models you may have selected at the same time in the file browser It does this by matching the parameter names in the motion file with the names of the generalized coordinates and muscles of eac
147. force generating properties The geometry is defined by a series of attachment points connected by line segments Each point is fixed to one of the body seg ments and its coordinates are expressed in that segment s reference frame A minimum of two points is required to define the muscle path In cases where a muscle wraps over bone or is constrained by retinacula you can intro duce intermediate via points to further constrain the path You can also specify a restricted range of a general ized coordinate over which these via points constrain the path Thus a via point near the surface of a bone can be 3 4 Muscle Files used to constrain the muscle path only when the path would otherwise pass through the bone Instead of or in addition to via points muscle wrapping objects may be added to body segments to provide a more automated form of muscle wrapping For more informa tion about wrap objects see Section 2 9 Wrap Editor and Section 3 3 9 Wrap Objects The isometric force generating properties of a specific muscle tendon actuator are derived by scaling a generic Hill based model To scale the generic model you must supply four parameters and three curves The four param eters are peak isometric muscle force Fv optimal mus cle fiber length M pennation angle a and tendon slack length amp The three curves are the active and pas sive force length relations of muscle and the force length relation of ten
148. fully specified the X Y and Z components must all be specified the button is deactivated This button lets you toggle the visibility of the current segment s reference frame in the model window This button lets you toggle the visibility of the normal vectors in the model window for all the bones in the cur rent segment This toggle button lets you turn on and off the display of the inertia vectors of the current segment show all mass centers show inertia 2 15 2 15 1 model gt help 2 15 Bone Editor 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 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 of the norm program 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
149. g 140 motion files 193 200 opening 13 saving 15 specifying in joint file 147 194 Motion Module 209 237 opening analog data files 217 opening C3D files 210 opening TRB C files 210 opening XLS files 217 real time import 220 motion objects 197 198 defined 193 specifying in joint file 177 specifying in muscle file 197 motions adding events 140 animating 25 29 cropping 138 displaying continuously 19 Muscle Editor 49 57 command menu 50 information header region 49 model window keyboard commands 60 moving muscle attachment points 59 muscle parameters form 55 selecting muscle attachment points 58 muscle files 184 192 opening 12 saving 14 specifying in joint file 147 184 muscle menu defined 8 muscle orientation defined 37 muscle parameters activation defined 56 editing 55 maximum isometric force defined 56 maximum thickness defined 189 minimum material defined 189 minimum thickness defined 189 optimal fiber length defined 56 pennation angle defined 56 tendon slack length defined 56 muscle wrapping see wrap objects muscles adding attachment points 59 deleting attachment points 60 displaying attachment points 26 displaying coordinates 52 displaying in model window 19 including in dynamics 133 moving attachment points 59 parameters see muscle parameters restoring from buffer 51 saving to buffer 51 selecting attachment points 58 surfaces 190 musculotendon length defined 35 N norm 203 208 Index 5
150. h 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 recreate a DLL e the number of muscles 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 torques at any gencoord e the orientations of any joint s rotation axes 2 16 Dynamics Tool ig Dynamics Tool model gt input amp output options working dir D Users Simm dynamicModel browse dll none specified browse input file Simm dynamicModel gait_cycle_IN mot output file Simm dynamicModel gait_cycle_OUT mot browse simulation time start 0 00000 end 99 00000 step 1 01020 motion for inverse dynamics output variables motion gt gait_cycle gt muscle activations y joint reaction torques muscle lengths gt joint torques smoothing low pass cutoff muscle forces y spring forces kinematics 10 Hz contact forces v muscle moment arms forces 25 Hz mass center positions muscle joint torques EMG non
151. h open model SIMM will automatically link the motion to those models with matching names 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 making plots see Section 2 5 Plot Maker Chapter 2 Tools 13 2 3 Saving Files 14 plot files 2 3 joint and muscle files Chapter 2 Tools 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 topmost SIMM will create a new plot window and add the curves to it In this way multiple plots from sepa rate files can be combined into a single plot if desired 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 navi gate to the directory where you want the file to go then either type the name of the file to create or select an exist ing file to be replaced When saving files to disk SIMM does not preserve any comments that may have been present in the
152. he cursor in the direction in which you want to move the points With this method the muscle points are constrained to move in the plane of the screen so you can change the model view as needed in order to move the selected points in any desired direction The other methods involve pressing keys while the model window is the active window These methods are described in detail in the next section The first method moves the muscle points along the X Y and Z axes of the body segment to which each point is attached The second method helps you position a single muscle point on the surface of a bone using the selected polygon You can select a polygon on the body segment of the muscle point by pressing the F9 key and moving the cursor over the polygons of the bone Each polygon is highlighted as you move over it To select a polygon click the left mouse button while it is highlighted This polygon becomes the selected one and you can then move the muscle point towards its vertices Adding and Deleting Attachment Points You can add and delete attachment points and change the body segment to which the points are attached using the buttons in the lower left corner of the tool window These buttons are described below This command lets you add an attachment point to a mus cle path It works by duplicating the selected muscle Chapter 2 Tools 59 2 7 Muscle Editor 60 delete muscle point segment gt Chapter 2 Tool
153. he left mouse button in the function plot area at the location where you want to Chapter 2 Tools 63 2 8 Gencoord Editor 64 delete point create new func save as new func Chapter 2 Tools add the new control point SIMM figures out which two points the new point should go between and adds it to the function The point is added to the function as soon as you press the left mouse button and if you keep the button pressed you can move the point around within the plot area before releasing the button This command does nothing if no function is currently displayed in the func tion plot area or if the function is inactive displayed in gray This command lets you delete a control point from the currently displayed restraint function After selecting it this item remains highlighted until you select the point you want to delete by clicking the left mouse button on the point You can cancel this command by clicking the left mouse button while the cursor is not on any point This command does nothing if no function is currently dis played if the current function has only two points or if the function is inactive displayed in gray This command creates a new restraint function for the cur rent gencoord SIMM gives the new restraint function a new function number greater than the highest one already defined The new function is created with 8 control points including a pair of coincident points at the star
154. he 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 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 y min y max scale offset 2 5 Plot Maker by editing 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 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 curv
155. he 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 but ton labeled object Clicking on it will display a pop up menu of the wrap objects that are currently associated with the muscle 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 mus cle and then reassign it to the end of the list You can start pt end pt hybrid midpoint axial 2 7 Muscle Editor use this pop up menu to choose which object s parameters you want to display and or change These two fields are used to specify the region of the mus cle path that is allowed to wrap over the wrap object Start pt defines the first muscle attachment point and end pt defines the last attachment point in the region Only mus cle 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 defini tion 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
156. he name field spec ifies the name of the spring floor The filename field spec ifies the name of the SIMM bone file which contains the polygon that comprises the floor only the first polygon in the bone file is used Type a name into this field or click on the browse button to browse for a file The visible Chapter 2 Tools 117 2 14 Segment Editor 118 show mass center show segment axes show normals Chapter 2 Tools show inertia checkbox controls whether or not the spring floor is dis played in the model window Once a spring floor is defined you can define one or more spring points on other body segments Note that although these points are defined on segments other than the cur rently selected segment they are only accessible in the Segment Editor when the current segment is the one to which their corresponding floor 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 associated 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 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
157. he x key and the Shift key will zoom out and similarly 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 pre cision of the displayed coordinates is increased so that you can more accurately note the point s location Wrap Editor The Wrap Editor allows you to create and edit muscle wrapping primitives wrap objects Wrap objects provide automatic muscle wrapping without the need to explicitly specify intermediate muscle points a k a via points Muscle 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 relative 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 Chapter 2 Tools 73 2 10 Wrap Editor 74 2 10 1 model gt help 2 10 2 wrap object gt Chapter
158. he zooming effect will be centered on the points under the cursor when you first press the two keys Press the Control key and the right mouse button 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 direction will rotate the model about an axis perpendicular to that direction The second method of changing the model view will func tion if the trackball toggle button in the Model Viewer window is turned off In this case the Control key and mouse buttons function as follows To rotate the model around the X axis of the world frame which always points horizontally to the right press the Control key and the left mouse button The direction and speed of rota tion are determined by the position 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 Chapter 2 Tools 27 2 4 Model Viewer 28 Chapter 2 Tools Ei fF amp e a 9 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 fash ion pressing the Control key and the middle mouse button ro
159. here 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 1 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 eighth vertices Chapter 3 Input Files 145 3 3 Joint Files 146 Chapter 3 Input Files 3 3 The third format supported by SIMM and norm is a binary format Previous versions of SIMM required bones to be in this binary format so norm would output binary bone files by default If you have some of these binary files you can load them into the current version of SIMM or you can use norm to convert them to ASCII which is rec ommended if you plan to manipulate or transform them in any way Norm is located in the directory where the SIMM execut able resides In addition to converting between different file formats norm processes bone files by calculating ver tex normals checking the vertex and polygon lists for inconsistencies and optionally translating and rotating bones and filling in holes in their surfaces see Chapter 4 Norm for details Joint Files Joint files define the body segments joints generalized coordinates and k
160. ht 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 Chapter 2 Tools 9 2 1 Introduction 10 slider toggle button Chapter 2 Tools the Shift key while pressing the left and right arrow keys to move one character at a time If some text is high lighted 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 Some form fields can contain only numbers e g the gen coord form in the Model Viewer When editing a numeri cal 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 cur sor is outside the field and not over any other menu item or form 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 edit ing it You can also press the Tab key when you are done editing
161. ifies the starting time for the dynamic simula tion 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 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 with the time of the last frame of data 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 Chapter 2 Tools 131 2 16 Dynamics Tool 2 16 4 motion gt 132 Chapter 2 Tools 2 16 5 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 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 usually want to choose the no motion option However if you would like to prescribe the motion of some of the gencoords during a forward simula tion then choose
162. ill 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 Chapter 2 Tools 95 2 11 Deform Editor 96 Chapter 2 Tools 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 modeled 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 by the auto reset deform because it would lie outside of the auto reset deform s outer box By default an auto reset deform will apply both transla tion and rotation to restore the segment s origin to its orig inal position and alignment However it is possible to specify that only translation be applied by including the translationonly keyword in the
163. imes difficult to determine which model or plot you are working on with a given tool In most cases the only indication is the information line at the top of the tool window After you have made a plot for example it is impossible to tell which model the curves were generated from Be careful when editing a function within the Joint Editor or Gencoord Editor SIMM limits the point you are moving so that it stays between the two points it started between but you can still create a bad function If you move the point to a side of the bounding region so that it has nearly the same X coordinate as another point the function may misbehave If you want to create a knot coincident control points in a spline function you should do it by typing the control point values into the function definition in the input file It is very difficult to create knots interactively using SIMM s graphical function editor When you select items from command menus the corresponding action is performed as soon as you press down the left mouse button You cannot abort the action by moving the cursor out of the box before releasing the button You cannot interactively change the names of muscle groups joints generalized coordinates world objects or materials You cannot interactively edit the generalized coordinate ranges for wrapping points You can A 2 Caveats and Limitations move the point itself by moving the joint so that the point is activ
164. inematic functions used in musculoskel etal models They can also include optional components such as world objects muscle wrap objects deform objects constraint 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 Segment 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 model name muscle and motion files inverse kinematics 3 3 Joint Files 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 parameters generally go at the top of the file although they can be placed anywhere The rest of this section describes these optional parameters To give your model a name use the keyword name fol lowed 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 c
165. ing Chapter 5 Motion Module 231 5 3 Using the Mocap Model 5 3 5 232 Chapter 5 Motion Module information consists of the name of the OrthoTrak seg ment and X Y and Z reference numbers that correspond to the unscaled length of the SIMM segment For exam ple the right femur in the mocap model contains the line gait scale R THIGH 0 3960 0 3960 0 3960 This tells the Motion Module that the unscaled femur is 0 3960 meters long Once the length of the corresponding OrthoTrak segment is known R_THIGH the femur can be scaled accordingly If the R THIGH segment were 0 35 meters long then the femur would be scaled by a fac tor of 0 35 0 396 In most cases the three reference values are the same number indicating that the segment should be scaled uniformly in X Y and Z The two exceptions are the TORSO and PELVIS which are scaled differently in two dimensions For SIMM segments that do not map directly to an OrthoTrak segment their scaling informa tion is copied from the most relevant segment For exam ple 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
166. ing object and still be an acceptable solution It does not affect SIMM s cal culation 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 calculated If the point is not within tolerance of its constraint object it is colored red to indicate this condition Chapter 3 Input Files 183 3 4 Muscle Files 184 Chapter 3 Input Files 3 4 3 4 1 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 muscle 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 key word 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 They are described in Section 3 4 2 Muscles Each muscle tendon actuator is defined by specifying its geometry and
167. it is assigned to a new segment However when the model is put in motion the constraint object will follow the move ment of the new segment to which it is attached Con straint 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 Chapter 2 Tools 105 2 13 Constraint Editor E Constraint Editor model gt constraint object gt segment transform translate Zz points gt segment gt save points restore points delete point E trackball tolerance object name rscap_cons segment ribcage radius x 0 0800 y 0 1800 z 0 0800 Bl active E visible rotate body fixed rotation transform in local frame y parent frame constraint points name scapulal segment scapula_r offset 0 0950 weight 1 0000 0 001000 y sphere w cylinder ellipsoid plane constrain to quadrant x E positive E negative n4 Z translation 0 0399 0 1799
168. la cal file to describe their for ceplate 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 237 5 4 Analog Configuration Files 238 Chapter 5 Motion Module A 1 Tips on Using SIMM Appendix A Tips and Caveats A 1 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 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 criterion 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 Appendix A Tips and Caveats A 1 A 2 Caveats and Limitations A 2
169. le menu in the Plot Maker To make it easier to select and unselect large groups of muscles the title bar of each muscle menu also has a spe cial function If one or more muscles in a menu are unse lected 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 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 longer displayed If any of the mus cles in the menu are selected when you put away the menu they remain selected even though you can no longer see the menu When you are finished 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 mus cle 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 highlig
170. le that contains the object s surface description must be in the same format as a bone file see Section 3 2 Bone Files and should be processed with norm see Chapter 4 Norm before being loaded into SIMM You can position the object anywhere in the world reference frame using the origin parameter Just specify the X Y and Z coordi nates of the object s origin with respect to the origin of the world reference frame To control the appearance of the object assign a material to it the same way you do for a body segment If you do not assign a material the default material def bone will be used The drawmode param eter gives you additional control over the shading of the object s surface As with body segments flat shading gouraud_ shading wireframe outlined solid fill and none are supported The default drawmode is solid fill name of this world object norm ed binary file describing surface vector from world ref frame to object use this material defined in joint file override default and use flat shading Figure 3 8 Example world object 3 3 8 3 3 Joint Files 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 mus cles 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 co
171. like but they must match the units used in the bone and muscle files meters are used in the sample leg model To make a dof a function of some generalized coordinate put the key word function after the name of the dof then enter a function name followed by the name of a generalized 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 defi nition 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 axisl axis2 and axis3 respectively The trans lation is divided into three orthogonal components tx ty 3 3 Joint Files tz where the X Y and Z directions are defined by the axes of the femur reference frame The rotation axes are also defined relative to the femur reference frame and their orientations can be changed by adjusting the axis definitions Since all of the translations and rotations in this joint are either constants or functions of a single gen eralized 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 win
172. luded in SIMM plots Chapter 5 Motion Module 235 5 4 Analog Configuration Files 236 5 4 1 force plate Chapter 5 Motion Module importVariables txt The importVariables txt file located in SIMM Resources mocap misc contains a list of variable names and attributes When SIMM processes an analog data file or an OrthoTrak XLS file it consults the importVariables txt file to decide which variables to import and how to inter pret them Each row in importVariables txt defines a variable to be imported The first column in a row specifies the name of the variable as it appears in the analog or XLS data file Since certain analog files support variable names with spaces in them the first column of the importVariables txt file must be terminated by a tab character SIMM consid ers 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 vari able names in an analog data file Therefore the name Rt Tibialis would be considered the same as rt tibialis The second column in a variable definition specifies the type of the variable It must be one of the following key words force plate muscles Of other data These keywords must be lowercase Following each keyword is information describing the variable This keyword specifies a ground reaction force variable
173. ly show up under the motion curves gt muscles menu when you use the motion curves command in the Plot Maker These col umns of muscle data do not count as otherdata Motion Objects SIMM allows you 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 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 ani mated The components that may be animated are e position px py pz e scale sx sy sz e vector vx vy vz e color Gr EG 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 Chapter 3 Input Files 197 3 5 Motion Files 198 beginmotionobject force scale 0 5 0 002 0 5 endmotionobject and force vx force vy and _force
174. m plete 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 keywords ambient diffuse specular and emission should each be followed by the red green and blue color components of that material property These values range from 0 0 to 1 0 Ambient refers to the background illumination which hits all sides of an object Diffuse illumination is brightest where the light source strikes the object perpendicular to the surface Specular lighting accounts for highlights or glare when MATERIAL default bone beginmaterial def bone ambient 0 7 diffuse 0 6 specular 0 7 emission 0 0 shininess 10 endmaterial ooooo o 7 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 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 Chapter 3 Input Files 165 3 3 Joint Files Figure 3 10 SIMM s default materials 166 Chapter 3 Input Files 3 3 9 3 3 Joint Files surface Finally the shininess value which ranges fr
175. m includes forceplates copy the file forcepla cal from your EVaRT 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 EVaRT 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 EVaRT Load the appropriate project Select File Load Tracks File and select the tracked marker file corresponding to the static trial for the subject Under Setup Misc click on the radio button for SIMM OrthoTrak Solver located in the Skeleton Options area Launch SIMM Select File Open Mocap Model and navigate to the motion folder Choose the tracked marker file containing the static pose Set the options as desired in the dialog box and click OK Chapter 5 Motion Module 221 5 2 Opening Tracked Marker Files 222 Chapter 5 Motion Module 4 4 Open the Model Viewer window In the Model Viewer window choose start gt realtime connection to lt hostname gt SIMM will display a dialog box allowing you to set some options for the connection The motion buffer size options control how many seconds of motion data are saved in SIMM s buffer The time scale options let you specify the minimum and maximum val ues in seconds for the time scale of the motion If you want the scale to remain fixed between minimum and maximum check the
176. mallest X coordinate 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 coordinate among all the vertices and subtract it from all the X coordinates translate the origin of the object along the X axis to the midpoint 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 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 capture system It reads files containing tracked marker data 3D positions of markers in global space using the TRC or TRB file format developed by Motion Analysis Corporation It can also read analog files in the ANB or ANC format with ground reaction force and EMG data that was recorded in sync with the motion The Motion Module can also read C3D files which contain both tracked marker and analog data in the same file Addition ally the real time version of the Motion Module can con nect to a Motion Analysis system and receive and display motion and analog data in real time as it is being recorded Files of tracked
177. mand in the Plot Maker the standard deviations will be displayed underneath the data in the same color When you load a motion file into SIMM the new motion is linked only to the current model so you should make the model window the topmost one in SIMM before load ing a motion file to link to it Chapter 3 Input Files 199 3 6 Plot Files 200 Chapter 3 Input Files 3 6 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 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 designed to allow you to compare data derived from other sources e g experimental data dynamic simulations with the data that SIMM computes from your model SIMM can also write out plot files containing curves that were com puted from your musculoskeletal 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 using the file browser see Sections 2 3 and 2 4 for more details An example plot file is shown in Figure 3
178. modi fied 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 3 5 3 5 Motion Files 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 generalized coordinate It can be used to animate the model and 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 5 Y variables In addition to specifying joint angles during a motion you can also specify muscle activation levels Because the thickness 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 dis play the relative activity levels of the muscles used to cre ate the motion An example motion file is shown in Figure 3 21 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 two built in motion objects a green arrow and a green sphere These two motion objects can be used to display force vectors and contact points respectively However you can add
179. 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 com bination of deform objects and thus are not tied to a par ticular body segment When moving muscle points be careful not to move mus cle points that are currently being deformed Although the muscle point may appear to follow the motion of the mouse correctly the next time you make a change to any 2 12 2 12 1 model gt help 2 12 Marker Editor 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 mus culoskeletal model Markers are used by the Motion Mod ule 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 coordi nates for the markers that were placed on the subject while a motion was recorded These files thus contain a series of marker clouds each one representing the 3D coordi nates of all the markers on the subject at a particular instant of time during the motion The Motion Module reads
180. mulations They transform external forces expressed in the ground refer ence 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 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 If the segment already has one defined the button will be grayed out and the force matte s parameters will be displayed The name field specifies the name of the force matte The filename field specifies the name of the SIMM bone file which con tains the polygon description 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 the model window Contact Object Contact objects are used only by dynamic simulations and they are used to model rigid contact between polygo nal surfaces To learn more about how they work 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 these appropriately
181. muscle with respect to a motion variable the submenu lists only true generalized coordinates 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 Tog gle Buttons and also on the current activation level if the active component is turned on muscle orientation motion curve 2 5 6 2 5 Plot Maker This variable does not generate a plot curve but rather writes out an ASCII data file with muscle orientation information For each selected muscle with an attachment point on the chosen body segment the one selected using the segment 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 seg ment the point pt2 is the next point on the muscle path and vec is the normalized vector pt2 ptl This informa tion is written to the file for each value of the correspond ing 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 This option lets you plot one column of motion data ver sus another The submenu contains a list of the motions linked to the current model and each of those has s
182. n Chapter 2 Tools 135 2 16 Dynamics Tool 136 muscle forces contact forces mass center positions mass center velocities System energy joint reaction forces Joint reaction torques Joint torques Chapter 2 Tools the dynamic forces in all of the muscles in the simulation the forces applied by the rigid body contact detection algorithm This includes the impulses applied during pen etrating contact and the forces applied during resting con tact 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 correctly in the dynamics code the total energy potential plus kinetic of the model dur ing the simulation If there are no muscle external or fric tion forces applied system energy will be conserved during the simulation the reaction forces at each joint 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 each joint These are the torques applied by the proximal segment to the distal seg ment
183. n curve A pop up menu of the motions will appear Choose 2 5 5 moment gt musculotendon length moment arm 2 5 Plot Maker the motion you want then move the cursor to the right to display the menu of motion curves These menu items correspond to the columns of data in the motion file When you release the left mouse button with a menu item highlighted the corresponding column of data from the motion file will be plotted in the current plot window Y variables The moment of the selected muscles with respect to the chosen generalized coordinate Moment is defined as force multiplied by the moment arm with respect to a gen eralized 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 general ized coordinates When selecting moment as the Y vari able you must choose a generalized coordinate from the submenu The origin to insertion length of the selected muscles This length depends only on the locations of the muscle attachment points and the current configuration of the model s joints The moment arm of the selected muscles with respect to the chosen generalized coordinate The generalized coor dinate is chosen from the moment arm submenu which appears when you move the cursor off the right side of the moment
184. n 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 shows the change These three fields contain the X Y and Z offsets from the origin of the segment to the marker To change the offset Chapter 2 Tools 101 2 12 Marker Editor 102 Chapter 2 Tools weight visible fixed 2 12 4 radius simply type in new values The units of the offsets are the implicit length units in your model usually meters The weight of each marker determines how much empha sis 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 regardless of the actual weight value the Motion Module treats all markers equally This checkbox controls whether or not the marker is visi ble 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 offsets in the mocap model are not automatically calcu lated when the static trial is processed Rather the offsets in the marker definition in the joint file are used t
185. n 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 Module to process any marker data To explain why this is so we must first introduce the concept of critical markers and non critical markers Critical markers are ones that must be present in the static trial in order for the Motion Module to load and scale the mocap model For the lower body these markers are V Sacral R ASIS L ASIS R Knee or R Knee Lateral R Ankle or R Ankle Lateral R Heel R Toe L Knee or L Knee Lateral L Ankle or L Ankle Lateral L Heel and L Toe If any of these markers is missing from the static trial the SIMM model of the lower body will not be loaded For the upper body the critical markers are V Sacral R ASIS L ASIS R Shoulder R Elbow R Wrist Chapter 5 Motion Module 233 5 3 Using the Mocap Model 234 Chapter 5 Motion Module L Shoulder 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 cent
186. n 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 muscle using the muscle button Editing Attachment Points Use the following technique to select muscle attachment points Once a muscle point is selected you can move it using the two methods described in the following section 1 Click on the model window to make it the active window 2 Press and hold down the Space Bar 3 Move the cursor onto each muscle point you want to select and click the left mouse button 4 Release the Space Bar when you are done selecting points The muscle points are highlighted in yellow when they are selected As you select and unselect muscle points the list of selected points is updated in the Muscle Editor window add muscle point 2 7 Muscle Editor The points within each muscle are numbered according to their order in the muscle definition in the muscle file Moving Selected Attachment Points There are three ways to move selected muscle attachment points The first involves pressing the Shift key and the left mouse button then moving t
187. n the knee is flexed beyond 80 degrees 3 4 Muscle Files 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 s M a Pennation angle must be specified in degrees Since the curves that specify the force length relations of beginmuscle defaultmuscle must use this name for default muscle begintendonforcelengthcurve force length curve for tendon 0 00000 0 000 0 00131 0 010 0 00581 0 065 0 00731 0 091 0 00881 0 123 0 01030 0 161 0 01230 0 227 3 00000 98 000 endtendonforcelengthcurve beginpassiveforcelengthcurve passive force length curve for 0 00000 0 000 1 00000 0 000 muscle fibers 1 10000 0 035 1 20000 0 120 1 30000 0 260 1 40000 0 550 1 50000 1 170 1 60000 2 000 endpassiveforcelengthcurve beginactiveforcelengthcurve active force length 0 000000 0 000000 0 403500 0 000000 curve for muscle 0 527250 0 226667 0 718750 0 856667 fibers 0 861250 0 950000 1 045000 0 993333 1 217500 0 770000 1 438750 0 246667 1 618750 0 000000 2 200000 0 000000 endactiveforcelengthcurve beginforcevelocitycurve force velocity curve 1 00000 0 000000 0 50000 0 166667 for muscle fibers 0 20000 0 444444 0 05000 0 791000 0 000000 1 00
188. nal form without having to save them first This command lets you add a control point to the currently displayed function After selecting this item it remains highlighted until you click the left mouse button in the function plot area at the location where you want to add the new control point SIMM figures out which two points the new point should go between and adds it to the func tion The point is added to the function as soon as you press the left mouse button and if you keep the button pressed you can move the point around within the plot area before releasing the button This command does nothing if no function is currently displayed in the func tion plot area This command lets you delete a control point from the currently displayed function After selecting it this item remains highlighted until you select the point you want to delete by clicking the left mouse button on the point You can cancel this command by clicking the left mouse but ton while the cursor is not on any point This command does nothing if no function is currently displayed or if the current function has only two points This command lets you change the type constant or func tion of each of the dofs Selecting it pops up a menu of the six dofs each with a submenu containing two items constant and function If you choose function then you must use the submenu to the right to choose which gener alized coordinate to use in the function the function
189. namics Pipeline Module or FIT Module options to SIMM there is a Dynamics Tool for interfacing SIMM to dynamic simulations 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 When you select a menu item it is highlighted and the box appears to be pressed into the menu Menu items such as save muscles Chapter 2 Tools 7 2 1 Introduction 8 Chapter 2 Tools muscle menu remain highlighted only as long as it takes to perform the necessary action In other instances a menu item is used to change modes within a tool in order to perform a more complicated action In this case the menu item is high lighted until you complete the action by pressing a key or mouse button For example the Joint Editor has a menu item called add point which lets you add a control point to a joint function When you select this option the box is highlighted to indicate that you are in add point mod
190. ne files can be specified in any of three formats The first format shown in Figure 3 1 is the recommended for mat for new musculoskeletal models It is an ASCII for mat that contains the following information The first line in the bone file must be the string NORM _ ASCII to indicate the file type The second line contains the number of vertices num_vertices followed by the number of polygons num_polygons The third Chapter 3 Input Files 143 3 2 Bone Files 144 Chapter 3 Input Files line contains the bounding box of the bone The six num ber are respectively X min X max Y min Y max Z min and Z max 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 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 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 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 seventh and sixth verti ces When listing the indices for
191. nematics for more information inverse kinematics solver on Another optional component of a joint file is the specifica tion of some model specific colors Shown below are the five colors that you can specify Background color refers to the background color of the model window Rotation axes color refers to the color of the rotation axes of the joints Segment axes color refers to the color of the axes of the body segment reference frames Vertex label color refers to the color of the polygon outline and vertex numbers of the selected polygon Crosshairs color refers to the color of the crosshairs in the model window All of the RGB values ranging from 0 0 to 1 0 in the example below are the default values that SIMM uses if you do not specify your own values background color 0 2 0 2 0 2 rotation axes color 1 0 1 0 0 0 segment _axes color 1 0 1 0 vertex label _ color 1 0 0 0 crosshairs color 1 01 01 0 0 O OH You can also specify the length and force units for your model When you specify units they are used for two pur poses First the Motion Module uses them to convert 3D marker coordinates and forceplate data in TRB C ANB C and C3D files into SIMM model coordinates Second the units are used for display purposes when cre ating 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 specifies the units of all window position windo
192. ns 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 proper ties you want to edit When a gencoord is selected its properties can be viewed and edited in the toggle boxes and gencoord form in the lower left corner of the editor window If the gencoord has a restraint function defined the function is displayed in the restraint function plot area on the right side of the 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 gencoord 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 This command lets you add a control point to the currently displayed restraint function After selecting this item it remains highlighted until you click t
193. nsform 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 parent segment s reference frame The constraint object s transform 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 cur rent constraint point for editing The remaining items in the pop up menu allow you select existing constraint points for editing Select this command 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 save points restore points delete point 2 13 6 point name segment offset 2 13 Constraint Editor However when the model is put in motion the constraint object will follow the movement of its new parent seg ment Constraint objects and points cannot
194. nstraint objects creating 105 defined 103 deleting 107 restoring 105 saving 105 specifying in joint file 179 transforming 108 constraint points creating 110 tolerance 112 contact objects Index 1 adding to body segments 116 creating markers 100 cropping motions 138 D def bone 152 164 165 default_value of generalized coordinates 67 159 of materials 166 Deform Editor 84 99 attributes panel 88 command menu 88 information header region 86 tips and techniques 98 transform panel 91 deform objects auto reset deform objects 95 combining multiple 85 93 creating 88 defined 85 deformity sliders 85 96 deleting 88 editing attributes 88 inner and outer boxes 85 specifying in joint file 172 tips and techniques 98 transforming 91 deformities specifying in joint file 176 deleting bones 122 markers 101 drawmode flat_shading 153 gouraud_ shading 153 Index 2 none 153 of body segment groups 20 outlined 153 setting in Segment Editor 113 setting interactively 20 solid fill 152 specifying in joint file 152 wireframe 152 dynamics including muscles in 133 input and output options 130 normalizing output 133 output variables 135 pausing a simulation 135 running in SIMM 127 setting simulation time 131 smoothing input data 132 specifying gravity 134 Dynamics Tool 127 137 information header region 130 E ellipsoid wrapping methods 81 83 axial 83 hybrid 82 midpoint 82 specifying in Wrap Editor 78 events
195. nt object will not be visible in the model window but it will still be enforced quadrant constraint points 3 3 Joint Files This parameter may be used to limit the constraint object to one half of the geometric primitive When the object is limited 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 ellipsoidal 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 num ber 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 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 correpsond
196. nts 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 Restraint Function Plot Area If the current gencoord has a restraint function it is dis played in the function plot area If the restraint function is inactive it will be shown in gray For an active function the control points are displayed in yellow the curve in white and the extrapolated parts of the curve in pink The gencoord range and current value are also displayed in the plot area Two red vertical lines show the start and end values of the gencoord range and the yellow vertical line shows the gencoord s current value When the IK solver is on it uses the restraint functions to calculate the residuals for each gencoord but only when the function is active and the gencoord is unclamped The IK solver tries to find a solution in which all of the gencoord s residuals are zero Tolerances showing the allowable range for the restraint function values values which result in accept Chapter 2 Tools 69 2 8 Gencoord Editor 70 Chapter 2 Tools able residual errors are shown by blue horizontal lines in the plot these lines only appear when you zoom in close enough The solver will never calculate a loop configura tion with a gencoord value where the restraint function is outside this tolerance envelope When a gencoord is clamp
197. o SIMM you use the Windows file browser Select File gt Open to browse for files to load By default the file browser displays all files with SIMM file name extensions jnt msl mot and plt You can use the Files of type popup menu at the bottom of the browser to limit the display to files of a single type to make it eas ier to locate a specific file As a convenience it is possible to select and open multiple files at once using the file browser This can be useful when working with multiple models motions or plots or when applying different muscle files to a single model To create a model the segments joints generalized coor dinates and kinematic functions must be defined in a joint file If muscles are to be part of the model they must be defined in separate muscle file see Chapter 3 Input Files 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 specified within the joint file 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 mus cle file was also selected in the file browser If a muscle file was selected in addition to a joint file in the browser SIMM will load the model from the joint file and add the muscles from the muscle file to it When selecting both joint and muscle files from the file browser remember that any muscle file specified within the joint
198. o posi tion 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 prop erty of a marker is relevant only to the mocap model since this property is used only when recalculating offsets dur ing 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 visible 2 13 2 13 Constraint Editor 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 their visibility Even if the markers are not visible they are still used by the Motion Module when importing tracked marker files 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 surface of a geometric primitive a k a constraint object on a second segment This mechanism is useful for creat ing joint kinematics that are too complex to be modeled with a traditional SIMM joint For example in the shoul der
199. o 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 muscle path segments that are between these start and end points will be checked for intersection with the wrap Chapter 3 Input Files 189 3 4 Muscle Files 190 Chapter 3 Input Files 3 4 2 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 corresponds to the last point in the muscle Note that these muscle 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 are still counted for the pur poses of determining 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 mus cle 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
200. odel appro priately Chapter 2 Tools 19 2 4 Model Viewer 20 look at gt drawmode gt Chapter 2 Tools This command lets you change the body segment that is fixed to ground for display purposes only The origin of this segment will not move as you flex the joints in your model but it is allowed to rotate about its origin as the joints move 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 seg ment will always be the fixed segment in the SIMM model see Section 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 polygons no shading outlined white polygons with highlighted 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 change the draw mode of several
201. of appearance in the muscle file If there is more than one muscle point selected these keys do nothing 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 Chapter 2 Tools 61 2 8 Gencoord Editor 2 8 1 Selector Menu The model selector lets you choose which model s genco model f 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 never have more than one model at a time loaded into SIMM then you do not need to use the model selector E Gencoord Editor Model Lower Extremity model gt oard ana select gencoord gt Sees Gencoord knee_angle save gencoord 28 restore gencoord function editing add point delete point create new func save as new func Ej function active E clamped locked value 34 000 tolerance 0 000 default value 0 000 knee_angle range from 90 000 to inverse kinematics loop tolerance 0 000100 Figure 2 5 Gencoord Editor window 62 Chapter 2 Tools help 2 8 2 gencoord gt save gencoord restore gencoord add point 2 8 Gencoord Editor Clicking on the help button ope
202. off frequency to use when 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 to use when smoothing the EMG data Enter a value of 1 for no smoothing System Parameters This button lets you choose which muscles you want to include in the dynamic simulation The following options are available no muscles all the muscles in the SIMM model all the muscles whose display is currently turned on in the Model Viewer all muscles that have EMG data in the currently selected motion all muscles that have excitation patterns defined for them This button lets you choose the normalization option for the output motion created by the dynamic simulation Normalization of the output can be useful if you want to compare several dynamic analyses to each other By default normalization is off and the output motion will Chapter 2 Tools 133 2 16 Dynamics Tool gravity gt 2 16 7 initialize 134 Chapter 2 Tools contain the appropriate 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 refer ence number will range from 0 0 to 99 0 Normalization does not aff
203. om 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 their default values are shown in Figure 3 10 Cameras Cameras formerly known as model views define the position 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 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 trans formation 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 trans lation should always be negative You can enter cameras directly into a joint file if you know the exact coordinates but it is usually
204. om the File menu a new row of information containing the model s current gener alized 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 dat arows variable to 200 see Section 3 5 Motion Files After saving your motion 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 accom plish 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 Chapter 2 Tools 15 2 4 Model Viewer 16 Chapter 2 Tools 2 4 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 Win dows file browser to specify the name and location of the plot file to be writ
205. on Files 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 levels and kinetic data when importing a motion SIMM uses a configuration file named importVariables txt to determine which analog variables to import from an analog file and how the data for each variable should be interpreted This configuration file is used for both TRB TRC import with corresponding ANB ANC analog files and for C3D import where the analog data is contained in the C3D file itself SIMM can 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 channels 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 classified as other data SIMM does not perform any cal culations on these data variables but they may be inc
206. on is the first deform in the list followed by Neck Shaft Angle Notice 2 11 Deform Editor in the picture 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 segment s 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 seg ment 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 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 transformations and automatically computes a deforming transformation that restores the segment s origin to its original undeformed position If the segment s reference frame is defined such that its ori gin coincides with the center of its proximal joint then the result of an auto reset deform w
207. onsisting of the word model fol lowed by a number name Lower Extremity You can also specify the names of the muscle and motion files that you would like to load with the joint file This is a convenient feature if you often load the same muscle and motion files with a certain joint file To specify the muscle file use the keyword muscle file followed by the muscle file name Then when you load a model by selecting the joint file with the file browser SIMM will also open the specified muscle file You can also specify motion files in this way up to 100 per joint file using the keyword motion file The corresponding motions will be added to the model when you load it The top of your resulting joint file would look something like this muscle file leg model msl motion file walk mot motion file run mot If there are loops in your model there is an optional parameter to specify whether the inverse kinematics IK solver is on or off it is on by default Just put the key word inverse kinematics solver and specify the Chapter 3 Input Files 147 3 3 Joint Files 148 colors model units Chapter 3 Input Files state on or off When SIMM loads the model it will turn the IK solver on or off appropriately 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 Ki
208. onstant thereby interactively increasing or decreasing 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 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 2 6 Joint Editor E Joint Editor Eg Model Lower Extremity model gt EE Joint knee femur to tibia rl 0 0000 r2 0 0000 r3 f knee_angle ty f knee_angle tz 0 0000 transform order _ axzis1 _ axis 2 _ axis 3 knee_angle Figure 2 3 Joint Editor window 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 6 2 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 45 2 6 Joint Editor 46 save add point delete point dof type gt Chapter 2 Tools This command saves the current joint of the current model It saves the joint 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 the joints so you can restore them back to their origi
209. ontains one item called new Initially new is the current 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 2 5 Plot Maker Plot Maker x Plot none plot gt Model Lower Extremity model gt help Flotting hip_flexion moment ys make curves delete curves muscles gt plot title motion curve gt curve name segment gt EA F glut_med1 Bj glut_min1 Aj tf Oo iliacus _ psoas lt lt done gt gt step size x min y min scale ETN F glut_med1 D glut_med2 Bj glut_med3 E glut_min1 E glut_min2 E glut_min3 _ sar aj tf D glut_maxl Oo peri lt lt done gt gt hip_flexion y variable gt x variable gt hip_flexion moment vs hip_flexion 2 00 activation 1 000 10 00 xmax 120 00 y max offset 0 0000 active B passive 1 0000 sum rectify a O glut_med3 O glut_min3 i quad_fem _ gem oO peri lt lt done gt gt act override E isometric Figure 2 2 Plot Maker window Chapter 2 Tools 31 2 5 Plot Maker 32 help 2 5 2 make curves delete curves muscles gt Chapter 2 Tools method the 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 Mak
210. options in Bone Editor 124 normalizing dynamics output 133 O offsetting plot curves 41 opening bone files 13 motion files 13 muscle files 12 plot files 14 tracked marker files 210 opening files 12 optimal fiber length defined 56 other data in motion files 199 outlined drawmode defined 153 P passive toggle button 42 password txt file B 4 pennation angle defined 56 plot curves clipping 40 creating see Plot Maker deleting 32 naming 39 rectifying 42 plot files 200 202 opening 14 saving 15 Plot Maker 30 44 command menu 32 generating curves from a model 33 Index 6 information header region 30 offset field 41 options form 38 plotting data from motion files 34 scale field 41 toggle buttons 42 X variables 37 Y variables 35 plot points creating 73 deleting 72 plot selector defined 11 Plot Viewer 71 73 command menu 72 information header region 71 plot window commands 72 toggle buttons 72 plots creating see Plot Maker deleting 32 showing cursor 72 showing events 72 Q quick solve defined 213 R real time import see Motion Module rectify toggle button 42 restoring body segments 113 camera positions 18 generalized coordinate values 18 generalized coordinates 63 joints 47 markers 101 muscles 51 restraint functions 161 163 adding control points 63 creating 64 deleting control points 64 making active inactive 65 saving as new function 64 S saving body segments 113 cam
211. orce motion object Chapter 3 Input Files 3 5 4 3 5 Motion Files 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 col umns 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 mes sage window so you can see which ones SIMM did not associate with a model component For any of the columns of data in a motion file except muscle 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 negative values for one standard deviation and label the column with the original data label appended by _std When you plot the data using the motion curves com
212. ord is clamped it is forced to remain within its specified range and cannot assume val ues 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 genco ord is unclamped and has an active restraint function this function will be used by the inverse kinematics solver If a gencoord is outside 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 cur rent gencoord When a gencoord is locked its value can not 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 gencoord command or by Chapter 2 Tools 65 2 8 Gencoord Editor 66 Chapter 2 Tools 2 8 4 value tolerance restoring a model s default configuration using the default config command in the Model Viewer Gencoord Form The gencoord form in the lower left corner of the Genco ord Editor window contains numerical fields for the gen coord 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
213. ords at their locked values When a model is loaded SIMM uses Chapter 2 Tools 67 2 8 Gencoord Editor 68 Chapter 2 Tools the solver to assemble the system and close all the loops using the default values If the solver is on when joint def initions are changed changing dof types editing func tions and when motions are applied to a model the solver tries to close all loops given the current configura tion If individual gencoords are changed by entering val ues 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 gen coord 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 objects that involve the same gencoords the IK solver will solve the 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 an
214. otation DEFORM END translation _DEFORM END active visible autoreset 3 3 Joint Files 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 deformation 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 the deform object s ending deformation 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 fol lowed by the word yes no true or false The default value is yes 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 obj
215. otting Muscle Properties Joint Editing and Gait Analysis A more complete version of the demo leg model is pro vided with the full version of SIMM You can use this model for a musculoskeletal analysis of the lower extrem ity or as a template for building your own model A detailed description of the lower extremity model and its development is beyond the scope of this manual For more details on the model and on using SIMM to create new musculoskeletal models consult the following docu ments Delp S L Loan J P A Computational Framework for Simulating and Analyzing Human and Animal Movement JEEE Computing in Science and Engi neering vol 2 2000 pp 46 55 Delp S L Loan J P A Graphics Based Software System to Develop and Analyze Models of Muscu loskeletal Structures Computers in Biology and Medicine vol 25 No 1 1995 pp 21 34 Delp S L Surgery Simulation A Computer Graph ics System to Design and Analyze Musculoskeletal Reconstructions of the Lower Limb Ph D Disserta tion Stanford University 1990 2 Tools 2 1 2 1 1 menu Introduction SIMM has thirteen tools that enable you to create modify and 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 and Plot Viewer Also if you have the Dy
216. ou notice erratic muscle motion e g skips or jumps when wrapping over an ellipsoidal wrap object or 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 orientation of your wrap object to achieve smooth wrapping motion Chapter 2 Tools 81 2 10 Wrap Editor 82 Chapter 2 Tools THE HYBRID WRAPPING METHOD The hybrid method chooses a wrapping path by comput ing 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 mus cles that use the hybrid wrapping method This is a side effect of the hybrid method that can occur as the weight ing 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 Mus cle Editor tools to restrict the choice of wrapping algo rithm to either the midpoint or axial methods thereby avoiding artifacts created as the hybrid method blends between the midpoint and axial methods In most cases however the hybrid method will produce the best wrap ping result
217. p j restore camera gt saye camera gt name Lower Extremity w 400 h 400 restore gc values Gear 0 080 gt m save gc values muscles gt Bl trackball muscle points shadows crosshairs start gt EDE lisat 2 hip_flexion ajr draw mode gt hip_adduction ajr gencoords gt hip_rotation ajr snapshot gt knee_angle ajr ankle_angle ajr subtalar_angle ar mtp_angle ar a a A i i i A at VIMIMIMMIMIMIV gait_cycle __kneciext E hinexot ankle of Bj pat_lig _ gem B flex_dig _ rect_fem Bj glut_med3 _ flex_hal _ vas_int Bj glut_min3 _ lat_gas Bj vas_lat Bj peri B med_gas E vas_med E quad_fem _ per_brev lt lt done gt gt lt lt done gt gt Bj per_long Bj soleus Bj tib_post lt lt done gt gt Figure 2 1 Model Viewer window Chapter 2 Tools 17 2 4 Model Viewer 18 2 4 1 model gt help 2 4 2 restore camera gt Save camera gt restore gc values gt Chapter 2 Tools 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 cur rent model setting the current model does not affect 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 abo
218. p the inverse kinematics solver will re evaluate the loop s default configuration potentially changing one or more gencoord s default val ues so that the loop remains closed If default values of other gencoords in the loop are changed a message win dow 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 from and to fields Both values can be changed by selecting the appropriate field with the left mouse button and then typ ing 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 The keys display show you which keys control the current gencoord See Section 2 4 6 Model Window Viewing Commands 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 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 satis fying 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 genco
219. 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 models of the human elbow wrist jaw and other anatom ical structures These models can be altered according to particular surgical procedures to study how the surgical alterations affect muscle function SIMM can also be used to analyze and display the mechanics of injuries 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 can use models created with SIMM to study musculoskeletal anatomy and func tion In addition to visualizing anatomical structures stu dents 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 can use SIMM to create three dimensional animations of a person s movement Movements
220. ptions 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 These fields allow you to specify the range of frames to read from the marker file as well as the increment To use them type into the first two fields the starting and ending frame numbers that you want to import The third field specifies the increment to use when reading frames from the file For example to read every other frame from the file enter an increment of 2 The starting frame number field and the increment field are initialized to 1 The end ing frame number 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 han dle cases in which several markers are missing from a Chapter 5 Motion Module 213 5 2 Opening Tracked Marker Files crop ends 214 Chapter 5 Motion Module 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
221. r extremity model and thus flexes and extends the knee The speed and direc tion of the gencoord movements work the same way as the model rotations described above If you keep the keys pressed to continue changing a gencoord you will eventu ally reach the end of the gencoord s range When this hap pens the value of the gencoord will stop changing and the model will stop moving However when you move the cursor to the opposite 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 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 g per cent of gait cycle were a gencoord Just press the key s that you specified in the motion file and move the cursor horizontally to move the model through the motion sequence 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 comman
222. raint Editor window will be blank except for the constraint object button which will let you add new con straint 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 2 13 2 constraint object gt segment gt save all restore all 2 13 Constraint Editor 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 constraint object creates a new constraint object adds it to the current model and makes it the current con straint object for editing object for editing When a con straint object is created 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 constraint object is attached defined as the parent segment When you select this item a pop up menu of the model s body segments is displayed Choos ing a segment from this menu will reassign the current constraint object to the selected segment The constraint object s overall position will not change when
223. 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 Each pair of data points in the function should be entered between parentheses with a comma separating the X and Y values You can also put blank spaces between the val ues commas and parentheses 3 3 Joint Files KINEMATIC FUNCTION Tx of the femoral tibial joint beginfunction f1 defines x translation from femur to tibia knee_angle degrees tx meters 120 0 0 100 0 0 80 0 0 60 0 O 40 0 0 20 0 0 10 0 0 0 0 0 endfunction 003 001 004 004 002 001 003 005 3 3 6 Figure 3 6 Example kinematic function Restraint Functions Restraint functions are used primarily for controlling gen coords during forward dynamic simulations performed with the Dynamics Pipeline The functions define forces or torques that are applied to the gencoords in order to restrain them from going outside their ranges of motion However restraint functions are also used by SIMM s inverse kinematics 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
224. rces 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 simulation will calculate the torques that are required at each joint to create the pre scribed 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 spec ify 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 calculate and apply any additional torques that are required to pre Chapter 2 Tools 127 2 16 Dynamics Tool 128 Chapter 2 Tools scribe 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 Module users cannot create their own DLLs but can choose from several pre built DLLs that come with the software 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 wit
225. reedom in the musculoskeletal model The definition of the generalized coordinate knee angle from the femoral tibial joint defi nition 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 generalized 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 win dow 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 gener alized coordinate in the Model Viewer When you include wrap in the definition you can repeatedly sweep through the range of motion for the generalized coordinate by knee angle name of gencoord range of motion for this gencoord press this key to flex the knee starting and default value of gencoord lets you loop through range of motion Figure 3 5 Example generalized coordinate Chapter 3 Input Files 3 3 Joint Files resetting to the beginning of the range when you reach one end This is de
226. rence The current con straint object s transformation can be modified interac tively in the model window or it can be modified precisely by entering values in the translate or rotate fields of the Constraint Editor window INTERACTIVE CONSTRAINT OBJECT TRANSFORMATION To interactively transform the current constraint object hold down the c key then click and drag in the model win dow The behavior of the left middle and right mouse buttons depends on the setting of the trackball toggle but ton at the bottom left corner of the Constraint Editor win dow trackball clear 2 13 Constraint Editor If the trackball toggle button is checked then the left mouse button will move the current constraint object left right up and down in the plane of the computer screen The middle mouse button will move the constraint object in and out perpendicular to the screen Finally the right mouse button will rotate the constraint object as if it were attached to a virtual trackball If the trackball toggle button is not checked then the left mouse button will rotate the current constraint object about the X axis the middle mouse button will rotate it about the Y axis and the right mouse button will rotate it about the Z axis Furthermore if the transform in local frame radiobutton is selected then the constraint object will rotate about its local XYZ axes If the transform in parent frame radiobutton is selected then the constraint
227. ri ables txt to map forceplate channels to SIMM variables This file is located in SIMM Resources mocap misc and EMG data other data 5 2 Opening Tracked Marker Files contains mappings for typical channel names for up to six forceplates 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 load ing ANB ANC files and when loading C3D files See Sec tion 5 4 1 importVariables txt for information on how to modify this file SIMM displays EMG data by varying the sizes and colors of the corresponding muscles in the SIMM model EMG data in an analog file are voltages measured by the EMG system SIMM rectifies and smooths these data and then scales them based on an MVC value maximum 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 val ues are not present SIMM will use each muscle s maxi mum voltage in the analog file to scale that muscle s EMG data thus each muscle s excitation will peak at 1 0 some time during the motion The file importVariables txt located in SJMM Resources mocap misc contains map pings between typical EMG channel names and the mus cle names in the mocap model It does not contain any MVC values See Section 5 4 1 importVa
228. riables 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 Chapter 5 Motion Module 219 5 2 Opening Tracked Marker Files 5 2 4 220 Chapter 5 Motion Module any calculations on 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 importVariables txt This configuration file located in SIMM Resources mocap misc contains mappings between OrthoTrak and the mocap model of all forces moments and powers for the hip knee and ankle joints You will only need to edit this file if you want to import data other than these 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 EVaRT SIMM is thus able to animate a muscu loskeletal model and plots of joint angles and muscle lengths while the subject s motion is being recorded For thi
229. rker are displayed in the Marker Editor window This command creates a new marker in the current model It is given default values for all its parameters which can then be changed as described in Section 2 12 3 save delete marker restore 2 12 3 name segment offset 2 12 Marker Editor 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 can restore them back to their original form without having to save them first This command deletes the currently selected marker 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 command 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 Marker Parameters 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 The segment butto
230. rors between the current Chapter 3 Input Files 149 3 3 Joint Files 150 loop_tolerance marker_visibility marker_radius Chapter 3 Input Files solver ordinates and the ideal ordinates Decreasing this value will cause the solver module to iterate longer and return a more accurate solution Shown below are the parameters with their default values These parameters can only be specified in a joint file they cannot be changed in SIMM once the model has been loaded solver accuracy 0 0001 solver max iterations 100 This parameter specifies the acceptance level for the solutions that the solver module reaches when implement ing 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 is not acceptable 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 dis tance is zero When the loop is not properly enforced the loop joint disarticulates and the two points are separated by a certain distance The loop tolerance parameter sp
231. s segment object name inner box outer box position deform start deform end 2 11 Deform Editor segment femur object name neckangle inner box outer box min max min max x 0 0500 x 0 0500 x 0 0700 x 0 0700 7 0 0500 fy 0 0500 y 0 0700 0 0700 z 0 0800 g 0 0250 z 0 1000 2 0 0050 y position auto reset deform start deformend E Figure 2 12 Deform Object Attributes Panel This field displays the name of the Deform Editor s cur rent 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 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 Chapter 2 Tools 89 2 11 Deform Editor 90 Chapter 2 Tools auto reset active visible inner and outer deform boxes together to specify how they are attached to the current body segment In
232. s 2 7 7 x Z See adog agao point then placing the copy a small distance away The duplicated point becomes the new selected point so you can then move it to the desired location If there is not exactly one selected muscle point this command does nothing This command lets you delete an attachment point in a muscle path It deletes the selected muscle point leaving no currently selected points If there is not exactly one selected muscle point this command does nothing This command lets you change the body segment to which the selected muscle points are attached When you change segments using the pop up menu the muscle points ini tially remain in the same positions on the screen but if you move the joints you will see that they now move with the new segment Model Window Keyboard Commands These keys constitute the second method of moving selected muscle points Pressing these keys while the model window is active moves the selected muscle points in the X Y and Z directions To move the points in the positive direction along these axes press the Shift key while pressing x y or z You can press any number of these keys simultaneously to move the points in several directions at once e g to move the points in the positive X and Z directions press the x z and Shift keys These keys constitute the third method of moving selected muscle points Pressing the number keys while the model window is the activ
233. s int msl mot plt SIMM Files jnt msl mot plt Joint Files jnt Motion Files mot Plot Files plt Figure 5 1 Windows File Browser Selecting Tracked Marker Files To import a tracked marker file into SIMM first make sure that the model you want to apply it to is the current model the topmost window in SIMM Then select File gt Open from the menu bar When the Windows file browser appears change the Files of type popup menu at the bottom of the browser to MAC Files or to C3D Files then navigate to the folder containing the tracked marker file s you want to import Next select the appropriate marker file s in the file browser Click the Open button to import the file s At this point SIMM will display a dialog box allowing you to specify several options for importing each data file into SIMM 5 2 2 import frames to increment quick solve 5 2 Opening Tracked Marker Files Note If your analog data files have the same base name as your TRB TRC file e g subject14 trc subjectl4 anb and subject 4 x s then it is not necessary to select analog files in the file browser SIMM will automatically 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 O
234. s new local Z axis this is known as an XYZ Euler rotation The default value for this field is 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 drawmode vectoraxis 3 3 14 3 3 Joint Files be a default SIMM material The default value for this field is arrow mat See Section 3 3 7 Materials for infor mation 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 value for this field is guuraud_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 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
235. s normal material and highlight 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 drawmode 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 values will be written to the joint file when you save the model The begingroups 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 shown in Figure 3 3 the shadow of the femur would be displayed 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 shadowcolor 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 segment s shadow in the model window use the shadows toggle button in the Model Viewer see Section Chapter 3 Input Files 153 3 3 Joint Files 154 Chapter 3 Input Files 3 3 2 2 4 5
236. s real time connection EVaRT solves tracked marker data using the mocap model It then sends generalized coordinate values as well as analog data over the net work to the SIMM computer 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 EVaRT and SIMM First time setup only Find the folder SIMM EVaRT on your SIMM computer and look for mocap jnt and solver dll solver dll may be hidden in the folder view because it is a system file Copy both files to the folder on the EVaRT machine where EVaRT resides you ll need to exit EVaRT first if it is run ning This will guarantee that EVaRT is using the same 4 4 4 4 5 2 Opening Tracked Marker Files mocap model and the same scaling algorithms as SIMM uses Open the text file SIMM Resources preferences in a text editor such as Notepad or Wordpad Locate the line that reads EVART_MACHINE lt hostname gt and change the host name to the name of your EVaRT machine Save and close the preferences file make sure that the file is saved as ASCII text with the name preferences Wordpad likes to surreptitiously append a txt extension when it saves files that don t already have a filename extension If your motion capture syste
237. s the kinematics of each joint Finally the muscle file contains a list of coordinates that describe the line of action of each muscle tendon actuator and 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 structure that represents the musculoskeletal model Each of these types of files is described in detail in Chap ter 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 seven software tools Chapter 3 Input Files details how to define a musculosk eletal model Chapter 4 Norm describes the utility pro gram that you use to preprocess bone files before loading them into SIMM Appendix A contains some useful tips and caveats on using SIMM Appendix B describes how to customize SIMM to better fit your needs and prefer ences We recommended that you read both of the appen dices before using SIMM to make your own musculoskeletal models SIMM Tutorials SIMM comes with a sample leg model built into the soft ware and includes several tutorials that will introduce you to the basic capabilities of SIMM The tutorials are located in the Help menu accessible from the SIMM Chapter 1 Introduction 5 1 6 SIMM Tutorials 6 Chapter 1 Introduction menu bar There are four tutorials Viewing a Musculosk eletal Model Pl
238. scle 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 muscle using the muscle button Chapter 2 Tools 55 2 7 Muscle Editor 56 Chapter 2 Tools Its tendon slack length the maximum length at which the tendon develops no force This param eter is used to find tendon strain which scales the X coordinates of the tendon s force length curve Fmo 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 pas sive force length curves lmo optimal fiber length the fiber length at which maximum active isometric force is generated This parameter scales the X coordinates of the muscle s active and passive force length curves pen 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 act level of activation which can range from 0 0 to 1 0 This parameter scales the active component of isometric muscle force Muscle Wrapping Form If t
239. scle line and the chosen axis increases Therefore the axial method automatically chooses the principal axis that is most parallel to the mus cle 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 situation 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 aver age 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 constrain wrapping to one side of a wrap object then mus cles will automatically wrap over the side that permits the shortest muscle path By constraining the wrap object you Chapter 2 Tools 83 2 11 Deform Editor 84 Chapter 2 Tools 2 11 can force muscles to wrap over the desired side of the object even if it is not the shortest path around the object However when calculating a muscle path other than the true shortest path SIMM may occasionally calculate
240. scribed in more detail in Section 2 4 Model Viewer To define a default value for a generalized coordi nate 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 gc 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 specify whether or not the gencoord is locked By default gencoords are unlocked If a gencoord is locked its value cannot change The keyword active is an optional parameter that can be used when a restraint function is associated with the gen coord 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 pipeline but don t want to use it to solve loops If you define a restraint func tion for a gencoord it is active by default Restraint functions can be specified for each gencoord These are used in the Pipeline 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
241. 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 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 ref erence frame not the rotated frame After the transforma tions 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 pro cessing 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 typing values into the fields described below remember to process the bone with norm using the norm bone 1 but ton in order to apply the transformations to the bone ver tices Until you do this the transformations are stored in a temporary 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 La
242. 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 5 3 Using the Mocap Model joint motion as closely as possible The joint file for this model is SIMM Resources mocap mocap jnt There is also a mocap model that has been customized for use with the FIT Module and dynamic simulations It is a simplified full body model that includes the mass and inertia properties for all of the body segments The joint file for this model is SIMM Models dynamic Model dynamic jnt There are also models of the right arm and left arm for use in upper extremity motion capture applications where full body capture is not appropriate These joint files are rightArm jnt and leftArm jnt in the folder SIMM Resources mocap SIMM keeps track of which mocap model to use by stor ing 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 The default setting for this variable is SIMM Resources mocap mocap jnt If you want to change the mocap model while SIMM is running 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
243. sliding checkbox otherwise the scale will continue to increase as new data is received SIMM will now wait to receive data from the EVaRT computer Once the connection is established SIMM will display connected in its message window and the SIMM model will begin tracking the motion of the subject in real time You can pan zoom rotate and change the draw mode of the SIMM model as it is tracking the motion You can also create plots of kinematic variables and muscle properties and see the plots change in real time To disconnect SIMM from the real time stream click the stop button in the Model Viewer You can play back the last N seconds of the motion 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 ben efit of the full data set This has the following implica tions To set the baseline for the forceplates the first frame of force data is used as the zero level Thus when 5 3 5 3 Using the Mocap Model you first connect SIMM to EVaRT 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 level will be kept and used to scale the EMG signals into the range 0 0 to 1 0 Thus if you want to accu rately scale EMG levels throughout
244. sly cursor in plot windows will be yellow heelstrike will be displayed in plot windows as a magenta vertical bar enforce loops when animating motion enforce constraint objs when animating motion seconds between each frame of data so SIMM can calculate derivatives of motion curves rf semimem knee_mom hip flexion _ vel 22 0 10 33 4217 0 0000 25 10 35 8324 1 8606 25 00 38 0823 3 6857 35 00 40 0734 12 2093 135 00 42 9230 11 5651 37 00 43 1642 10 8911 aoe 00 45 3475 9 7498 Figure 3 21 Example motion file 3 5 1 events derivatives 3 5 Motion Files Motion File Header A header in each motion file names the motion defines the range of values for the motion usually percent of activity and lists the keys that are used to animate the model as in a generalized coordinate definition You can specify either one or two keys to control the motion and they must be on the same line as the word keys in the motion file To make it easier to correlate the animation of your model with plots of the data you can specify some parameters in the motion file header that will show up in your plots of the motion data If you put the keyword cursor in the motion file followed by an RGB color value see the example in Figure 3 21 a vertical bar will move along the plot data as you animate the model according to that motion To place markers in the plots representing events in the motion e g heelstrik
245. solution using the algebraic form of the cubic spline 2 9 2 9 Plot Viewer 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 window Like the Model Viewer see Section 2 4 Model Viewer some of the Plot Viewer commands are available from within the plot windows These plot win dow commands are described in Section 2 9 3 E Plot Viewer plot gt reset view i show cursor delete points i show events Figure 2 6 Plot Viewer window Selector Menu The plot selector lets you choose the current plot which is the one affected by the reset view and delete points com mands All other viewing commands are performed in the plot windows so the plot selector does not affect them Clicking on the help button opens a window containing helpful text about the Plot 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 Chapter 2 Tools 71 2 9 Plot Viewer 72 2 9 2 reset view delete points Chapter 2 Tools 2 9 3 show cursor show events o P 0 oJ 5 w 2 r Command Menu This command resets the view of the current plot to its ini tial view The plot curves are zoomed and or translated so that they are all visible within the window
246. splayed 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 A 2 Caveats and Limitations 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 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 Appendix A Tips and Caveats A 3 A 2 Caveats and Limitations A 2 A 4 Appendix A Tips and Caveats Caveats and Limitations The following is a list of warnings and limitations of SIMM It is strongly recommended that you read through the entire list before using SIMM for any of your work It is somet
247. stics just like you can with any other body segment You can specify one or more bone files so that you can see the ground segment in the model window 3 3 3 3 3 Joint Files 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 segment with this command that segment becomes the new fixed segment If you write the model to a file how ever this new fixed segment is not marked as such in the output file 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 seg ment to another The body fixed transformations are per formed in a user defined order and consist of three orthogonal translations and three rotations around user defined axes Each translation and rotation is either con stant i e independent of body position or a function of a generalized 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 rotations to the generalized coordinates are called kine matic functions A sample joint definition is shown in Fig ure 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 trans
248. sting files without prompting put all output files in the specified directory If the direc tory doesn t already exist norm will create it process all files in the current directory that match the specified filter These files will be overwritten with the output write out each polyhedron that is in the input file to a sep arate 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 check ing for 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 duplicate vertices Chapter 4 Norm 205 206 Chapter 4 Norm fill es num con tri CCW rn opt 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 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 addi tional 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 trian
249. stly you should frequently 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 convexify polygons triangulate separate bones fill holes vertex tolerance tx ty tz 1X VY YZ SX SY SZ 2 15 Bone Editor 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 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 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 Thes
250. 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 mus cle strengths when designing products or work stations can use SIMM to study how posture effects muscle 1 3 1 3 Design Goals strength Limits on joint ranges of motion can also be taken into account Biologists interested in animal movement can create mod els to quantify limb function Investigating movement strategies 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 verification 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 ex
251. t and end of the gencoord s range This command does nothing if the current gencoord already has a restraint function This command saves the current restraint function to another function number It is useful when you have used the same function for several gencoords in the joint file but now you want to edit the function for just one of the gencoords that uses it You should use this command to save the function to a new number before editing it If the function is edited before being saved and the function is used by other gencoords the changes will appear in the restraint function plots for the other gencoords as well To 2 8 3 function active clamped locked 2 8 Gencoord Editor restore the original function for these gencoords use the restore gencoord command Toggle Buttons This button allows you to toggle the restraint function from active to inactive 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 If there is no restraint func tion for the gencoord this button does nothing This toggle button allows you to clamp or unclamp the gencoord If the genco
252. t column contains the values of the X vari able and each of the rest of the columns contains one plot curve of data 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 different range of the X variable ankle angle 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 into SIMM The main purpose of norm is to compute surface normals for the polyhedra in the files but it can also perform other functions such as removing duplicate vertices making the polygons convex and translating or rotating the poly hedra These features can be useful if you are creating new object files from medical image data or 3D digitiza tion 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 simple polygon and vertex editing functions which norm does not However the stand alone version of norm contains some file conversion and advanced normal calculation functions that are not accessible in the Bone Editor Before you begin modifying your bone files it is recommended that you learn about the
253. t corner of the Deform Editor window as described below If the trackball toggle button is checked then the left mouse button will move the current deform object left right up and down in the plane of the computer screen The middle mouse button will move the deform object in and out perpendicular to the screen Finally the right mouse button will rotate the deform object as if it were attached to a virtual trackball If the trackball toggle button is not checked then the left mouse button will rotate the current deform object about the X axis the middle mouse button will rotate the deform object about the Y axis and the right mouse button will rotate the deform object about the Z axis Furthermore if the transform in local frame radiobutton is selected then the deform object will rotate about its local XYZ axes If the transform in parent frame radiobutton is selected then the deform object will rotate about its parent segment s major axes 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 rotate fields then click the button below the text fields one or more times to apply the trans form If the transform in local frame radiobutton is selected then the specified transform will be applied rela tive to the deform object s local XYZ axes Otherwise the transform will be applied relative to the deform obj
254. tarts up so to see the effects of your changes you will need to restart SIMM each time you make a change to simmcolors Additionally each time SIMM opens a joint file jnt it looks for a file named simmcolors in the same directory as the joint file Note model specific colors and materials are specified in the joint file for that model not in the simmcolors file See Section 3 3 Joint Files and Section 3 3 7 Materials for more information on changing model specific colors and materials Appendix B SIMM Resources B 3 B 3 Password txt B 3 B 4 B 4 Appendix B SIMM Resources Password txt The first time you run SIMM on your computer you will be prompted to enter your SIMM password At that point SIMM will automatically store your password in a file named Password txt This file is created by SIMM simply as a convenience to you so you will not need to reenter your password each time you run SIMM SystemInfo txt Each time SIMM runs it creates a file named SystemInfo txt containing information about your computer This informa tion can be useful to us when helping you resolve technical problems with SIMM If you request technical support by sending email to support musculographics com please include a copy of the SIMM SystemInfo txt file with your message B 5 B 5 Bones Bones The bones subdirectory in the SIMM resources directory contains the bone files used to display the SIMM demo model The bones in this
255. tates the entire model around the Y axis which always points straight up Pressing the Control key and the right mouse button rotates the model around the Z axis which points out of the screen towards you In addition to the two methods described above you can also translate the model by pressing certain keyboard keys These keys function independently of the two view ing methods described above so they will operate regard less of which of the two you have chosen The speed with which they move the model depends on the current gear These keys are described below Pressing this key moves the model in towards you mak ing it larger Pressing this key moves the model out away from you making 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 moving the joints animating motions changing display properties 2 4 Model Viewer 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 window the values of the generalized coordinates will change For example pressing the k key changes the value of knee_angle in the sample lowe
256. ten SIMM can write plot files in two formats tab 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 columns and add a pit extension to the file name if necessary Tab delimited plot files are designed to be easy to read or import into word processing or spreadsheet programs Note SIMM cannot read plot files in Postscript format Plots that you intend to load back into SIMM later should be saved in the tab delimited p t format Model Viewer The Model Viewer allows you to change the views of the musculoskeletal models You can rotate scale and trans late a model into any viewing perspective as well as choose which muscles to display on the bones There are also commands to display shadows of the body segments and start or stop a continuous animation of a model Figure 2 1 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 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 2 4 Model Viewer i Model Viewer x Model Lower Extremity model gt hel
257. tensible 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 anal ysis tools Figure 1 1 Each tool is contained within its own window and has a distinct function such as control ling the viewing of the models Model Viewer altering the muscles Muscle Editor and making plots for analy sis Plot Maker Muscle Editor Ye Wrap Editor EA EA EN N muscle force moment arm ne son mas 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 and Model Viewer Information is extracted from the model by making plots movies or by exporting edited joint muscle and motion files Chapter 1 Introduction 1 5 1 6 1 5 About the Manual A musculoskeletal model is specified with three types of input files The bone files contain lists of the polygons representing the bone surfaces The joint file specifie
258. 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 closest one If the current gencoord is locked its value cannot be changed by typing in a new value If the genco ord 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 import ing 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 computa tion time This feature is especially useful when you are importing a motion in real time with the Motion Mod ule and want the SIMM animation to be as fast as possi ble The default value for tolerance is 0 0 default value range from to keys 2 8 5 inverse kinematics 2 8 Gencoord Editor 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 gencoord that is used in a loo
259. the Helen Hayes or Cleve land Clinic marker sets plus your own additional mark ers 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 personal 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 possi ble to the OrthoTrak algorithms This was done so that motion information in SIMM e g joint angles EMG lev els 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 information 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 default model is a full body model that has been custom ized for gait analysis but can be used to import and dis play 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 approxi mately 175 cm tall with a mass of 78 kg The model is scaled to match the
260. 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 3 4 Muscle Files because the Plot Maker uses the 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 acti vation 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 If the muscle is to automatically wrap over a wrap object specified in the model s joint file then an association between the muscle and the wrap object must be made Include the wrapobject keyword in the muscle defini tion 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 n
261. the appropriate partial motion For inverse dynamics choose a motion with data for all of the gencoords When you choose a motion SIMM will auto matically 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 Pass Cutoff SIMM will gener ate 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 simulation time fields with time values taken from the motion data 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 kinematics forces EMG 2 16 6 muscles gt none all visible with EMG data with excitations normalize gt 2 16 Dynamics Tool simulation you can perform smoothing of that data only by entering the appropriate column labels in the file itself This specifies the low pass cutoff frequency to use when smoothing the gencoord data Enter a value of 1 for no smoothing This specifies the low pass cut
262. the lengths of the OrthoTrak segments and use them to scale the mocap model to match the size of the subject The reference frames for the foot shank thigh pelvis and torso are all determined using the procedure described in Appendix H of the OrthoTrak manual OrthoTrak does not create reference frames for the upper and lower arms but the Motion Module does this using one of several methods If medial elbow and wrist mark ers 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 deter mined 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 measurements in personal dat then the foot length is assumed to be 1 4 times the distance from the heel marker to the toe marker the toe marker is actually placed on the top of the foot just posterior to the toes Each body segment in the mocap model contains scaling information that tells the Motion Module how to scale it based on an OrthoTrak skeletal segment The scal
263. the restore gc values command This command lets you choose which muscles are dis played 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 selecting 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 window the model window is redrawn to show the new muscle selections This command lets you continuously loop through motions without having to press keys or mouse buttons When you select it a pop up menu is displayed containing a list of the motions that have been linked to the current model When you select one of the motions the model is continuously animated according to that motion data and the button name is changed to stop This will continue until you click on stop to stop it Because this procedure repeatedly draws the model in the model window it can slow down the computer making it difficult 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 chang ing the model view while the animation is proceeding If you need to change the view of the model stop the anima tion first then restart it after positioning the m
264. 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 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 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 99 2 12 Marker Editor Marker Editor Ea Model Mocap Model model gt help choose marker name R Elbow new marker segment gt humerus_r save delete marker restore offset 0 00136 0 34388 0 05078 weight 2 00000 H visible fixed global parameters radius 0 00500 E visible 2 12 2 choose marker new marker 100 Chapter 2 Tools Figure 2 16 Marker Editor window 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 highlighted in the marker window The parame ters for the chosen ma
265. tically sub tracts these baseline values from the data thus zero ing out the force data In order to display forceplate data that is in the analog file SIMM creates graphical objects in the model window rep resenting the forceplates Each time you load a tracked marker file with corresponding analog data SIMM creates a new graphical object for each forceplate in the file In most cases you will want to remove the existing forceplate objects from the model when loading a new file so that the display is not cluttered with multiple or redundant sets of objects Thus this option is turned on by default If you load a series of marker and analog files that all have the same forceplate definitions then you should leave this option turned on For C3D import only This option allows you to choose from which parameter field in the C3D file to read the save HTR file save motion file 5 2 3 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 EVaRT 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
266. ton controls the use of the universal acti vation level in the options form When it is turned on the activations 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 parameters form in the Muscle Editor it merely sets the activations for plotting purposes only to reset activations in the parameters form to their defaults see reset activa tions in Section 2 7 2 Command Menu When act over ride is turned off the muscles individual activations as listed in the parameters form will be used This toggle but ton is particularly useful when you have loaded a motion file which contains muscle activations 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 However 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 individu ally changing each muscle s activation in the Muscle Edi tor There is no way to override just a subset of the muscle activations The current setting of act override has no effect if you are plotting data from plot data files or col umns of data from motion files This toggle button gives you control over th
267. two or more points on the scapula can be con strained to remain in contact with the ribcage which is represented as an ellipsoid Once this constraint is acti vated when you change the value of one of the general ized coordinates in the shoulder SIMM will adjust the values of the other generalized coordinates 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 associ ated 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 reference frame of their associated segment and follow the movement of that segment Constraint objects can take the form of planes spheres cylinders or ellip soids Chapter 2 Tools 103 2 13 Constraint Editor 2 13 1 104 Chapter 2 Tools Figure 2 17 Sample Constraint The constraint object is an ellip soid fixed to the ribcage There are two constraint points both fixed to the posterior edge of the scapula 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 cur rent model has no constraint objects in it then the Const
268. ub menus 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 dis played 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 indi vidual 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 Chapter 2 Tools 37 2 5 Plot Maker 38 motion curve Chapter 2 Tools 2 5 7 plot title plot computed muscle properties over a smaller range you should edit these form fields before generating your plot curves 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 an
269. ues 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 meaning ful 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 interactively within SIMM Chapter 2 Tools 97 2 11 Deform Editor 98 Chapter 2 Tools 2 11 6 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 joint s DOFs and kinematic functions are not deformed 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
270. ut 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 five buffers is displayed Selecting one will restore the camera view to the one saved in that buffer See the save camera com mand for directions on saving a camera view This command saves the current camera view of the model to one of five buffers When you select this com mand a pop up menu of the five view buffers is displayed Selecting one will save the current model view to that buffer See the restore camera command for directions on how to restore the camera once you have saved it This command restores the gencoords to their default val ues If there are closed loops in the model and the inverse kinematics solver is on SIMM will try to satisfy the loop constraints and close all the loops in the model If the IK solver needed to change gencoord default values in order save gc values gt muscles gt start gt 2 4 Model Viewer to close the loops a window will pop up with some options for handling this new default configuration This command saves the current gencoord values as their default values Once they are saved you can restore the model to this configuration at any time using
271. w _size gravity solver_accuracy solver_max_iterations 3 3 Joint Files lengths and translations in your model Force units specifies the units of muscle force length_units m force units N This parameter lets you specify 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 lets you specify the size of the model win dow when the model is first loaded into SIMM The num bers following the keyword are the width and height respectively window size 400 600 This parameter specifies the direction of the gravity vec tor 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 two parameters you can specify to control the 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 specified maximum number of itera tions has been reached The accuracy value corresponds to the sum of the squares of the er
272. w to use these parameters 2 14 1 model gt help 2 14 2 segment gt restore segment drawmode Sa save segment Sal Sa 2 14 Segment Editor 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 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 all 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 combina tion with the save all button to help you undo changes made while editing segments This command lets you change 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 polygons no shading outlined white polygons with highlighted edges
273. wer 24 2 4 3 generalized coordinates Chapter 2 Tools name shot images that include a 3D model with one or more 2D plots superimposed Note that this technique is dependent on the organization of your computer s video memory and may not work on all systems 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 is not clamped any values outside its range will be displayed 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 general ized coordinate Thus you can also position the model at a specific time step in a motion sequence by selecting the motion variable field and entering a value The gencoord command can be used to toggle the visibil ity 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
274. 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 Chapter 2 Tools 93 2 11 Deform Editor 94 Figure 2 14 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 Chapter 2 Tools 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 understanding of how multiple deforms behave In Figure 2 14 above the larger box in 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 Anteversi

SIMM User`s Guide - Stanford University

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