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NMSBuilder User`s Manual v.1.0

1. In the options there is the possibility of real time being able to act on the time scale or to select the number of frames for second to display The user can also select the loop playback to see video nonstop Application Settings E General Creal time O Appieation E Storage speed NG 4 O Application Layout frames em L User Interface Preferences step 0 00200401 O Interaction Manager loop playback O Interface language O Measure Unk 3 aa E Network Connection ative view playback Carinae in cubrange 5 5 Menu WINDOW and HELP Window When the user opens many views he she can use the standard command of Windows OS for order the windows Cascade It allows to order all windows at minimise dimensions in cascade Tile Horizontally It sorts all open view windows in the work area in horizontally order of opening Tile Vertically It sorts all open view windows in the work area in vertically order of opening Arrange Icons If the windows are minimized this command orders the windows down in the work area Next It activates the next view window in opening order Previous It activates the previous view window in opening order Help About It opens a dialog window with the version information 46
2. 4 4 Interaction and Interface Elements MAF framework supports the interaction within MAF applications The features provided by this library include User re configurable list of input and output devices to be used for interacting with the application Assignment of available devices for different actions to be performed inside the application Dynamic reconfiguration of the device assignment on the basis of the current application state running operation or application logic state UO semantic abstraction layer represented by interactors objects Many off the shelf interactors for 2D and up to 6D interaction with 3D objects support for haptic interaction by means of the OpenHaptic extension library fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 4 5 Integration with OpenSim APIs and specialised components In order to integrate the OpenSim APIs into the NMSBuilder application a number of components were identified to be developed as specialisation of MAF basic features VMEs Views and Operations The scheme below presents the integration approach for MAF and OpenSim NMSBuilder integration components e Simulation results Simulation Results Views OpenSim Model SimBos Engine Creation Editing Operations OpenSim compliant XML model Simulation input parameters C d Spanne Simulation Operations OpenSim Model VME C
3. It imports output file mot generated by Inverse Kinematics simulation in OpenSim The values of the generalized coordinates will be automatically stored as vtk data ASCII format in the corresponding joint frame in child having the same name of the generalized coordinate OpenSim Inverse Dynamics simulation results 19 fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system It imports output file sto generated by Inverse Dynamics simulation in OpenSim The values of the joint moments will be automatically stored as vtk data ASCII format in the corresponding VME joint frame in child having the same name of the generalized coordinate 5 1 2 Exporters All geometric format exporters STL INP MTR the VTK exporter and the Ansys Input File exporter expose the apply absolute matrix option This option let the user export the VME applying the current absolute pose matrix that describes the position of the VME with respect to the global reference system to the original data contained in the dataset Images Raw It stores a VMEVolume in raw binary format both as single binary file or stack of binary images Images BMP It stores a VMEVolume in a set of bmp files Files can be saved in RGB or Grayscale format It is also possible to set an offset different from zero for the first bmp file Progressive numeration is used for the other image files Geometries ST
4. or press down the scroll wheel to translate pan e The right mouse button to zoom in out If a Laptop is used please see in the computer manual on how to simulate the central button of the mouse from keyboard There is a basic structure for any MAF application it comprehends a well defined GUI environment composed by a main Working Area a lateral Control Bar showing the VME hierarchical structure a Log Bar for the system messages and the main menu Menu Bar with at least five items e Menu FILE this item contains all the commands related to input output operations in the application skeleton the basic features are open save new commands to respectively load store or initialise a new msf MAF Storage Format session file 10 fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system e Edit this item contains the commands to cut copy paste delete any VME from the tree There are also the undo redo commands The Find VME operation allows searching a VME by name in the data tree e Menu VIEW this item contains the list of the available views To add a new view simply select Add View and select the desired view It is also possible to select which of the other bars Control Bar Log Bar Tool Bar and Time Bar have to appear in the principal window e Menu OPERATIONS this item contains a list of available operations within the application to perform an operat
5. API commands Schematic representation of the components involved in the MAF OpenSim integration In black the components specialised from MAF and in red the communication flow In particular on the left side of the image the general components of the MAF framework described in the previous sections are presented while on the right side the components of OpenSim involved in the integration are listed In the central part of the scheme we represented the specialised components that have been developed during the NMS Physiome project to achieve the integration They consist in anew VME type which represents a general OpenSim model C commands of the API to be used as a template for the construction on the patient specific OpenSim model and simulation three specialised operations to edit the template model define the simulation to be run and compile the C commands of the API to generate the OpenSim model specialised views for the post processing and visualisation of the simulation results The red arrows represent the flow of information among the modules In summary NMSBuilder provides a model template which can be edited to include the patient specific information provided by the data in the NMSBuilder data tree The model is composed by commands from the OpenSim API in C When completed a specialised operation run the model by calling a compiler which generates the osim model file to be then opened into the Op
6. The list of VMEs selected as meter mid points appears in the window below It is possible to add remove or modify the VMEs sequence using the Add Remove Up and Down buttons respectively The visualisation of the meter is similar to that of the distance meter and changeable in the visual props tab derive muscle wrapper The Muscle Wrapper is a particular VME which takes as input the following VME s Muscle surface VME representing the muscle to be wrapped Wrappers wrapped action lines in the Rest Pose and the Current Pose Origin and Insertion areas single landmark or landmark cloud 34 im Zug NMSBuilder v 1 0 NMS PHYSIOME 3 User s Manual Personalised models of the neuromusculoskeletal system The operation gives as output a VME representing the deformed muscle surface based on the VME s defined in the rest and the current pose The deformation is governed by the difference between the output from wrappers in the rest and the current pose The information regarding the origin and insertion areas is used to compute the fibres direction In the Muscle Wrapper VME tab the user will find the following parameters I imported From Wtest2 msf S Rl imported from y3_wrapping msF vme output visual props vme Si Fast checks Muse rs Cl Generate fibers Muscle Surface Rectus Femaris Select Wrappers RP E RP_RS PRS te rectus
7. can be activated pressing with right mouse button in any view background and it provides some actions specific for the views e Rename view allows to assign a specific name to the current view e Normal size maximize allows to restore the size view to maximised or normal for compound views there is the command both for the view as a whole and for the selected sub panel 11 im KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system Save as image allows to save the content of the view in a standard image format bmp jpg tiff etc for compound views there is the command for the view as a whole or for the selected sub panel Export Scene VRML allows saving the content of the rendered view in VRML format e VME contextual menu it can be activated pressing with right mouse button on any VME displayed in any view and it adds to the previous actions some others specific for the VMEs Hide allows to remove from the display list the selected VME Delete allows to delete from the Data Tree the selected VME Move launches the Move operation on the selected VME Visual props it opens a GUI exposing the visual properties of the VME according to the selected View or sub panel e Tree contextual menu Save MSF layout saves the layout of the current views with their display list into the msf at the next opening of the msf it will be asked to the user if he
8. element 1 and element 2 of the selected VMEMesh ELEM EPTO1 0 26600E 04 0 52000E 02 In case the attributes are time varying they should be stored in different files for each time stamp having the same prefix to be declared and consecutive numbered suffix e g for three time stamps attributes file will be namefile001 namefile002 namefile003 Attributes are associated by default to the first consecutive time stamps 1 2 3 etc The association of attributes files to different time stamps can be optionally obtained from a time stamp file e g suppose a VME is made of 100 time stamps but attributes are given only for time stamps 1 30 and 60 the attributes file will be stored as namefileO01 namefile002 namefile003 but the time stamp file containing the numbers 1 30 60 should be specified to associate attributes stored in namefile001 to time stamp 1 those in namefile002 to time stamp 30 and those in namefile003 to time stamp 60 time reduce This operation allows the user to subsample the time stamps of a time varying VME It can be chosen the number of frames to be deleted VME Metadata It adds a new tag to the VME type can be numeric or string It is possible to use tab key for fast navigation of text entries editing and saving Example Create a tag named Vector3 corresponding to vector 1 5 25 Press Add A new attribute named New Tag will be added Rename New Tag to Vector3 Set molteplicity to 3 Set comp
9. has been further extended by an additional software layer called MafMedical MafMedical contains all MAF components that are specific to the biomedical application domain A generic MAFMedical application such as NMSBuilder is defined by choosing from the framework the necessary components and eventually specialising them It is also possible to develop ad hoc components that are necessary only to the application itself and plug additional 3rd parties libraries There are four types of components that form any MAF application Virtual Medical Entities VMEs which are the data objects Views that provide interactive visualisation of the VMEs Operations that create new VMEs or modify existing ones and the Interface Elements generic GUI components that define the user interface of the application Special Operations are the Importers that let you import and convert into VME almost any biomedical dataset and the Exporters that can convert the VME into files formatted according to the most common standards 4 1 VME It provides the data Representation Examples of VME are surfaces of muscle imported and segmented from DICOM images AVME represents a data entity VMEs are organised in a hierarchical tree VME Tree or data tree and they are all composed by a time varying dataset a time varying matrix that defines the pose http www openmaf org 3 http www vtk org fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Person
10. norm vis C edge vis 7 property material bone lut 7 x scalar vis In the Surface view it is possible to visualize the Landmark trajectories The user must set the interval that you wants visualise default 0 in the visual props of a single landmark Fie Edt View Operations Tools Window Heip 8x SEIL RER L PE AAG material A new material deploy it e J 1 56 ume 0168 PER free mem 2769 mb In the Surface view it is possible to visualise the Ground Reaction Force GRF The platforms and the vectors are visualized singularly In the visual props tab of a single vector the user can select the visualisation of the vector arrow the Centre Of Pressure COP and the Vectogram 28 findi Zur NMSBuilder v 10 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 5 3 Menu OPERATIONS An Operation can create a new VME modify an existing one by modifying its data and or its attributes The operations are grouped according to their aim e Create anew VME is created in the data tree i new for the operations that do not require another VME to create the new one ii derive for the operations that require another VME as input to create the new one e Modify the dataset and or the attributes of the VME are changed e Measure to perform measurements on the VME e Manage to perform operations related with external services The principal operat
11. she wants to load also the corresponding layout Hide show it is present if the VME can be displayed in the active view and it allows to hide or show the VME Show sub tree it is present if a view is opened and it allows to display in the current view all the VMEs of a sub tree Show same type it is present if the selected VME can be displayed in the active view and it allows to display in the current view all the VMEs of the same type of the selected one present into the data tree Hide sub tree it allows to remove from visualisation in the active view all the VMEs of the sub tree Hide same type it allows to remove from visualisation in the current view all the VMEs of the same type of the selected one Crypt applies encryption to the selected VME Enable crypt sub tree applies encryption to all VMEs of a sub tree Disable crypt sub tree removes encryption from all VMEs of a sub tree Sort children nodes allows to sort children nodes in alphabetical order Keep tree nodes sorted allows keeping the alphabetical sorting even when new VMEs are added to the data tree 5 1 Menu FILE This menu allows managing the input output of data to and from the application in different formats The NMSBuilder files are stored in the internal msf format Apart from the usual open save save as close and quit operation there are different importers and exporters for different data types Importers Exporters are grouped according to the t
12. user applies a filter to a surface the program alerts that a new VME Surface if you try to act on an imported surface will be created The user can use many type of filters and set the parameters for each one For example with the smooth filter it is possible to define the iterations number volume density With this operation the user can modify the density of a VME volume i e the scalar attribute e g Hounsfield Units in volumes derived from a CT scan The modification is applied over a volume of interest specified by a surface VOI surface The user is asked to choose a VME surface from the tree that defines the volume of interest and the scalar value with which the VOI will be filled deform surface The operation Deform surface deforms the surfaces accordingly to differences between two polylines and a chosen deformation method It takes as input a VME surface and two polylines The operation opens a pop up window where the GUI allows the user to e Automatically create a base curve to deform e Selecting from the three two curves the original curve and the deformed curve e Edit both the original and the deformed cure by adding moving deleting and other editing options on curve points e Sow Hide in the preview window curves and surfaces 39 Zuse NMSBuilder v 7 0 NMS PHYSIOME User s Manual e Selecting alternative deformation methods Blanco s method Modified Blanco s method and simple warping e Sav
13. L It stores a VMESurface in STL format both binary and ASCII Geometries INP Exporter operation for the INP format described in the importers section Geometries MTR It is exporting single landmark cloud in case input node has Landmark cloud type or all children of input node having Landmark cloud type in the other case MTR file that contains data for one or several landmarks is generated as result Other VTK It stores a VMESurface or a VMEVolume in vtk format Other Action Line It exports a txt file of the action line information The first rows of the txt file contain the name of the action line the second row the data headers Data contain the timestamps and the trajectories of all points that define the action line Other Meter It exports a txt file of the meter information The first row contains the timestamp while the other rows contain the information of the meters group selected for the export operation Each meter is characterised by a set of 9 rows where the first row contains the meter name and the other 8 rows are as follow one row named Origin followed by 3 rows containing the 20 fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system coordinates x y z of the meter starting point and a row named Insertion followed by other 3 rows containing the coordinates x y z of the meter ending point Motion Analysis Landmark It stor
14. NMS PHYSIOME Personalised models of the neuromusculoskeletal system NMSBuilder User s Manual v 1 0 be KE NMSBuilder v 10 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 1 Tu dee We ge 3 2 Hardware reouirements 4 3 Installation and software reguirerments ronciers dateen niron inamana 5 3 1 NMSBuild r installation essensen es eene e aee a e Eiee eegen 5 3 2 OpenSIM API Integration reguirements 5 3 3 Visual Studio 2008 GT 5 3 4 CMake eegene Sege 5 3 5 OPENSIME2 2 DEE 5 A MAF the NMSBuilder Core cccsssccccecessesesseaeeececeseeseeeaeeececeseeseeaeaeeesecsseeseaeaesesecsssesasaeaeeeeseessesenaaas 7 4 1 VME ics ee 7 4 2 WAG WS ee 8 4 3 Operations soceri esenee E E ete Moti Meson Ek cea es 8 4 4 Interaction and Interface Elements 8 4 5 Integration with OpenSim APIs and specialised components 9 5 NMSBuilderap plication cc cc2iecsscateececvecheeeacaceecces eigen gsccaeaced eege eege den 10 5 1 ON RTR 12 5 1 1 utile lege 13 5 1 2 Beleeg TEE 20 5 2 Menu NEW eege Ee dee 22 5 2 1 eL n ENEE AEN 22 5 2 2 DRR eelere gegen 23 5 2 3 Analog Gra TE 24 5 2 4 Eet E e EE 24 5 2 5 IEN 24 5 2 6 OrthOSliCE s Ssazcesese sock ias aeaaaee aE e a E NEE aia Ee aeea SEEE e E ARE EEEN 25 5 2 7 RE eege eech 26 5 2 8 le 26 5 2 9 Si later 26 5 3 Men OPERATIONS sscedsecccececssaecebdecscnes e E e e E a E EEEE 29 5 3 1 Create SUD GAUL srir E EE EEEE ERS 29 5 3 2 M
15. NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 5 2 3 Analog Graph The view called Analog Graph shows the scalar value of the analog signals i e EMG signals of the muscle electric activity The user can select one or more signals among those imported It is possible to visualise one or more signals in different windows In order to plot a signal this must be selected in the visual props tab and the Plot button must be used The signal name can be modified and visualized by flagging the button Legend and each signal can be assigned a specific Colour The user can also modify the axes range deselecting the Autofit plot checkbox and then defining into the text boxes the axes ranges X Title and Y Title text boxes allow assigning user defined label to the axes 5 2 4 Global Slice The Global Slice View shows a slice obtained from the intersection of one or more volumes with a user selectable coordinate plane In the View Settings it is possible to choose the orientation of the plane with respect to the coordinate system select the position of the plane in the chosen direction change the transparency with the opacity slider or the LUT of the selected volume An indication of the slicing plane position origin and director cosines is reported in the bottom left corner of the view 5 2 5 Isosurface In the View Isosurface a VMEVolume is displayed as a surface ext
16. TERIAL NUMBER 2 EX 18456 NUXY 0 33000 DENS 1 1476 Each element having a 1 in the second column of the file defining the list of elements will be assigned properties of material number 1 and so on Note additional rows defining more properties can be added e g MU 0 54000 to define a frictional coefficient Once a mesh has been imported the number of the material card as well as the material properties of each element can be visualised using the visual props panel or right clicking on the VME in the compound views by selecting enable scalar field mapping and browsing the desired field to be visualised among those available ControlBar x data tree view settings operation le type Ansys Text KA nodes file open elements file materials file optional open l ok J cancel Finite Element Ansys Input file This importer creates a VMEmesh directly from an Ansys ASCII input file The importer currently supports only the following entities nodes linear and quadratic solid elements 2D elements can be created as degenerated solid elements and material cards Finite Element Ansys CDB file This importer creates a VMEmesh directly from an Ansys ASCII archive cdb file which can be written directly by the Ansys program The importer currently supports only the following entities nodes linear and quadratic solid elements and material cards OpenSim Inverse Kinematics simulation results
17. View is a compound view made of two panels In the left panel the user can change using gizmos the position and the orientation of an arbitrary plane in the right panel the corresponding volume section is showed in a 2D parallel view 22 im Zug NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system The view properties can be changed from the View Settings panel where the user can change the slice visualised in two ways e Gizmo Interaction It is possible to translate or rotate the slice with three arrows for the translation or three rings for the rotations By selecting the desired gizmo and holding pressed the left button of mouse the gizmo moves and the plane is updated accordingly e Text Interaction The user can write the value in the corresponding text box The user can also change the LUT of the VMEVolume and with the reset button restore the initial plane position 5 2 2 DRR The DRR View is a special volume renderer window that displays a VMEVolume as the result of a digitally reconstructed radiography DRR algorithm while a VMESurface is rendered with a 3D representation In the visual props panel the DRR settings can be used to change the generated DRR e g colour or the level of the project with the gamma value The camera settings can be used to modify the position of the projection instead of using the mouse interaction 23 im Zug
18. Z direction the user can import a text file with the Z coordinates as in the Import Raw Volume Moreover the user can set the header size to be skipped in the import In the file offset field the user can set an offset for the first slice number e g 6 and in the file spc can set a spacing in the numbering of the images if different from unity If the information provided are compatible with the files a preview of the images appears in the window and the slices can be seen using the slice num slider Analogously to the DICOM importer the user should define a memory limit beyond which the raw images will be stored as a VMEVolumeLarge Finally a VMEVolume or a VMEVolumeLarge is created in the tree upon pressing the ok button Geometries STL It loads a Stereo Lithography File which contains a polygonal surface model A VMESurface is created in the data tree Geometries VTP 14 fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system It loads a 3D geometry in a vtp file format which contains a VTK XML based description of a polygonal surface model A VMESurface is created in the data tree Geometries INP INP_AF It imports geometries from INP files INP format is usually generated by AMIRA to describe geometries triangle meshes The INP format is the following 1 Each line starting with is a comment line the future description assumes that all comments
19. algorithm ControlBar data tree view settings operation smooth B Labels cortical 1000 923 1844 soft_tissue 100 209 197 ok cancel 5 3 2 Modify sub menu fuse register landmark cloud The operation Register Landmarks Cloud allows the user to register a source Landmarks Cloud onto a target Landmarks Cloud by the Single Value Decomposition SVD method This registration provides as output a new Landmark Cloud if the apply registration matrix to landmarks option is not selected generated from a rigid affine and similar transformation that applied to the source cloud best fits the landmarks coordinates with respect to the target ones The registration is performed by matching landmarks that have the same name in the two landmark clouds This implies that the two landmark clouds must have a sub set of landmarks with common names This operation is enabled only if the two landmark clouds are collapsed see Add Landmark to know how to explode collapse a cloud It is possible to make spatial registration with three different types of registration rigid similarity or affine with the reg type box Moreover it is possible to carry out registration for a single or more frames In the last case the user must flag the option multi time The follower surface button allows to select a VME surface that will get applied the same transformation of the registered cloud The weighted registration button allows to assig
20. alised and all other VMEs into the view are sliced in correspondence of the slicer The slicer can be moved using the standard Move operation 5 2 9 Surface The Surface View displays VMESurfaces and landmarks in a three dimensional perspective render window VMEVolumes are displayed only with their bounding box 26 im i VPHOP NMS PHYSIOME Personalised models of the neuromusculoskeletal system NMSBuilder v 1 0 User s Manual 1E Juge stew The control bar tabs for this view and for a VMESurface are Visual Props O O Display List This checkbox allows to speed up the rendering of VMESurface Scalar Vis The user can visualise with different colours possible scalar values associated to the VMESurface Norm Vis The user can visualise the normal to the cells on the VMESurface Edge Vis The user can visualise the surface free edges i e border of a hole The edge is visualised with a colour complementary to that of the surface Property This checkbox applies the Material properties to the VMESurface Material Opens a window for creating or modifying the visualisation properties of the VMESurface The user can choose among several pre defined materials that have different rendering characteristics or define a new one The user can specify the colour and intensity of the ambient diffuse and specular setting A preview is shown on the top of the window In addition the user can s
21. alised models of the neuromusculoskeletal system of the VME with respect to its parent in the VME tree and a set of metadata that provides all the textual attributes of the VME 4 2 Views They allow the data Examination There are various views that permit to analyse the Medical Data A View provides an interactive representation of the VME Tree For each view the system maintains a display list of the VMEs that must be rendered in that view and a Compatibility list that specifies which types of VME can be rendered in a single instance and which in multiple instances The user can control certain properties and the behaviours of the view through the View Settings tab in the upper part of Control Bar 4 3 Operations Operations create new VMEs or modify existing ones At any time the user selects a VME and then chooses one of the available Operations The Operation may accept only a particular type of VME e g the Resample Volume Operation accepts only VMEVolumes At any time it is possible to run only those operations that accept the currently selected VME Operations that need more than one input may request the additional VME to the user The user can control certain properties and the behaviours of the operation through the Control Bar Operations are modal when an operation is running it is not possible to run another operation and it is not possible to change the selected VME Operations support the Undo Redo feature
22. and the landmark coordinates at the given timestamp e Static each row contains only the landmark coordinates When the operation is launched the user is able to indicate if the file to be imported is tagged or not If the file is tagged each row contains the landmark name followed by its coordinates Motion Analysis Raw Motion Data An ASCII file containing a sequence of points either static or time varying can be imported as a landmark cloud In the file each row corresponds to a time frame In each row each point coordinates are defined by three consecutive numbers Dot delimits integers and decimals one or more blanks delimits one coordinate from another A dictionary may be optionally chosen Example of a raw motion data for two landmarks two time stamps Landmark1 has initial coordinates 0 0 0 and moves to 2 2 2 Landmark2 has initial coordinates 1 1 1 and moves to 4 4 4 Motion Analysis ASCII Analog X Y This importer loads an ASCII file with the analog signals The file must be formatted as follows VPH2_ANALOG t t1 t2 tn X xX1 x2 xm y11 y12 yin y21 y22 y2n vm yme2 ymn where the first line must be always present the second line contains the time bar the third line contains the x values and the matrix below contains the y values for the given t x according to the format above Motion Analysis ASCII Analog VWs This importer loads an ASCII file with the analog signals from
23. are skipped by the importer 2 The first line contains three numbers separated by spaces lt NumberOfVertices gt lt NumberOfTriangles gt 0 0 0 3 The following lt NumberOfVertices gt lines contain information about vertices lt VertexIndex gt lt XPosition gt lt YPosition gt lt ZPosition gt 4 The following lt NumberOfTriangles gt lines contain information about triangles lt Trianglelndex gt 0 tri lt VertexIndex1 gt lt VertexIndex2 gt lt VertexIndex3 gt Geometries MTR Files in MTR format are usually generated by FARO arm during measurements NMSBuilder is able to import groups containing landmark clouds from MTR files Format description is the following 1 First line contains names of the following columns usually it is looking like Index Xmm Ymm Zmm A deg B deg C deg 2 Each following line contains landmark index in cloud and 6 values recorded from FARO Currently only first coordinates are used they are specifying landmark position 3 Indexes in lines define grouping of points when index in current line is not greater than in previous one it means that new group begins Importer is generating a VME group containing Landmark clouds Point grouping into clouds is based on grouping present in the MTR file Other VTK It loads data stored in vtk format The type of VME created into the data tree depends on the information contained into the vtk file Other MSF It is possible to import in the cur
24. cle actuator The user can assign the values of the following muscle parameters through the VME Metadata facility maxlsometricForce optimalFiberLength tendonSlackLength creating the corresponding tags If not defined default values will be passed to the source code 10 Create Marker Set Create a block of cpp commands to create marker sets from the position of landmark clouds and the corresponding target body 11 Run Inverse Kinematics Simulation Launch an Inverse Kinematics simulation using the selected OpenSim model The user has to specify IK Task Ser and Marker external files and can edit the setup file Running the simulation the program calls the OpenSim executable to perform the simulation The results will be automatically visualized and stored as attributes of the corresponding RefSys defining the joint reference frame in Child 12 Run Inverse Dynamics Simulation Launch an Inverse Dynamics simulation using the selected OpenSim model The user has to specify External Loads and Coordinates external files and can edit the setup file Running the simulation the program calls the OpenSim executable to perform the simulation The results will be automatically visualized and stored as attributes of the corresponding RefSys defining the joint reference frame in Child 5 3 3 Measure sub menu 2D measure The 2D Measures tool lets the user to interactively take some measurements default units are mm for distances and
25. d after Installation the following directories structure will be created c CMake 2 8 bin c CMake 2 8 doc 3 5 OpenSim 2 2 1 Download OpenSim 2 2 1 win32 VC9P exe from https simtk org frs download php file_id 2700 Install it in C and leave the default option for the system path during the installation After the installation you should have the following directories structure c OpenSim2 2 1 bin findi KE NMSBuilder v 10 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system c OpenSim2 2 1 doc Beware c OpenSim2 2 1 bin should be the only OpenSim in your PATH In order to check how many OpenSim installations you have in your path open the DOS command prompt and write echo PATH There should be Se some stuff C OpenSim2 2 1 bin some more stuff only in your path fns i vPHoP NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 4 MAF the NMSBuilder Core The Multimod Application Framework MAF is an open source freely available framework for the rapid development of applications based on the Visualisation ToolKit and other specialised libraries It provides high level components that can be easily combined to develop a vertical application in different areas of scientific visualisation see figure below lhpBuilder Application MAF Medical 3rd parties libraries MAF
26. degrees for angles onto 2D representations of VMEs i e on the CT Slices of the RXCT View e Points the distance between two points e Lines the distance between two parallel lines e Angle by lines the angle between two independent lines e Angle by points the angle between two lines with a common point e Indicator creates an arrow with a label Any measurement can be stored in the msf file with a description VOI density The VOI Density operation takes as input a VMEVolume and a VMESurface The operation can compute the volume and the average volume density in the region defined by the surface Compute Inertial Tensor The operation allows calculating mass center of mass 3x3 inertial tensor in the local reference frame and the principal inertial tensor with respect to the principal inertial 44 fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system axes of a closed single surface or multi surface VME The user can assign a density to each surface through the VME Metadata facility creating a DENSITY tag The bodies are assumed to be homogenous To calculate the properties pick the single surface VME or the multi surface group VME and proceed with the operation The results will be stored as attributes of the corresponding VME and displayed in the VME Metadata attributes 5 3 4 Manage sub menu open with external program This operation let
27. e element e Columns from the second to the sixth indicate some properties that respectively define associated material element type associated set of constants element refsys section properties The last 4 columns contain the element properties according to the ANSYS standards Particularly the second column indicates the material cards contained in the materials file This file contains the list of materials in the following format 21 WEE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system MATERIAL NUMBER 1 EX 20932 NUXY 0 30000 DENS 1 2508 MATERIAL NUMBER 2 EX 18456 NUXY 0 33000 DENS 1 1476 Note additional rows defining more properties can be found e g MU 0 54000 defining the frictional coefficient 5 2 Menu VIEW Every VME can be analysed and managed through a combination of views and operations Many instances of the same view with different VMEs displayed and or different views can be opened at the same time according to the user s needs M NMSBuilder File Edit View Operations Tools Window Help CZ PEEL Eee e lun vente view OA op a oC vo Dk opcgz a DI crac rom Demo3 msf legisteredvol msf app stamp NMSBulder Lie 3 IBID free mem 2355 mb The views available in the current release of NMSBuilder are described further on 5 2 1 Arbitrary The Arbitrary
28. e the threshold grey level to define the iso density surface called contour value It is possible to navigate the volume to check the surface contour and to pick a new threshold value on the volume slice The volume slice can be removed from the visualisation slice checkbox or changed of position with the corresponding slice position slider The optimize option activated by default automatically applies a filter to 36 E if vPHOP NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system the surface before creating the VME in the data tree which deletes the closed surfaces internal to the extracted surface Extract Isosurface contur value 356 5 B l slice position 124 es J V optimize X sice reset camera ok Il cancel derive decompose time Decompose time is an operation which takes as input a time varying VME and gives as output a desired number of static VMEs following a user defined mode The Decompose Time panel shows the following options e Timestamps mode The user specifies a list of timestamps The operation creates a static VME freezing the input time varying VME at the specified time stamps e Interval mode The user specifies a time interval The operation creates a static VME freezing the input time varying VME for all frames within a specified time interval e Periodicity mode The user specifi
29. enSim user interface or launch the OpenSim simulation which calls directly the SimBody Engine The results can be then loaded back into NMSBuilder which will provide specialised visualisation tools https simtk org home opensim http www nms physiome eu im Zug NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 5 NMSBuilder application When launched the application interface looks like M_NMSBuilder Ek File Edit View Operations Tools Window Help ControlBar S data tree view settings operation Be root EI D imported 8 ALs_cal_cnBc1b02 DR Do Gene mz Ml WALKING SKELETON D movie E B FORCE PLATES o hop a D cnbe1 o hop a D opCH lt gt vme output visual props vme maf MEGroup name Demo 10 43 20 058 executed operation MSF on input data root 10 43 20 058 operation MSF generate imported from DemoFiga msf as output 10 44 03 775 executed operation Select on input data root 10 44 03 775 node selected imported from DemoFiga msf 10 44 15 572 executed operation Select on input data imported 10 44 15 572 node selected imported from Demo4_3 msf v 19 isetime o MID welcome free mem 2792 mb In all visualisation windows the user can interact with the objects with the mouse in this way e The left mouse button to rotate e The central mouse button
30. es a VMELandmarkCloud in ASCII file The output format is structured in blocks where the first row correspond to the time frame and the rows below contains the location of each landmark for the given time frame For each landmark it is given in sequence the label and the x y and z locations An example of the output format is reported here below Time 0 C7 0 0 0 0 RA 0 0 0 0 LS4 0 0 0 Time 1 C7 0 0 0 0 RA 0 0 0 0 LS4 0 0 0 Time 2 C7 0 0 0 0 RA 0 0 0 0 ae B i Finite Element Ansys Input File This exporter creates an ASCII input file inp that can be directly read by Ansys program The exporter can deal with the basic finite element entities supported by the NMSBuilder application nodes linear and quadratic solid elements and material cards usually containing Young s modulus density and Poisson s ratio values In the exported file elements are grouped according to either element type and material properties Finite Element Generic Mesh This exporter allows the creation of three separate files one containing the nodes coordinates one containing the elements description and the other containing the material cards The node file contains a matrix where e The first column indicates the node number e Columns from second to fourth define the x y z nodal coordinates The file defining the list of elements and the connectivity contains a matrix where e The first column indicates the ID of th
31. es a periodicity The operation creates a static VME freezing the input time varying VME at the periodicity indicated in the time bar derive AFRefsys This operation is designed to create anatomical reference systems for different segments following ISB recommendations Currently it is using some hardcoded landmarks names for calculating reference system for lower limb bones and PNT1 PNT2 PNT3 landmarks for generating reference system for arbitrary segment 6 DOF placement modification of final result is possible using vme tab for RefSys VME derive average landmark Operation is applicable to any landmark cloud It appends to the cloud a new landmark that has position positions in case of animated cloud averaged from positions of landmarks initially present into the cloud 37 im Zuse NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system derive extract label Extract label can be launched when a Volume or a Labeled Volume is selected It enables the user to identify portions of the volume that have a defined value or label and creates a VME Surface that includes these regions In the operation tab the user can define the value or label name to extract and select whether a smoothing has to be performed default setting off on the resulting surface In case the smooth checkbox is activated the user is allowed to modify the parameters of the surface smoothing
32. et a transparency level opacity and the wire frame representation The new material can be saved with a custom name in the material library to recover it when necessary LUT The user can modify the LookUpTable for displaying the scalars associated to the VMESurface LOD This is a multiscale option If activated it modifies the visualisation of a VME in relationship with its dimensions with respect to the camera position e g if a VME is zoomed in it becomes first transparent then it disappears while it is zoomed out below a certain dimensions the VME is substituted with a glyph 27 Doft fAveHOP NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system e View Settings This tab shows the properties of the View It is possible visualise the grid or the axes and modify their colours The user can create new camera positions The control bar tabs for this view and for a VMELandmarkCloud are a subset of those available for the VMESurface namely o Display List This checkbox allows to speed up the rendering of VMELandmarkCloud o Scalar Vis The user can visualise with different colours possible scalar values associated to the VMELandmarkCloud o Material Opens a window for creating or modifying the visualisation properties of the VMELandmarkCloud with the same options described above for VMESurface and shown below vme output visual props vme displaylist
33. femoris Remove Add New Wrappe Sp Select E DES RPRS HESS CPRS Select dd Fibers Options oi Select D Select Type pennate zl Wach Res 14 Thick 0 25 J Z Smooth fibers Smoothing Opti windowing I Steps 5 weu ei T EE free mem 2714 mb In the Muscle Wrapper VME tab the user will find the following parameters e Name to assign the VME name in the data tree e Operational Mode specify the mode that will be used for the wrapping o Simple the input muscle VME at the time O is deformed according to the differences between outputs from wrappers at the time O and outputs at the current time o Advanced the user needs to specify different wrappers they may not change in time for the rest and current pose e Use RS if checked the deformation algorithm will use the origin of Reference System VME specified for wrappers whenever it is available e Generate fibres if checked the outputs are muscle fibres instead of deformed muscle e Muscle Surface Selects the VME to be wrapped e Wrappers Shows the wrappers added in the next box e Add new wrappers Selects VME s with the wrapper o RP CP Rest Pose Current Pose o RP RS CP RS optional selects a VME that serves as a coordinate system for deformation e Fibres options defines the fibres settings 35 fns i vPHoP NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system o O selects the VME
34. fiable implicit surface The user can choose the form of the new surface sphere cone cylinder cube and plane and set the corresponding parameters For example if the user creates a sphere surface the parameters to set are radius and the number of triangles that are generated by the curvature resolution new add landmark With this operation the user creates a VMELandmark Cloud child of the VME selected when the operation is launched The user can either choose a dictionary to firstly select a landmark name using the load dictionary button then the list of available names appears in the upper side of the tab or can assign a name to each landmark writing in the landmark name text box The landmark is created either picking on the selected VME or directly writing the landmark coordinates in the Position text boxes An example of dictionary is the file called dictionary diclocated in the subfolder NMSBuilder Config Dictionary In this file the anatomical landmarks of the femur described in Kepple TM et al A three dimensional musculoskeletal database for the lower extremities J Biomech 1998 Jan 31 1 77 80 can be found Once created the landmark cloud the user can add other landmarks by performing the Add landmark operation having selected the landmark cloud VME To perform the last action the landmark cloud has to be exploded The user can change the cloud status using the Explode checkbox in the VME tab In the VME tab also the radi
35. force platforms and ElectroMyoGraphy EMG systems produced by means of Vicon Workstation employed in Human Movement Analysis Example of the header 4 rows in the ASCII file for Analog Data 17 Ka Zumuoe NMSBuilder v 1 0 NMS PHYSIOME 3 User s Manual Personalised models of the neuromusculoskeletal system ANALOG 2000 000000 Hz Sample Fx1 2 Fx3 4 Fy1 4 Fy2 3 Fz1 Fz2 Fz3 Fz4 Fx1 2 Fx3 4 Fy1 4 Fy2 3 F21 Fz2 Fz3 Fz4 CH1 CH2 CH3 CH4 Units N N N N N N N N N N N N N N N N mV mV mV mV Motion Analysis ASCII Forces Plates VWS This importer loads an ASCII file with the GRF Ground Reaction Force data produced by means of Vicon Workstation employed in Human Movement Analysis Motion Analysis ASCII Trajectories VWS This importer loads an ASCII file containing all landmarks trajectories i e the position of any marker for any single frame that composes the marker trajectory Particularly this file is produced by means of Vicon Workstation www vicon com employed in Human Movement Analysis Example of the header 4 rows in the ASCII file for landmark trajectories TRAJECTORIES 100 000000 Hz C7 RA LA L5 RPSIS RASIS LPSIS LASIS RGT RLE RME RTT RHF Field X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z Finite Element Generic mesh This importer allows the creation of a VMEmesh from an Ansys Text file The user selects two text files
36. given VME Volume on a regular grid The user can remove from the display both the gizmos for the bounding box dimensions definition and for the bounding box orientation using respectively the check box Show handle and show gizmo transform The dimensions of the bounding box can be also set inserting numerical values into the text boxes in the ROI selection part while in the ROI orientation part the user can first select from the combo box if he she wants to translate or rotate the bounding box Translations and rotations can be set also inserting numerical values into the Bounding Box Origin and Bounding box orientation text boxes The user can set the output volume spacing and it is also possible set the auto spacing of volume 40 im Bug NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system scale dataset move The scale transform lets the user to scale isotropic scaling an input VME This can be done using gizmos with the mouse by clicking on a rectangle of the reference system axis By keeping pressed the mouse button and moving the cursor the user can set the dimension along the chosen direction It is also possible to enter directly the values in the corresponding text boxes The user can save intermediate scaling configurations and restore them at need The Move Operation modifies the pose matrix of a given VME The user can apply a transform by direct i
37. ideoRam 256Bit Memory Bus Interface fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 3 Installation and software requirements 3 1 NMSBuilder installation Installation is automatically handled by NMSBuilder installer which is provided in a fat version all inclusive with necessary integrated libraries included the following information is provided in order to help trace installation issues 3 2 OpenSIM API Integration requirements In order to use the NMSBuilder OpenSim API integration features you need to have installed Visual Studio 2008 Express free of charge CMake 2 8 3 OpenSim 2 2 1 As previously said this should be handled by the installer itself but in case of problems you might read the next sections 3 3 Visual Studio 2008 Express Express edition is free of charge and can be downloaded from http www microsoft com visualstudio en us products 2008 editions express Download the visual C 2008 with SP1 version and install it in the default directory it should be Program Files under XP or Program Files x86 under Windows 7 Please DO NOT CHANGE Visual Studio 2008 Express DEFAULT INSTALL DIR 3 4 CMake 2 8 3 Download cmake 2 8 3 win32 x86 exe from http www cmake org files v2 8 cmake 2 8 3 win32 x86 exe Install it and when asked leave the default option do not add to system path Select C as installing directory an
38. ing both the original and the deformed curve apply trajectory The operation Apply Trajectories applies a trajectory to a static only VME by loading the instantaneous VME s poses from an external ASCII file The VME s trajectory written in the file describes the instantaneous pose of the VME s coordinate system with respect to the global reference system The trajectory input file must be formatted as a matrix nx7 where n is the number of time stamps and the 7 columns contains in sequence the timestamp and the pose parameters x y z alpha beta gamma e x y z displacement of the VME refsys with respect to the father refsys e alpha beta gamma the Euler angles sequence Euler213 that describe the orientation of the VME refsys with respect to the father refsys surface mirror The Mirror surface allows the user to mirror a static surface along any of the coordinate axis crop volume The Crop Volume Operation lets the user to select a rectangular volume of interest from a given volume The user has two ways for selecting the region of interest The first is with interactive gizmos With the mouse the user select the face handle to move and generate a parallelepiped to crop The second way is to use the text boxes where the user writes the dimensions of the ROI Both the handles and the ROI can be taken off the visualisation by un checking the corresponding boxes volume resample The Resample Volume Operation resamples the
39. ion select your input if any and select the desired Operation in Operations menu if an operation cannot be run with the selected VME as input the operation name appears in grey e How To Customize NMSBuilder Menu Tools it defines a list of available settings for any MAF application The Control Bar is formed by three sub windows e Data Tree shows the loaded VMEs with the relationship degree and for the selected VME three other tabs in the bottom part of the Control bar e VME output shows the un modifiable attributes of the VME related to the VME data structure e Visual props shows the rendering properties of selected VME according to the active view e VME shows the modifiable attributes of selected VME such as the name the encryption etc Any VME is represented by colour and icon Blue the correspondent VME is loaded in memory and can be used Pink the VME has not been already loaded in memory Grey the VME could not be displayed in the active view mA MB apc The display check box near the VME icon can be a square or a circle If it is a circle the view is mutually exclusive for that type of VME which means that only one VME of that type can be display in the selected view e View Settings shows the settings of selected view e Operation shows the setting of operation in progress The user has available also some contextual menus there are three types of contextual menu e View contextual menu it
40. ion line The Pivot set method e Wrap it defines the method used to compute the meter curved path It can be set through a popup window as manual automated or IOR_automated O O Manual additional inputs intermediate points are chosen from a list of the VMEs in the tree The outputs are the sum distance of all point to point segments and the current locations of all VMEs composing the meter Automated the additional input to define the meter path is a Parametric Surface to be used as wrapping surface Outputs are the length of the meter curved path and the current locations of the two tangent points used to compute the overall distance To predict wrapping it is necessary that assumed the origin as a light source the insertion point lies in the parametric surface shadow IOR outomoted the additional input to define the meter path is a Parametric Surface to be used as wrapping surface Outputs are the length of the meter curved path and the current locations of the two tangent points used to compute the overall distance This method allows the action line to wrap around the parametric surface for up to 270 depending on the orientation of the coordinate system of the parametric surface e Reverse direction checkbox this option is active if the selected wrap method is automated It switches the meter path from a side to the other of the parametric surface e MidPoints this option is active if the selected wrap method is manual
41. ions are listed and described further on The Validate Tree operation allows the user to check after saving the integrity of the saved msf file The operation will check the binary data associated to each VME and will provide the found errors into the log area 5 3 1 Create sub menu new group The VMEGroup is a particular VME that defines a branch of the data tree By default it is created as child of the selected VME in the tree and is named group then the name can be changed in the VME tab new refsys Reference System It is possible to create an orthogonal reference system VMERefSys A new VMERefSys that inherits the parent s pose matrix is automatically created when clicking on the operation and checked as normal in the checkbox shown in the VME tab The user can subsequently reposition it by defining an origin clicking on select origin in the proper checkbox and selecting a VME Landmark from the data tree with the Origin button or both an origin and a XY plane clicking on select plane in the proper checkbox and choosing two other VME Landmarks Point 1 and Point 2 buttons from the data tree In addition within the VME tab the user can change the RefSys name and the visualisation scale 29 fns KE NMS PHYSIOME Personalised models of the neuromusculoskeletal system NMSBuilder v 1 0 User s Manual new parametric surface It creates a Parametric Surface VME This kind of VME is a run time modi
42. l be used as Parent Body Ball Joint Add a 3 DOF spherical joint between two Joint Reference Frames RefSys defined in the Parent and Child Body local frames Further information to specify is Parent and Child Bodies and the two RefSys identifying the joint Pin Joint Add a 1 DOF rotational joint between two Joint Reference Frames RefSys defined in the Parent and Child Body local frames Further information to specify is Parent and Child Bodies and the two RefSys identifying the joint The rotational axis has to be the common z axis blue axis 3 Create Marker Sets Add markers to bodies It is possible to select the source landmark cloud previously defined in the tree and the corresponding target body Marker positions and target bodies will be automatically passed to the source code 4 Add muscles Add muscle actuators Thelen2003Muscle class to the model It is possible to select a Wrapped Action Line defining each muscle actuator The user can assign the values of the following muscle parameters through the VME Metadata facility maxlsometricForce optimalFiberLength tendonSlackLength creating the corresponding tags If not defined default values will be assumed Actuator paths i e position of muscle points and target bodies and muscle parameters will be automatically passed to the source code derive slicer When the user wants to create a customized slice of a VMEVolume he she can use a Slicer When launched the o
43. n The range can be defined directly typing in the values in the 32 im KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system boxes or calculating the values from the initial meter length If the absolute mode is chosen then the initial length of the meter set by the user in the init field is an absolute value expressed in the same units of the meter length e g mm and the delta field sets the upper boundary of the range as a percentage of the initial length If the relative mode is chosen then the init field indicates the lengthening always in mm for example of the actual meter with respect to the initial one The percentage field works in the same way as explained above derive wrapped action line The Wrapped Action Line is a particular VME which takes as input two VMEs as starting and ending points and gives as output the length of the curved path plus the current position of a number of intermediate via points when present If the user moves a VME the meter updates itself automatically The two groups of methods currently implemented are the Geodesic method and the Pivot set method see the image below Fle Eat View Drogen Took Window Hap SEA gga L DE AXA z 707 tme 0460 FACOS free mem 2753 mb The Wrapped Action Line VME tab exposes the following parameters and sub panels Name to assign the VME name in the data tree Geodesic me
44. n weights to the landmarks to be used in calculating the registration fuse reparent to 38 im KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system The VME absolute position in a MAF application is given by the concatenation of the VMEs pose matrices in a given branch of a data tree If a VME is moved from a branch to another one in the hierarchy its absolute position can change With the Reparent Operation a user can move a VME from a branch to another one without changing its absolute pose When launched the operation opens a window to select the VME to be reparented to fuse register surfaces The operation Register Surface allows the user to register a source surface or landmark cloud onto a target surface or landmark cloud The operation uses the ICP Iterative Closest Point technique for surface registration The registration operation output is a new VME generated from an affine transformation that if applied to the source VME makes the points of the source fit the target ones If the source or target is a landmark cloud this operation is enabled only if the two landmark clouds are collapsed The user can set the iteration number of the algorithm in conv step inside the operation tab filter surface The Filter Surface operation takes as input a VME Surface and applies to it a combination of vtk surface filters smooth decimation etc When the
45. nds to define rigid bodies from multi surface VME with their attributes previously defined in the tree Geometric and inertial properties mass center of mass and 3x3 inertial tensor of each body will be automatically passed to the source code 4 Create Geometry Create a block of cpp commands to define vtp geometry from single surface VME with their attributes previously defined in the tree The vtp file will be automatically created in the working directory 5 Create Free Joint with ground Create a block of cpp commands to define a free joint 6 DOF between any selectable Child Body and the Ground 6 Create Pin Joint Create a block of cpp commands to define a 1 DOF rotational joint between two Joint Reference Frames RefSys defined in the Parent and Child Body local frames 7 Create Ball Joint Create a block of cpp commands to define a 3 DOF spherical joint between two Joint Reference Frames RefSys defined in the Parent and Child Body local frames 8 Create Muscle Multi Point Create a block of cpp commands to define a muscle actuator Thelen2003Muscle class from its path i e the position of muscle points and the target bodies 9 Create Muscle from Meter 43 im KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system Create a block of cpp commands to define a muscle actuator Thelen2003Muscle class from a Wrapped Action Line defining each mus
46. nteraction through mouse by interaction through gizmos or by editing the desired values in edit boxes Steps for the translations and rotations can be set in the step parameters section Constrains can be defined for the transformation if the gizmos are used to perform the operation An auxiliary reference system can be chosen with the choose button the reference system can be that of any VME into the data tree 41 im KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system VME dataset attributes adder This operation lets the user add static or time varying scalar fields to a VME currently implemented only for a VMEMesh so that it can be subsequently visualised The user should specify to which entity of the VME the attributes have to be associated currently the option is between cells and nodes of the unstructured grid of a Mesh The user can browse the file in which attributes are written It should be a txt file organised as a matrix The first row defines the name of the entity first column and of the scalar fields to be imported subsequent columns note that more than one field at a time can be imported while only one at a time can be then visualised The following rows indicate the entity ID first column and the scalar field value to be associated with it subsequent columns Example of a file from which a scalar field called EPTO1 is attributed to
47. odify sub menu 38 5 3 3 Measure sub menu siise teraiisen ririt s inete a EnaA EREE ETRE EENS rre RE ENERE EES RERaT 44 5 3 4 WEE E aa E E E E E E 45 5 4 How to customize NMSBuilder Menu Tools 45 5 5 Menu WINDOW and HELR 46 fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 1 Introduction NMSBuilder is the client application developed within the NMSPhysiome project to perform the musculoskeletal modelling pre processing This program executes on the user s PC and makes possible to import any kind of biomedical data interactively visualise them and fuse them into a coherent representation which can then use to build the model and simulation files for the OpenSim software The manual is divided into the following sections e Hardware requirements e Installation and software requirements e MAF the NMSBuilder Core e NMSBuilder application e Menu FILE e Menu VIEW e Menu OPERATIONS e How to customize NMSBuilder Menu Tools e Menu WINDOW and HELP https simtk org home opensim fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 2 Hardware requirements These are the minimal hardware requirements to run the NMSBuilder software e Microsoft Windows XP 2000 e 1GB of RAM e Intel Pentium 4 Processor e 500 MB of available hard disk space e High End 3D Graphics Card 512MB V
48. of VME resulting from the import before completing the process by clicking Finish dr ven importer data les Gctionsy open dere che Folder become D bowrtoad per Sea man 15 SA Images Raw Volume This importer can load a raw binary volume file A VMEVolume is created in the data tree The user should choose the file name browsing with the open button should specify the endianity the scalar type char short int float double the number of components e g 3 in a RGB Volume and specify if signed or not in the check box The user should also provide the dataset dimensions number of pixels and the spacing in mm pixel in all directions The import can be limited to a part of the whole defining a volume of interest VOI through specifying the x y and z pixel intervals to be considered VOI x VOI y VOI z fields If the spacing along Z is not uniform the user can specify a text file from which the Z coordinates are 13 fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system read browsing with z coord load button The Z coordinates file should be a text file whose format is the following the coordinates should be written in ascending order Z coordinates 109 1 107 8 106 5 105 2 103 9 Moreover the user can set the header size to be skipped in the import process The guess button makes the system to automatically e
49. of a point from a line line distance mode the user selects the point with the start button and defines the line with two VMEs selected through the end and 2nd point buttons The angle line angle mode is measured between the two lines that origin at the start point and are defined by the other two If the user moves one of the Meter origins the meter updates itself automatically If the plot profile checkbox is activated a histogram dialog is opened With the Probed button the user can selected a volume from the tree and see the histogram of the volume densities along the meter line File Edt View Operations Tools Window Hel 2x S DEER a a S PEN ae eae Histogram Dialog maf MEMeter name meter mode pant distance H n Jerdmark Start pluto Endt plot profile 7 est_volume Probed Ue 5 dom lt setme o FODD inns fraa mam 424 mh The meter can be visualized with a thin line or with a tube of user defined radius that can be capped or not visual props tab when a Surface view is active The visualisation of the meter can be set to change the meter colour depending on its actual length The user can define a range of length so that if the meter is shorter than the minimum length that is its initial length defined as follows then its colour is set to blue if it is longer than the maximum length calculated as follows its colour is set to red and it is changed from blue to red in the range in betwee
50. one for the nodes and other for the elements Eventually the user can select a file with the material properties The file defining the list of nodes should be a matrix where e The first column indicates the node number e Columns from second to fourth define the x y z nodal coordinates The file defining the list of elements and the connectivity should be a matrix where e The first column indicates the ID of the element e Columns from the second to the sixth indicate some properties that respectively define associated material element type associated set of constants element refsys section properties These columns are present because Ansys was taken at first instance as a reference program and this is how Ansys handles element properties At the moment these columns have to be included also when creating a mesh from scratch and not deriving it from Ansys However they represent a quite straightforward way to group elements in certain subsets The second column in particular can be very useful since it indicates which material the element is made of This becomes meaningful if the user specifies also a materials file when importing The optional file defining the list of materials should be formatted as follows 18 E i vPHoP NMSBuilder v 1 0 NMS PHYSIOME s i User s Manual Personalised models of the neuromusculoskeletal system MATERIAL NUMBER 1 EX 20932 NUXY 0 30000 DENS 1 2508 MA
51. onent 0 to 1 Set component 1 to 5 Set component 2 to 25 Press OK Now the attribute will be persisted for selected VME inside MSF tree You can press the VME button in the VME panel to see the attribute ASCII dump 42 fns KE NMS PHYSIOME Personalised models of the neuromusculoskeletal system NMSBuilder v 1 0 User s Manual Name Vector3 Type NUMERIC 1 Components 1 5 25 NumComp 3 OpenSim model It allows performing operations on a cpp source code of a previously created OpenSim model visible in the tree These features represent an alternative to create an OpenSim model from wizard see next section generating blocks of cpp commands for each model part that can be edited and copy pasted into the model source code The created cpp source codes will automatically show up in the text editor 1 Editing Tools Facilities for model generation Particularly the Generate Model option allows to compile the source code and generate the osim model which will automatically show up in the text editor and can be directly imported in OpenSim 2 Create Body from Surface Create a block of cpp commands to define rigid bodies from single surface VME with their attributes previously defined in the tree Geometric and inertial properties mass center of mass and 3x3 inertial tensor of each body will be automatically passed to the source code 3 Create Body from Surface Group Create a block of cpp comma
52. peration asks which VMEVolume has to be used for the slicing For changing later on the volume to be sectioned use the button Volume in VME tab derive freeze vme This operation allows the user to freeze a procedural VME by fixing once for all VME parameters such as position and displayed dimension of a reference system or the type and parameters of a parametric surface The type of VME created from the operation depends on the input VME i e a parametric surface gives as output a VME surface a meter a polyline etc derive distance meter The Distance Meter is a particular VME which takes as input two or three VMEs and gives as output the distance or the angles between them It is possible to measure a distance between two points between a point and a line or the angle between two lines 31 S une NMSBuilder v 1 0 NMS PHYSIOME Personalised models of the neuromusculoskeletal system User s Manual ControlBar x data tree view settings operation D root OW Cir CardiacCire 3 O Cir CardiacCire 3 Isosurfa la new landmark cloud Cla landmark2 o new_landmark OR meter sl gt vme output visual props vme _ maf MEMeter name meter mode point distance lv In the VME tab the user can find all the meter parameters definition To measure the distance between two VMEs the user selects line distance mode and the VMEs with the start and end buttons To measure a distance
53. racted with an iso density contour filter The user can interactively change the density threshold contour and the transparency threshold alpha in the visual props panel 24 S une NMSBuilder v 1 0 NMS PHYSIOME Personalised models of the neuromusculoskeletal system User s Manual 5 2 6 OrthoSlice The OrthoSlice View is a compound view made of four panels and three gizmos A perspective panel shows a volume intersected by the three orthogonal planes and the other three panels show a parallel view of each other slice As for the RXCT view a VMESurface is represented with a 3D rendering in the perspective panel and as contours in the other three Free mem Deg The user can modify the LookUpTable for displaying the VMEVolume When the Snap on checkbox is activated the slices are blocked to move on the slices of original CT dataset When this checkbox is deactivated the user can see slices created with the interpolation technique The border slider also activates when a surface is selected and it allows setting the thickness of the contour representing the surface into the slices panels 25 fin HOP Zus NMSBuilder v 710 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 5 2 7 RXCT The RXCT View is a compound view made of eight panels and six gizmos A gizmo is a particular handle that is instantiated by a View or an Operation to allow di
54. rect interaction with the mouse A VMEVolume is displayed in this View as a digitally reconstructed radiograph on the Anterior Posterior plane and on the Medial Lateral plane The other six panels show six CT slices that can be moved arbitrarily using the six gizmos If a VMESurface is displayed in the same window it will appear as a 3D surface in the projection panel and as the contour coming out from the section in the slices REECH In the RXCT view the View settings panel reports the properties of the view It is possible to choose the side to view for the medio lateral projection and to move all slices at the same time When the Snap on checkbox is activated the slices are forced to move on the slices of original CT dataset When this checkbox is deactivated the user can see the slices created with the interpolation technique The move all checkbox allows to move all slices together The adjust slices button activates when a VMESurface is selected and it allows to automatically set all the six slices within the surface bounding box The border slider also activates when a surface is selected and it allows to set the thickness of the contour representing the surface into the slices panels 5 2 8 Slicer The Slicer View is a compound view made of two panels the left one is a perspective one while the right one is a 2D parallel view When a VME slicer is displayed in this view in the right panel the section of the slicer is visu
55. rent VME tree a MSF session file previously created with NMSBuilder The data tree saved in the MSF file the user wants to load is imported in the current VME tree and grouped under a VME Group called imported from Other External data 15 fns i vpHoP NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system It loads a general file into the data tree such as doc xls etc When the msf is saved the imported file is stored in the folder of the msf file A VME is created which consists of a label that can be selected and opened with Open With External Program if an appropriate application is properly installed on the user s computer for the specified type of file In this case the standard application associated to the file extension is used to open the VME Motion Analysis C3D BTK It is able to read the following formats Vicon Workstation users refer to User Preferences in File menu e C3D data save format Integer and Real e C3D real data format PC DEC and MIPS e C3D analogue format Unsigned and Signed In the Control Barthe user can select the various parameters that wants to import into NMSBuilder It is possible to import e Trajectories it will create a landmark cloud containing all the landmark saved in the c3d file e Analogue Data as signals from force platforms and ElectroMyoGraphy systems e Force Plate Data as platform surface Centre Of Pre
56. representing the origin area single landmark or landmark cloud I selects the VME representing the insertion area single landmark or landmark cloud Type selects the geometry type of fibres through a popup window Num specifies the number of fibres to be created within the muscle volume Res specifies the resolution of the fibber o Thick specifies the thickness of the fibber e Smooth fibres if checked a smoothing process is applied on the generated fibres e Smoothing options specifies the number of smoothing iterations in terms of steps and weight O OO O vme output visual props vme medyMEMusclewrapper name gluteus minimus Operational Mode O Simple Advanced Fast Checks v use RS Generate fibers Muscle Surface Rectus Femoris Wrappers RP GR RP_RS CP_RS meter rectus femoris Add New Wrapper RP RS CPRS Fibers Options P E Select Type pennate w Num 50 Res 14 Thick 0 25 v Smooth fibers Smoothing Options Steps 5 Weight 4 Show template Show fitting Show fitting result It is possible to show checking the options the template the output is a set of fibres with a target cube the fitting process and the fitting result derive extract isosurface With the Extract Isosurface operation the user can extract a VMESurface from a given VMEVolume by selecting an iso density threshold The user can chang
57. s the user open a VME previously imported with import as External Data Menu FILE with the default application associated by the OS to the specific file extension To avoid problems with the Microsoft office versions it is advised to use OpenOffice to open excel or word files 5 4 How to customize NMSBuilder Menu Tools Options From this menu the user can modify the settings of the application It is possible to change the program language the measure unit and other The user can choose the layout of windows at program opening and can set the parameters for the remote storage The user can modify the interaction device like mouse haptic etc It is possible to customize the user interface preferences lt img src tools_menu jpg gt It is also possible to customize the Storage Settings The changes will take effect when the application restart The Network Connection options allow the user to set proxy name and port in case of access to the LHDL repository using a firewall proxy connection Application Settings O General D Apptcation Layout D User Interface Preferences Defaut settings for HTTP storage D Interaction Manager O Interface language O Measure Unt D Time be E Network Connection changes vl take effect when the akion restart It is also possible to customize the Time Bar 45 fns i vpHoP NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system
58. ssure COP Ground Reaction Force GRF and Moments to the platform centre data tree view settings operation Be root le cnBC1b02_TRAJECTORIES 3 cnBC1b02_ANALOG J C cnBc1b02_FORCE_PLATFORM_1 IO pc er Cl pc bon 3 a Ich cnBC1b02_FORCE_PLATFORM_2 CIO enbc1bo2_GRF_2 CIQ cnBC1b02_MOMENT_2 Example after the import of a common C3D file i e cnBC10b02 c3d data tree view settings operation Select Trajectories Analog Data Force Plate Data Dictionary Also a dictionary saved in the disk in an ASCII file can be specified to group the landmarks trajectories in different groups The format of the dictionary is 16 fns KE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system LAND1 CLOUD1 LAND2 CLOUD2 LANDn CLOUDn Where in the first column it is specified the landmark name and in the second column it is specified the cloud name If no dictionary is input the landmarks trajectories will be loaded in a single landmark cloud e g the group cnBC1b02_TRAJECTORIES in the second image above Motion Analysis Landmark The user is able to import a landmark cloud from an ASCII file The imported landmarks are stored in the data tree in a VMElandmark cloud with the same name of the imported file The imported file can represent a landmark cloud that is e Time varying the first row indicates the TimeStamp the following rows contain the landmark name
59. thod it compute an action line wrapping around one sphere or cylinder or two sphere cylinder parametric surfaces The method assumes that the action line lies on a plane and among all planes containing the action line origin and insertion the shortest one is chosen Pivot set method it allows the user to define the action line through ploy lines by defining a series of intermediate via points or by wrapping the action line around a parametric surface sphere cone cylinder cube plane or an ellipsoid This method assumes that the action line lies on the plane identified by the origin the insertion and the origin of the parametric surface the action line is wrapping on The two panels expose the following parameters The Geodesic method 33 im KE NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system NMSBuilder v 1 0 Wrap it defines the method used to compute the meter curved path It can be set through a popup window as single_sphere single_cylinder or sphere_cylinder Start it defines the landmark taken as starting point of the wrapping action line End it defines the landmark taken as ending point of the wrapping action line PathNum it defines the accuracy of the identification of the shortest geodesic path Higher it is more accurate and slower is the computation of the shortest path Sphere cylinder it defines the wrapping surface s the algorithm uses to wrap the act
60. us and the resolution of the landmarks may be changed new OpenSim Model The operation allows creating a cpp source code of an empty OpenSim model It is possible to edit this source code using the Editing Tools facilities new OpenSim Model from wizard The operation allows creating the cpp source code of an OpenSim model defined by the user through a step by step guided procedure from GUI The source code will be automatically updated at each procedure step and can be edited and compiled later using the Editing Tools facilities 1 Create Bodies from Surfaces Add rigid bodies to the model It is possible to select single surface or multi surface bodies with their attributes previously defined in the tree Geometric and inertial properties mass center of mass and 3x3 inertial tensor of each body will be automatically passed to the source code 2 Create Joints Add joints to the model Joint positions and orientations will be automatically passed to the source code The range of generalized coordinates will be set by default to 5 5 for 30 fns KE NMS PHYSIOME Personalised models of the neuromusculoskeletal system NMSBuilder v 1 0 User s Manual translational DOF and 2n 27 for rotational DOF Available types of joint selectable from the drop down menu are Free joint with ground Add a 6 DOF joint between a Parent Body and a Child Body Further information to specify is Child Body Ground wil
61. valuate the header size from the dataset dimensions inserted and the file size Analogously to the DICOM importer the user should define a memory limit beyond which the raw images will be stored as a VMEVolumeLarge Finally a VMEVolume or a VMEVolumeLarge is created in the tree upon pressing the ok button Images Images This importer can handle images in several standard imaging formats jpg png bmp A VMElImage is created in the data tree Images Raw Images This importer can load a stack of raw binary images and automatically creates a VMEVolume The raw images should be stored in a single directory and should be named with the same prefix and a progressive number e g Rawlmage_0006 raw Rawlmage_0007 raw etc The user should choose the name of single files in the folder through the prefix e g Rawilmage_ the pattern e g s 04d and the extension of the files e g raw The user should also specify if the images are 8bits 16 bits Little Endian 16 bits Big Endian 24 bits RGB and whether they are signed or not In case of 24 bits images also the presence of interleaving should be specified The user should then set the overall dimensions of the volume in pixels and the spacing along the axes in mm pixel Ticking on a checkbox a ROI can optionally be specified on the xy plane drawing and adjusting a red box with left mouse button whose real time dimensions are reported below If the spacing of the images is non uniform in the
62. ype of data they are dealing with In the current application version they are Images Geometries Other Motion Analysis and Finite Element 12 WEE NMSBuilder v 1 0 NMS PHYSIOME User s Manual Personalised models of the neuromusculoskeletal system 5 1 1 Importers Images DICOM This importer loads medical images stored in DICOM format and creates as output either a Volume Mesh or Image VME The user has first to select from a standard window for folder selection the directory in which the DICOM files are stored Once performed the folder selection a new wizard window appears in which the user can subsequently 1 see the images preview with some options to interact choose the number of study id if multiple ones are present in the folder and slide across the slices or the time stamps if a time varying dataset is being imported with appropriate sliders and perform windowing on the images 2 proceed to the optional Crop stage in which cropping is performed in the slices plane by drawing with the mouse the crop area and in the direction orthogonal to the slices by moving the z crop slider The in plane crop area can be changed by moving each side of the area and controlled over the different slices with the slice num slider 3 proceeding to the Build stage only the cropped area is kept The user can review the selected and cropped images and choose among Volume Mesh and Image type the type

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