User Manual
Contents
1. Figure 6 e Grey the VME could not be displayed in the active view 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 5 2 2 2 View Settings It shows the settings of the selected view Figure 7 Surface 2 De LL NA 724 724 amera parameters Focal pnt zi 88 627 25 019 748 8 position 199 36 1327 0 721 5 grid O grid norm 7 axes mo J grid pos 0 grid color se E t show axes back color Ea EJ link camera orientation fps gt Attach camera gt Text kit gt Light kit gt Animate kit Figure 7 5 2 2 3 Operation It shows the setting of the operation in progress 5 2 3 Contextual Menus 5 2 3 1 View contextual menu It can be activated pressing with right mouse button in any view background and it provides some actions specific for the views Figure 8 e Rename view allows to assign a specific name to the current view 11 Bonemat User Guide v 1 0 e Normal size maximize allows to restore the size view to maximised or normal in compound views this command is available for the view as a whole or for the selected sub panel e Save as image allows to save the content of the view in a standard image format bmp jpg tiff etc in compound views2. Absolute difference v ifference Absolute difference Relative abs a b mean a b cancel Figure 41 ControlBar Surface E E ES data tree view settings operation Mi root o OB Bonemati 183 Bonemat2 x Hi Bonemat2 Compare vme output visual props vme C wireframe C Element Edges Property material 3 new material Enable scalar Field mapping CELL EX v Figure 42 31 Bonemat User Guide v 1 0 output is a modified VME with a matrix pose applied to it please note the original dataset stored in vtk format is not changed just a pose matrix is applied to it whenever visualising or interacting with it The user interface Operation panel in the data tree lets the user apply the transformation either by inserting text or interacting with Gizmos Figure 43 If interacting with Gizmos the user has first Surface EIE data tree view settings Operation Choose Transform Translate w Apply upon mouse release Transform Entries Translate X 9 Translate Y 9 Translate Z 0 Rotate X ol Rotate Y 0 Rotate Z 0 Scale X 1 1 1 Scale Y Scale Z Figure 43 to select the transformation mode translate rotate scale Figure 44 The user Surface Surface data tree view settings operation Surface DER data tree view settings
3. mm I data tree view settings operation WW root E O volume an Save MSF Layout Hide Show Show same type Hide same type Crypt Sort children nodes Keep tree nodes sorted Figure 10 Importers Exporters are grouped according to the type of data they are dealing with In Bonemat the user can import medical images finite element meshes or previously stored vtk files Vtk files and finite element meshes can also be exported 6 1 1 Import Dicom Path File Import Images DICOM This importer loads medical images stored in DICOM format and creates as output either a Volume Mesh or Image VME most times a Volume VME The user has first to select from a standard window for folder selection the directory DICOM Importer DICOM Importer 648 J windowing 1764 n me JL windowna ies slice J Sort type uo JE ze gt Jl t92_ Ox slice OY Oz irorm spacing study series CT 0 512x512x193 Figure 11 Figure 12 in which the dicom files are stored Once performed the folder selection a new 14 Bonemat User Guide v 1 0 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 were present in the folder and slide across the slices with appropriate sliders and perform windowing on the images Figure 11 2 proceed to the opt
4. Figure 36 32 Bonemat User Guide v 1 0 erature review Clin Biomech 2008 Feb 23 2 135 46 Schileo E Taddei F Malandrino A Cristofolini L Viceconti M Subject specific finite element models can accurately predict strain levels in long bones J Biomech 2007 40 13 2982 9 The user can set a minimum value for the elastic modulus to be assigned optional All the material modelling parameters are shown in Figure 36 6 3 1 2 Algorithm parameters e HU integration vs E integration specifies whether performing the integration on the native HU field on each element and then calculate the E values called HU integration or vice versa E integration See the following references to choose among the averaging strategy Taddei F Schileo E Helgason B Cristofolini L Viceconti M The material mapping strategy influences the accuracy of C I based finite element models of bones An evaluation against experimental measurements Med Eng Phys 2007 Nov 29 9 973 9 Taddei F Pancanti A Viceconti M An improved method for the automatic mapping of computed tomography numbers onto finite element models Med Eng Phys 2004 Jan 26 1 61 9 Zannoni C MantovaniR Viceconti M Material properties assignment to finite element models of bone structures a new method Med EngPhys 1998 Dec 20 10 735 40 e Integration steps specifies how many integration points the application will set within each element e Gap value specifies the m
5. User Guide v 1 0 Bonemat User Guide v 1 0 Abstract This document is aimed to get the User able to use Bonemat software showing how to perform all basic operations and parameter setting To understand what is under the hood the User is redirected to the specialized literature describing philosophy and algorithms related to the Bonemat Bonemat User Guide v 1 0 Contents 1 Disclaimer 9 2 What is Bonemat 5 3 System Requirements 5 4 What is MAF 5 AlL VRE ARE 6 Mee AI bou w sx Gat Ee REE EE sak li ew ek D S3 EN BENY 6 A LIONE lt RBA EHR EERE SEES SEY SEE OHSS 7 5 GUI introduction 8 al Deer erat se sase t be sd W fk mom od AAA 8 5 2 GUI environment o 8 5 2 1 Menu DAE oe eee ai s n e died ioa AAA 9 Sad Pe ge aba be ra eee w d 95x59 91 9 Eo ew eee sen E di fE SE 9 Rug TIW socorro 9 ti 4e 308 908 36 9 d RS 9 0 4144 Operations won en pon w n RR OR ew 3 ORO EX 9 Mido cs so o won R X SY RE ee Wm 9 ls COL 22 99 55x39 3 925 WE OE nE 9 mal Data TGs corses 03 f an a ii x ee ew ELE 98 4 10 5 2 2 2 View Settings uuu s dot w wou ma W WE dok 11 mas UNES cs ded RR Bp dh o UE de dik ees 11 5 2 3 Contextual Menus 11 5 2 3 1 View contextual menu 11 5 2 3 2 VME contextual menu 12 0 2 8 9 Tree contextual menu 12 6 Key Commands 13 6 1 Data Importers and Exporters menu File 13
6. 611 MOTE DitOm is xo ko A a ri moi ninini 14 6 1 2 Import Raw Volume 15 Ds Import Raw IMages ox ROS ap w 9o 39 9 x xc an 3 16 DIS Import VIK 4 449 393 3994 dex 39 18 6 1 5 Import Generic Mesh 18 6 1 6 Import Ansys CDB File 19 6 1 7 Import Ansys Input File 20 6 1 8 Export Generic Mesh 20 6 1 9 Export Ansys CDB File 20 6 1 10 Export Ansys Input File 20 BLA Emon IR 4999390094 09 eee eee m 20 Bonemat User Guide v 1 0 6 2 6 3 Views Menu View 4 res 2 Dl Wiew AIDIEBEW coc nur eee ee od W tw A 21 022 View Orthoslice au lt ss eb Xo eom Ro B diy da EOS 24 Dono View RAC uuu uso um medo hm rra 26 6 24 View BIIN uoo ooo neo Ro nt Xo B ede KO 27 Operations menu Operations o 29 Dod I uuu w w w won X ad edef Ge ae 4 doi w Ni A5 29 6 3 1 1 Material modelling parameters 31 6 3 1 2 Algorithm parameters 33 6 3 1 3 Advanced configuration settings 34 Oe Bonemst DARIE wou w cs ce ee Rew eee ee y 34 6 3 3 Compare Mesh Data 36 EE IAN AE 37 Bonemat User Guide v 1 0 1 Disclaimer This is a brief manual of the Bonemat software It is intended to be a guide to the user and we hope it can help rather than confuse you Please be aware that the manual is still in a pr
7. Li ao Z 2 9 15 5 424 windowing f 1806 472 J _ windowina J 100 386 windowna J 243 424 J windowing J 1806 Fi 26 Figure 27 29 Bonemat User Guide v 1 0 6 2 9 View RX CT The RXCT View is a compound view made of eight 2D panels two planar pro jections in the XZ and YZ planes and six slices in the XY plane whose Z quotes are identified in the two planar projections by six gizmos Figure 27 The RX CT View supports the visualisation of e VMEvolume one at a time displayed in the projection panels as a digitally reconstructed radiograph usually resembling anatomical planes projections e g Anterior Posterior and Medial Lateral and sliced along the Z direction in the slice panels VMEvolume visual properties visual prop panel acces sible through contextual menu the user can change or define the LUT of the volume scalars and its opacity in the visualisation the z quote can also be changed manually Figure 28 Figure 28 e VMEmesh even more than one simultaneously as a 3D rendering in the projection panels and as sliced contours in the slice panels VMEmesh Visual properties visual prop panel accessible through contextual menu the user can define checkboxes whether to have a wireframe visualisation to show or hide element edges to show or not the visual properties colour opacity etc to visualise the scalars associated to the mesh e g el
8. even more than one simultaneously with a 3D rendering in the left volumetric view panel and the sliced contour in the right slice view panel e VMEmesh Visual properties visual prop panel accessible through contextual menu the user can define checkboxes whether to have a wireframe visual isation to show or hide element edges to show or not the visual properties 21 Bonemat User Guide v 1 0 Surface a ES OrthoSlice ze J 5 0 0 0 0 india 1806 Figure 19 DEAR lt Orthoslice Figure 20 22 Bonemat User Guide v 1 0 Figure 21 colour opacity etc to visualise the scalars associated to the mesh e g elas tic modulus and if so with which LUT i e look up table i e contour scale Figure 22 material e wireframe Flat A material 3 new material Enable scalar field mapping Enable scalar field mapping Ine CELL EX Figure 22 The view properties can be changed from the view settings panel Figure 23 i The user can change the position and orientation of the visualised slice through Gizmo or Text interaction 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 Text Interaction The user can write the value in the corre
9. which lists how many elements share the same elastic modulus for all the sampled elastic moduli in the model In the graphical interface the selected VMEmesh is taken as primary input Then the user has to specify the secondary input VMEvolume If a unique VMEvolume is 29 Bonemat User Guide v 1 0 OrthoSlice data tree view settings operation Mi root OW volume OU mesh x H1 Mesh Bonemat LutEditor Presets LUT FESTIS inumber of entries 1 256 256 mapped value range 383 105 21076 lt il gt select user LUT v a Lyme C wireframe El 7 Element Edges Property material o wireframe flat Enable scalar field mapping CELL Ex vi shade in rgba space shade in hsva space red 0 hue 0 green 0 sat 0 blue 0 val 0 alpha 0 color prev ok cancel apply 907 windowing 1806 Figure 33 Choose Volume Surface BE data tree view settings operation B3 root E m 99 volume 1 f li 5 volume 2 l x H3 Mesh All gt wmeouput visual pros ame v wireframe Thickness 1 g9 Element E jge You Y Property material e wireframe Flat C Enable scalar Field mapping POINT id iit Figure 34 30 Bonemat User Guide v 1 0 present in the whole MSF file that VMEvolume is automatically taken as secondary input otherwise the user can select a VMEvolume
10. 0 3 A F Taddei A Pancanti and M Viceconti An improved method for the auto matic mapping of computed tomography numbers onto finite element models Medical Engineering and Physics 26 Jan 2004 F Taddei E Schileo Helgason B L Cristofolini and Viceconti M The mate rial mapping strategy influences the accuracy of ct based finite element models of bones An evaluation against experimental measurements Medical Engineering and Physics 29 973 9 Nov 2007 C Zannoni R Mantovani and M Viceconti Material properties assignment to finite element models of bone structures a new method Medical Engineering and Physics 20 735 40 Dec 1998 40
11. it is not possible to change the selected VME The user can control the behaviour of the operation through the Control Bar Operations support the Undo Redo feature 5 GUI introduction When launched the application interface looks like Figure 3 SEE Bonemat File Edit View Operations Tools Window Help Bs oo EA O ControlBar data tree view settings operation M root vme output visual props vme 18 31 54 382 welcome Figure 3 5 1 User Interaction In all visualisation windows the mouse interaction with the available objects happens as follows e left mouse button to rotate e central mouse button or press down the scroll wheel to translate pan e right mouse button to zoom in out If a laptop is used please look up in the manual for how to simulate from keyboard the central button of the mouse 5 2 GUI environment There is a basic structure for any MAF application it consists of a GUI environment composed by Bonemat User Guide v 1 0 e Menu Bar e Main Working Area e Lateral Control Bar showing the VME hierarchical structure e Log Bar for the system messages Contextual menus upon clicking right mouse button are also available for Views VMEs and for the VME tree 5 2 1 Menu Bar 0 2 1 1 File This item contains all the commands related to input output op erations in the application skeleton the basic features are open save new commands to respec
12. operation Choose Transform Choose Transform Rotate vi Scale MM Y Apply upon mouse release Apply upon mouse release Transform Entries Transform Entries 417 17 pa 625 695 Rotate X 9 Rotate X Rotate Y 40 4786 Rotate Z a n SceX 1 Scale Y Scale Z 1 Rotate Z Scale X Scale Y Scale Z 1 4967 1117 66 0 Rotate Y 0 1 1 1 1 ScdeZ 0 Choose Ref sys Choose Ref sys Choose Ref sys VME local centroid vi YME local centroid v vme local centroid vi Ref sys Ref sys Ref sys Change Ref sys Origin Ref sys Origin Ref sys Origin X 401 075 x asss X 88 8538 Y 0 76343 YIZZ903 Y 22 9035 PITA Z 74675 Z 746 75 ok cancel ok cancel Figure 44 can activate the Apply upon mouse release option Figure 45 that allows him to visualize the transformation only after the mouse release and not interactively following mouse movement The pose parameters shown in the text are interactively updated when moving Gizmos The pose parameters and the Gizmos can be shown in the following reference systems Figure 46 e Absolute i e the global reference system e VME base ref sys i e the local reference system of the selected VME at the beginning of the operation so that the VME base reference system is fixed 38 Bonemat Us
13. or the ASCII file Figure 18 data tree view settings Operation volume wv Ek File file type binarv absolute matrix Force UNSIGNED SHORT scalar output Figure 18 6 2 Views Menu View Every VME can be visualised 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 users needs Views can be single or composed by different sub views visualisation panels Figure 19 Each visualisation panel views can be i perspective i e visualising a VME in space through a camera that can be rototranslated or zoomed or ii slice i e slicing a VME through a defined plane Figure 19 Special interaction objects Gizmos i e particular handles instantiated by a View or an Operation to allow direct interaction with the mouse are present in the slice views to facilitate the definition and the fine tuning of the view settings Figure 20 6 2 1 View Arbitrary The Arbitrary 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 Figure 21 The Arbitrary View supports the visualisation of e VMEvolume one at a time Windowing for the volume scalar is available It applies to both view panels e VMEmesh
14. this command is available for the view as a whole or for the selected sub panel e Export Scene VRML allows to save the content of the rendered view in VRML format Save as Image Export Scene VRML Figure 8 5 2 3 2 VME contextual menu It can be activated pressing with right mouse button on any VME displayed in any view provided it is also the one se lected in the VME tree Figure 9 It adds to the actions of the View contextual menu some other actions that are specific for the VMEs e Hide removes from the display list the selected VME e Delete deletes from the Data Tree the selected VME e Move launches the Move operation on the selected VME e Visual props opens a GUI exposing the visual properties of the VME according to the selected View or in compound views the view sub panel 5 2 3 3 Tree contextual menu It can be activated by pressing with the right mouse button on any VME in the VME tree Figure 10 It provides some visualisation shortcuts e Save MSF layout saves the layout of the current views with their display list into the msf at the next opening of the msf the user will be asked if he she wants to load also the corresponding layout 12 Bonemat User Guide v 1 0 ControlBar Surface data tree view settings operation 93 root OA volume Hide x Bi Mesh Delete Move Ctrl T visual props Rename View Maximize Save as Image Export Scene VRML
15. vme output visual props vme type mafvMEOutputMesh cells 209777 Figure 9 e Hide show present if the VME can be displayed in the active view hides shows the selected VME e Show sub tree present if a view is opened displays in the current view all the VMEs of the sub tree related to the selected VME e Show same type it is present if the selected VME can be displayed in the active view It displays in the current view all the VMEs of the same type of the selected one e Hide sub tree removes from visualisation in the active view all the VMEs of the sub tree of the selected VME e Hide same type removes from visualisation in the current view all the VMEs of the same type of the selected one e Crypt applies encryption to the selected VME e Enable crypt sub tree applies encryption to all VMEs of a sub tree e Disable crypt sub tree removes encryption from all VMEs of a sub tree e Sort children nodes allows to sort children nodes in alphabetical order e Keep tree nodes sorted allows to keep the alphabetical sorting even when new VMEs are added to the data tree 6 Key Commands 6 1 Data Importers and Exporters menu File The Import and Export classes accessible through the menu File allows the user to import export data to and from the application in different formats When in use in the Bonemat application the files are stored in the internal msf format 13 Bonemat User Guide v 1 0
16. User Guide v 1 0 in that view The Views available in Bonemat are Arbitrary Orthoslice RX CT Surface Figure 1 The user can control several properties of the active View Bonemat File Edit YER Operations Tools Window Help SI Gor w ToolBar c 0 X Ba I a amp TimeBar wv LogBar w ControlBar Add view Arbitrary OrthoSlice Surface RACT Figure 1 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 can select VME and then choose one of the available Operations An Operation may accept only a particular type of VME as primary input e g the Bonemat operation accepts only VMEMesh At any time it is possible to run only those operations that accept the currently selected VME Figure 2 Operations that need more than Bonemat Surface E File Edit View Memes Tools Window Help Bonemat Ctrl B Bonemat Batch Compare Mesh Data M 6e E ro Transform Ctrl T F data tree view settings operation w B root A OA volume x H1 Mesh Figure 2 one input may request additional VMEs to the user e g the Bonemat operation requires as additional input a VMEVolume The Operations available in Bonemat are Bonemat Bonemat Batch Compare Mesh Data and Transform Bonemat User Guide v 1 0 Operations are modal when an operation is running it 1s not possible to run another operation and
17. astic modulus and if so with which LUT i e look up table i e contour scale quite the same than in other views Figure 22 The view properties can be changed from the view settings panel Figure 29 e side Left right changes the projection direction of the lateral projection 26 Bonemat User Guide v 1 0 e snap on grid the user can select whether to avoid interpolation between slices and perform slice cuts only at values of the original grid The user can change the layout of the panels in the view e move all by checking it the user moves all gizmos simultaneously e reset slices brings back all slices to their original positions Contro data tree view settings operation O Right Left C Snap on grid Move all nterpolation Figure 29 6 2 4 View Surface The Surface View is a three dimensional perspective render window Figure 30 The Surface View originally intended for the visualisation of VMESurface and VMELandmarkCloud which are not core component of the Bonemat application supports in Bonemat the visualisation of e VMEvolumes displayed only with their bounding box e VMEmesh VMEmesh visual properties visual props panel of the control bar below the VME tree or visual props in the contextual menu quite the same than in other views Figure 22 i e the user can define checkboxes whether to have a wireframe visualisation to show or hid
18. browsing the data tree Figure 34 The user has then to define some operation parameters related either to the material modelling relationships to be used and to the algorithm The specified parameters can be saved save configuration file command in a XML file which is by default stored in the parent directory The configuration file can be reloaded open configuration file command or updated save configuration file as com mand Figure 35 Please consider that the application itself is adimensional so datatree view settings operation Configuration File open configuration File save configuration File save configuration File as Figure 35 the user is responsible for setting coherent measurement units to the variables 6 3 1 1 Material modelling parameters e CT densitometric calibration pgor a bHU specifies CT densitometric calibration parameters usually obtained through a calibration phantom e optional Correction of the calibration pash a bpocr applies a linear correction rule if available to the CT densitometric calibration There is the possibility of specifying up to three different linear corrections on three differ ent density ranges See the following reference for details on the opportunity of using such a correction Schileo E Dall Ara E Taddei F Malandrino A Schotkamp T Baleani M Viceconti M An accurate estimation of bone den sity improves the accuracy of subject
19. convert the VME into files formatted according to the most common standards e Interface Elements generic GUI components that define the user interface of the application Each session of a MAF application can be saved and reloaded as a msf MAF Storage Format file which is an XML file describing each object properties and object relationships including links to a complementary folder in which the datasets relative to each object are stored in binary format 4 1 VMEs VMEs provide the data representation A VME represents a data entity There are many VME types in MAF that can be used to represent almost any biomedical image or signal The VME types Bonemat can directly handle are VMEVolume VMEMesh Other VME types can be imported through the Import vtk function and some of them can be visualised e g VMESurface in the View Surface but no interaction through Operations is foreseen for them in Bonemat VMEs are organised in a hierarchical tree VME Tree or data Tree and they are all composed by a dataset a matrix that defines the pose 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 Views allow data examination There are various views that permit to examine the VMEs A View provides an interactive representation of the VME Tree For each view the system maintains a display list of the VMEs that are currently rendered Bonemat
20. d and the extension of the files e g raw The user should also specify if the data stored in 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 ROI dimensions are shown un derneath If the spacing of the images is not uniform in the Z direction the user can import a text file with the Z coordinates just like in the Import Raw Volume Moreover the user can set the header size to be skipped in the import The user can set an offset for the first slice number file offset field and a spacing in the numbering of the images file spc field if different from unity If all the information provided are compatible with the actual files fed in the appli cation a preview of the images will appear in the window to be optionally scrolled through the slice num slider Finally VMEVolume is created in the tree upon pressing the ok button raw importer raw Folder browse D dataset file pref file patt s 04d file ext raw bits pixel 16 bits Big Endian signed dimensions x y z z is the number o
21. e element edges to show or not the visual properties colour opacity etc to visualise the scalars associated to the mesh e g elastic modulus and if so with which LUT i e look up table i e contour scale 6 The view properties can be changed from the view settings panel Figure 31 26 Bonemat User Guide v 1 0 Surface Figure 30 e camera parameters the user can control the camera with text entries rather than with the mouse if a predefined exact camera position has to be set e grid commands make it possible to visualise the grid or the axes and modify their colours e show axes shows or hides the reference system gizmo e back color lets the user set the background colour the other settings below are part of Surface View in MAF but are of little use in Bonemat Surface m JE data tree view settings operation re aoa Vaval IRIE A Ce Camera parameters focal pnt 89 702 21 533 746 81 position 405 04 1408 2 699 9 orientation grid grid norm Z axes wv grid pos 0 grid color Ea m show axes back color Es 3 link camera orientation fps gt Attach camera gt Text kit b Light kit P Animate kit Figure 31 28 Bonemat User Guide v 1 0 6 3 Operations menu Operations 6 3 1 Bonemat This Operation is the core of the appl
22. eliminary and rudimentary shape It may not be complete or updated and we cannot ensure all the information in it is 100 correct Bonemat is not intended for commercial nor for clinical use You use it at your own risk and you are responsible for the interpretation of any results Being a research tool under continuous development Bonemat may not work exactly as documented and sometimes it may not work at all loop crash etc Please report to us if you find any bugs developers bonemat org or would like to suggest improvements info bonemat org 2 What is Bonemat Bonemat is developed by Istituto Ortopedico Rizzoli in Bologna Italy as a tool for mapping on a Finite Element mesh bone elastic properties derived from Computed Tomography images Bonemat can import CT images and FE models interactively visualise them fuse them into a coherent representation and export the updated FE mesh once bone properties have been mapped Though developed for computa tional bone biomechanics it may be intended as a more general tool for numerical integration of entities from a regular to an unstructured grid Bonemat is developed using the Multimodal Application Framework MAF for short see below for a detailed introduction to MAF 3 System Requirements To use Bonemat you just need a PC running Microsoft Windows we are sorry but currently other oprative systems are not supported The minimum system requirements are e Operating Sys
23. er Guide v 1 0 data tree view settings operation E Choose Transform Apply upon mouse release Figure 45 Choose Ref sys VME base ref sys VME local centroid Relative Relative centroid Arbitrar cancel Figure 46 and the user can control at each instant the transformation entity on the text entries e VME local centroid i e a reference system centered at the centroid of the selected VME the user can modify the coordinates of the reference system origin to control the transform entity e Relative i e a reference system specified by the user among the VMEs present in the data tree e Relative centroid i e a reference system centered at the centroid of a VME specified by the user among the ones present in the data tree e Arbitrary i e an arbitrary reference system that the user can define from the global reference system by modifying the coordinates of the reference system origin References 11 B Helgason E Perilli E Schileo F Taddei S Brynjolfsson and Viceconti M Mathematical relationships between bone density and mechanical properties a literature review Clinical Biomechanics 23 135 46 Feb 2008 2 E Schileo F Taddei A Malandrino L Cristofolini and M Viceconti Subject specific finite element models can accurately predict strain levels in long bones Journal of Biomechanics 40 2982 9 2007 39 Bonemat User Guide v 1
24. erties and nodal connectivity and optionally iii an array of material properties All fixed rules for the sintaxis of the files are the same as for the Importer 6 1 9 Export Ansys CDB File Path File Export gt Finite Element gt Ansys CDB File This exporter creates an ASCII file that can be read by Ansys as an Ansys archive file cdb The exporter can deal with the basic finite element entities supported by the Bonemat 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 into Ansys components according to either element type and material properties 6 1 10 Export Ansys Input File Path File Export Finite Element gt 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 Bonemat 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 into ANSYS components according to either element type and material properties 6 1 11 Export VTK Path File gt Export Other gt VTK Each VME can be exported as its vtk representation The user can choose whether 20 Bonemat User Guide v 1 0 to export the binary
25. f slices 512 si2 Ji define ROI spacing in mm pixel x v z z coordinates File header size File offset File spc cancel use lookup table Figure 15 17 Bonemat User Guide v 1 0 6 1 4 Import VTK Path File Import gt Other gt vtk The VTK importer loads data stored in vtk format The type of VME created into the data tree depends on the information contained into the vtk file 6 1 5 Import Generic Mesh Path File Import gt Finite Element gt Generic Mesh This importer allows the creation of a VMEmesh from two optionally three files i a matrix of nodes IDs and coordinates ii a matrix of element IDs element properties and nodal connectivity and optionally iii an array of material properties Figure 16 i ii ControlBar datatree view settings Operation type Ansys Text w nodes file open elements file materials file optional open cancel Figure 16 The file defining the list of nodes should be a matrix where the first column indicates the node number columns from second to fourth define the x y z nodal coordinates The file defining the list of elements should be a matrix where the first column indicates the ID of the element columns from the second to the sixth indicate element properties that respectively define material
26. ic moduli bins is not necessarily the gap value The Grouping Density options lets the user decide whether to assign to the bin the highest elastic modulus value contained in it or the mean one This option does not usually imply big or mechanically relevant differences in the output when e g analysing a whole bone ranging from 50 to 20000 MPa in Young s modulus but can be relevant in niche applications where small ranges are analysed or if few material bins are used e Poisson s ratio while waiting for the implementation of a consistent relation ship if any between density and Poisson s ratio a fixed value is set The default is 0 3 here the user can specify a different value e Output frequency file specifies the output filename and folder address de fault on the install directory of the file that lists how many elements share the same elastic modulus for all the sampled elastic moduli in the model All the advanced configuration settings are shown in Figure 38 w Advanced Configuration Density Output Use rhoQCT vi Grouping Density Mean wv Poisson s Ratio 0 3 Output Frequency file Freq file save Mesh Freq txt Figure 38 34 Bonemat User Guide v 1 0 6 3 2 Bonemat batch The Bonemat batch Operation allows a user to run a series of Bonemat operations on multiple volumes and multiple meshes using a single text file txt format Fig ure 39 The text file has to inc
27. ication The Bonemat operation allows the user to assign to each finite element of a bone mesh an average material property derived from the Hounsfield Unit HU of the tissue in that region as reported in the CT dataset thus generating an inhomogeneous FE model based on the density information contained in the CT The most common and here implemented pro cedure to relate CT data to bone mechanical properties is to extract a density value from the CT numbers densitometric calibration achieved by scanning a phantom and from this calculating an elastic modulus by applying a density elasticity rela tionship An additional correction to the densitometric calibration parameters may be introduced since it has been shown that densitometric phantoms are not free of errors when mimicking bone characteristics The core of the Bonemat algorithm is the numerical integration that maps the voxel wise properties of the CT grid to element wise properties of a unstructured mesh grid The input data are a VMEvolume and a VMEmesh the mesh has to fit within the volume bounding box The operation is accessible when a VMEmesh is selected Figure 32 The output of the operation is an updated VMEmesh in which each Figure 32 element has been assigned an elastic modulus value on the basis of CT data The elements are grouped by their material card Figure 33 An additional output is given in terms of a so called frequency file
28. inimum gap between two subsequent material cards e g given a typical elastic modulus range in the order of 50 to 20000 MPa the user may want to avoid defining 19950 different materials but rather group them each e g 500 MPa resulting in maximum 40 material cards All the algorithm parameters are shown in Figure 37 6 3 1 3 Advanced configuration settings This small sub menu lets the user set some minor yet possibly interesting parameters e Density Output since a list of bone density values comes as output with the list of elastic moduli and different density measurements can be set in the ap plication the user can decide whether to list the density coming directly from 99 Bonemat User Guide v 1 0 Young s modulus E calculation E integration bul Integration steps Gap value 0 Figure 37 the densitometric calibration named Rho QCT default or that resulting from the optional correction to the densitometric calibration e Grouping Density by default elastic moduli bins are assigned by Bonemat starting from the highest modulus among each element and then grouping to that value all elements within the specified gap value Then the algorithm searches again for the highest value among the remaining elements and the game goes on until all elements are assigned an elastic modulus or the mini mum value specified above optional is reached This means that the distance from two consecutive elast
29. ional 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 Figure 12 3 proceed to the Build stage when only the cropped area is kept The user can review the selected and cropped images and choose among Volume default and Image the type of VME produced by the Import Operation before completing the process by clicking Finish Figure 13 DICOM Importer Figure 13 6 1 2 Import Raw Volume Path File Import gt Images Raw Volume This importer can load a raw binary volume file i e a stack of images already stored in a single file Figure 14 A VMEVolume is created in the data tree as a result The user needs to choose the file name browsing with the open button specify the endianity the scalar type char short int float double through which the images are represented the number of components for each pixel value e g 1 in a greyscale image 3 in a RGB 15 Bonemat User Guide v 1 0 Volume and to specify if data are signed or not check box The user has also to enter the dataset dimensions number of pixels and the spacing in mm pixel in all directions The import can be limited to a par
30. lude for each Bonemat operation the following Bonemat File Edit view MEN Tools Window Help Z El BAnanna atch Com Mesh Data ransrorm f data tree view settings operation vme output visual props vme 19 36 11 033 welcome Figure 39 information e path of the VMEmesh FE model cdb or inp or vtk file formats e path of the VMEvolume CT volume vtk file format path to the calibration file conf or xml file formats path for the output FE model FE model inp or cdb or vtk file formats Paths can be absolute for example the text file can be formatted as follows C NWindows mesh mesh cdb C NWindowsNvolumeNvolume vtk C NWindowsNcalibration filesNcalibration xml C Windows results batch inp Even relative paths can be used as in the following example mesh mesh cdb volume volume vtk calibration_files calibration xml results batch inp 30 Bonemat User Guide v 1 0 with the condition that the text file is in the same directory of the folders in which there are the VMEmesh the VMEvolume and the calibration file In the example above the output will be saved in a folder located in the same directory of the text file It is not necessary to specify the paths when the text file is in the same folder of the VMEmesh the VMEvolume and the calibration file The output will be automatically located in the same directory of the text file if its path is
31. nable scalar field mapping Figure 17 and browsing the desired field to be visualised among those available Surface SE vme output visual props vme C wireframe 1 C Element Edges v Property material 3 new material Enable scalar Field mapping CELL material CELL ANSYS ELEMENT REAL ELL Ex Figure 17 6 1 6 Import Ansys CDB File Path File Import gt Finite Element Ansys CDB File This importer creates a VMEmesh directly from an Ansys ASCII archive cdb 19 Bonemat User Guide v 1 0 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 6 1 7 Import Ansys Input File Path File Import gt Finite Element gt 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 associated material cards 6 1 8 Export Generic Mesh Path File gt Export gt Finite Element Generic Mesh This exported is symmetric to the Import Generic Mesh feature A VMEmesh is translated into two or three if materials are present files i a matrix of nodes IDs and coordinates ii a matrix of element IDs element prop
32. not specified Comments can be added to the text file by adding before them Please observe that a calibration file in xml format is recommended because it contains the advanced options explained in more detail in the Advanced configuration settings section of the Bonemat operation It is anytime possibile to update the configuration file in the Bonemat operation by saving it in xml format 6 3 3 Compare Mesh Data This Operation allows the user to compare the scalars associated to two meshes that share the same topology i e connectivity The Operation can be run when a VMEmesh primary input is activated Another VMEmesh secondary input has to be chosen by the user for comparison Figure 40 Element Edges property material 3 new material Enable scalar field mapping CELL Ex vi Figure 40 The user can choose in the Comparison mode menu of the Operation panel which kind of comparison to perform among difference absolute difference relative difference Figure 41 The output is a new VMEmesh whose scalars are the result of the comparison between the two input VMEmesh Figure 42 6 3 4 Transform This Operation allows the user to perform affine transformation roto translation and non uniform scaling on the VMEs The input is any VME in the data tree The 36 Bonemat User Guide v 1 0 data tree view settings operation Comparison Mode
33. number element type set of constants reference system section properties the following columns indicate the nodal connectivity The mid columns 2nd to 6th are present because Ansys was taken at first instance as a reference program and this is how Ansys handles the association of properties to elements when listing elements 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 18 Bonemat User Guide v 1 0 iii 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 MATERIAL NUMBER 1 EX 20932 NUXY 0 30000 DENS 1 2508 MATERIAL 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 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 e
34. rspective view panel and the sliced contour in the orthogonal slice panels VMEmesh Visual properties visual prop panel accessible through contex tual menu or visual props of the control bar below the VME tree the user can define checkboxes whether to have a wireframe visualisation to show or hide element edges to show or not the visual properties colour opacity etc to visualise the scalars associated to the mesh e g elastic modulus and if so with which LUT i e look up table i e contour scale quite the same than in other views Figure 22 24 Bonemat User Guide v 1 0 plume pipe gu lut opacity 1 X 100 Interpolation windowing windowing JL 1806 Figure 24 Figure 25 The view properties can be changed from the view settings panel Figure 26 i layout the user can change the layout of the panels in the view ii LUT the user can set or define the look up table to be assigned to the scalars of the VMEVolume currently visualised iii Snap on grid the user can select whether to avoid interpolation between slices and perform slice cuts only at values of the original grid x 54 RXCT x data tree view settings operation a ES IhpyieworthoSlice layout T m sd Snap on grid reset slices All Surface Bord 1 m v Interpolation
35. specific finite element models J Biomech 2008 41 11 2483 91 e density elasticity relationship EH a bpasn specifies the law relating bone density to bone elastic modulus usually taken from the many empirical density elasticity relationships available in the literature There is the possi bility of specifying up to three different power laws on three different density ranges so as to account for discontinuities e g one for cortical and one for trabecular bone given a threshold Density elasticity relationships have been extensively reported and discussed in the literature see e g the following ref erences for a critical review and a FE application respectively Helgason B Perilli E Schileo E Taddei F Brynjlfsson Viceconti M Math ematical relationships between bone density and mechanical properties a lit ol Bonemat User Guide v 1 0 CT densitometric calibration RhaQcCT a b HU a 0 00393573 b 0 000791701 Correction of the calibration Rho4sh a b RhaQCT Apply calibration correction Single interval Single interval a 0 079 b 0 877 d Density elasticity relationship E a b Rhodsh c Minimum Elasticity Modulus 1e 006 Three intervals w 4 Three intervals Rhodsh1 RhoAshz 10 RhaAsh lt Rho4sh1 a b 14664 Cc 1 49 Rhoashi lt Rho sh lt RhoAshz a b 14664 211 49 Rho4sh gt RhoAsh2 ij a b 14664 C 1 432
36. sponding text box and restore the initial plane position with the reset button 29 Bonemat User Guide v 1 0 ii Reset button the user can reset the initial position of the slice ii LUT the user can set or define the look up table to be assigned to the scalars of the VMEVolume currently visualised Interpolation v Interpolation translation gizmo abs position Translate X 74 6731 translation gizmo abs position Translate Y 4 68009 4 68 rotation gizmo abs orientation Rotate X 90 0551 Rotate Y 0 Rotate Z 9 39436e 018 Translate Z 745 728 rotation gizmo abs orientation Figure 23 6 2 2 View 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 Figure 24 The Orthoslice View supports the visualisation of e VMEvolume one at a time Windowing for the volume scalar is available It applies to all view panels VME volume visual properties visual prop panel accessible through contextual menu the user can change or define the LUT of the volume scalars and its opacity in the visualisation the z quote can also be changed manually Figure 25 e VMEmesh even more than one simultaneously with a 3D rendering in the pe
37. t of the original volume defining a volume of interest VOI through x y and z pixel intervals VOI x VOI y VOI z fields If the spacing along the z spacing axis is not uniform the user can specify a text file from which the Z coordinates are read browsing with z coord load button The Z coordinates file should be a text file whose format is like the following the coordinates should be written in ascending order Z coordinates 109 1 107 8 104 0 Moreover the user can set the header size to be skipped in the import pro cess A guess header function is available throug the guess button Finally a VMEVolume is created in the tree upon pressing the ok button raw importer endian Little Endian M scalartype sport signed dimensions x y z voix fan voyo s vozo e spacing in mmjpixel x y z Ro H a z coords header size memory limit MB gt use lookup table Figure 14 6 1 3 Import Raw Images Path File Import gt Images gt Raw Images This importer can load a stack of raw binary images automatically creating a VMEVolume Figure 15 The raw images should be stored in a single directory 16 Bonemat User Guide v 1 0 and should be named with the same prefix and a progressive number e g Raw Image_0006 raw Rawlmage 0007 raw etc The user needs to specify the name of single files in the folder through the prefix e g Rawlmage the pattern e g Yo87004
38. tem Windows XP Windows Vista Windows 7 Windows 8 e Processor 1 0 GHz RAM 1GB 3 GB recommended Graphics Card Compatible with OpenGL 1 2 e Hard Disk 30MB 4 What is MAF The Open Multimod Application Framework openMAF is an open source freely available framework www openmaf org for the rapid development of applications Bonemat User Guide v 1 0 based on the Visualisation Toolkit www vtk org 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 OpenMAF 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 Bonemat 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 applica tion itself and to plug in additional 3rd parties libraries There are four types of components that form any MAF application e Virtual Medical Entities VMEs which are the data objects e Views that provide interactive visualisation of the VMEs e Operations that create new VMEs or modify existing ones special Operations are the Importers that let you import and convert into a VME almost any biomedical dataset and the Exporters that can
39. tively load store or initialise a new msf MAF Storage Format session file All importers exporters will be described in detail in the following 0 2 1 2 Edit This item contains the commands to cut copy paste delete any VME from the tree Undo redo commands are also available Find VME allows the user to search a VME by name in the data tree Each command has a keyboard shortcut displayed in the menu 5 2 1 3 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 should be visible in the global application window All views will be described in detail in the following 5 2 1 4 Operations This item contains a list of available operations within the application to perform an operation first select your input VME if any then select the desired Operation in Operations menu if an operation can not be run with the selected VME as input the operation name appears in grey All operations will be described in detail in the following 5 2 1 5 Tools Through the command options a list of available settings for any MAF application can be set It is possible to change the program language the measurement unit and other settings For example the user can choose the layout of windows at program opening and modify the interaction device e g mouse It is also possible to cus
40. tomize the user interface preferences The changes will take effect when the application restarts 5 2 2 Control Bar The Control Bar is formed by three sub windows Bonemat User Guide v 1 0 5 2 2 1 Data Tree It shows the loaded VMEs with their hierarchical struc ture For the selected VME three other tabs are active in the bottom part of the Control bar e ume output shows the un modifiable attributes of the VME related to the VME data structure Figure 4 data tree view settings operation Mi root OS volume x rz KE Surface E vme output visualprops vme type mafvMEOutputMesh cells 209777 Figure 4 e visual props shows the rendering properties of the selected VME according to the active view Figure 5 vme output visual props yme yi v wireframe Thickness 1 9 C Enable scalar field mapping POINT id NN 5 Figure 5 e ume shows the modifiable attributes of selected VME such as the name the encryption etc Figure 6 Any VME is represented by colour and icon e Blue the correspondent VME is loaded in memory and can be used e Pink the VME has not been already loaded in memory 10 Bonemat User Guide v 1 0 a Hox iag view settings operation mi Mi root an OS volume x H3 Mesh vme output visual props vme maf MEMesh name l Mesh not animated crypt
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