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1. File Edit RES Applications Analysis Tools Help Display Viewports Orientation Background te AutoCenter F E Wwidth le Magnifier al Width ial Level MO Menu items followed by an arrow gt indicate a second level menu is available under that title Second level menus can be pulled out onto the desktop in the same manner as the main menus from the menu bar Menu items followed by will prompt the user for further information sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 10 File ques aaa Open CNI File a Opens an existing CNI file Save XML File Saves the active CNI file in XML format and extension Save CNI As Saves the active CNI file with a new name drive or path Open CHI File Save XML File Save CNMI As Import Export Close Exit Import Image Data Imports image files with formats Plain Raw Explicit Raw Photoshop SDT Stimulate IMG Analyze AIR and BMP Geometries Imports geometry data in Visualization Toolkit VTK format Thayer School Mesh File format WPI Mesh File formats See appendix for details CNI File Export Exports Images in a variety of formats such as Raw or sequential slices Exports geometries node and element files etc in a variety of formats Close Closes all files currently opened Exit Qu
2. Thresholds wk IO Hich Ad a Falete Primary Comp Hattral o Iraga Manipalation sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 36 a 2 panel view and select one image set for each window as shown below This setting provides side by side image comparisons One might need to adjust the orientation such as axial view for each viewing pane Under Tools Slice Control move the slide bar of each image set until the same distinct regions of the brain can be identified in each volume set Preferably select a slice towards one end of the brain Ideally we want to have 3 locations identified on this slice For our example dataset we selected slice No 154 for the Rat Atlas and slice No 3 for Ana One Rat brain Slice numbers here are counted in original slice views Another adjustment might be to decrease the increment step between slices If the user toggles between two adjacent slices but the image seems to skip over the desired features the slice increment can be reduced Markers need to be created in both image sets Select Tools gt Marker Type in a new label for a group ex Atlas Markers and Add this group Select the Create button and identify the 3 locations on the Rat Atlas image set The 3 target points are M4 M5 and M6 as shown in the Figure The user
3. The drag bars on the Registration menus are available to manually alter the images Numerical values may be input as well for more accurate results sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 47 b Geometry Open File K Select the Open CNI file option from the File pull down menu O Geometry images Under the browsing window find and click on the eee e file to be opened Eilersinmesh cr Examples BrainMesh BrainMesh cni Click on H RegistrainMesh2 cn Open to load the file The blue bar at the bottom left i RegisBrainMesh cni of the program window indicates file opening progress The opened file will be displayed on the screen When working solely with a file containing geometry you have the option of changing the viewport to one single 3D window for better viewing In this viewport n 5 Wie Metano Filename BrainMesh cri el you may manually change the size of the program Places Files oftupe EE Cancel window by clicking and dragging a corner of the RA window The menu bar should be automatically displaying the options of the Image application If you would like to work pressi Ea in the Geometry application select Geometry from the View pull down menu Use the Display property tab to fia Jf manipulate the geometry and toggle the dif
4. either Rotate Spin or Pan and click the direction arrows to move the model The Measure Performance function 1s not operational at this time Note One of the options available is Backface Culling This is a VTK related function that enhance the visualization at times However at times it produces inconsistent results If the visualization appears somewhat unexplainable check the status of the Backface Culling flag Measure Performance sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI Za Applications There are three main applications currently available in CWBench These applications are Registration Mesh Generation and functional MRI Registration The Registration application can be used to modify the size shape and location of an E 4 image slice a set of slices and or geometry models so as to conform to other images or e Wee E geometry models The manual alterations work interactively ee A Matrix The Matrix tab displays the current 4x4 transformation matrix for the Active Matrix selected The transformation matrix entries can be changed manually via the 4x4 window However the primary mode is via the Manual tab options The Identity button purges the current 4x4 matrix and replaces it with the identity matrix The Invert button takes the current 4x4 matrix and provi
5. analyzed and tabulated relative to the regions identified by the user CWBench Prof John Sullivan Copyright 2004 WPI File Edit View Applications PRESE Tools Help Image Manip Histogram Domain Filters Operate Help Active Dataset Defol ume El Analysis This menu pull down will be expanded in future software updates It will provide direct access to analysis routines such as the fMRI t test module However at this time the menu selection is limited to a histogram function Histogram The user can select an image set for analysis The frequency of pixel intensity groupings is displayed Adjustments in the histogram distribution are available Shot np 1 Fie Edit view Applications Analysis lE Help Refresh Information Slice Control Marker Import Export Vem Setting Slice Control View Setting Annotation Annotation Active Dataset RAT bas ita Conversion Record Movie Conversion Record Movie Tools Marker Geometry based coordinate markers fiducial markers can be added by the user on 2D 3D view windows Markers are grouped in user specified lists A group or list must be active prior to any operations such as add delete select points etc Multiple groups or lists can be created sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 15 Operations on Markers First select
6. back ground settings in the Slice Control application File Edit view Applications Analysis Tools Fie Edt view Applications Analysis Tools Width Level sets which pixel values will have the most visible Images Images o range You can set these values manually or allow CWBench to eee TE m do it for you automatically by selecting the appropriate button Threshold Set visible thresholds at Low High ends Again you can set these values manually or allow CWBench to do it automatically by selecting the appropriate button Press Apply when you have finished setting the thresholds to impose these changes onto the slices Palette select the color scheme for the data Interpolation indicate whether to interpolate between voxels Active Volume b te fo Toggle this option On or Off meo Import Carm To import image datasets Select file s that you wish to import by browsing for the first image file CWBench will automatically detect the last slice in the same directory or you may specify otherwise in the input box Select the header tab to display modify header information for the images sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 22 The DICOM tab allows that specific type of medical image format data to be imported to CWBench Once the data is selected press Apply Ifthe images do app
7. data Display Import Other Help Image Data fea Under File hover cursor over Import and press Image Data on the menu appearing Properties leader DICOM adjacent to File menu This action will open up the Import tab under the Image application You may choose to open up to this tab manually by first choosing Image Data from the View menu if it is not already there and then clicking on the Import tab Next to First Image File click the Browse button This will bring up a menu where you may select the file from your dgtive Volume computer which will be the first image you would like to import Properties example Examples BrainMesh Images BrainSag 001 When you press Open the program will automatically detect the remaining image data files in the current folder and put the number of the last image in the box labeled as such ge Headers Auto Manus The next few input boxes are automatically set for you as well You may change any information in the input boxes to your Image Uata Grayscale abel Map discretion Make the required selections for Image Headers automatically if available or manually and type of Image Data either as grayscale for label map You may give the files a name and or a description Press Apply to import the files cancel to abort sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Co
8. going to the Applications pull down menu and selecting Registration The Active Matrix is automatically detected to be the boundary that was loaded p You may use the Matrix Definition chart under sell rr the Matrix property tab to make adjustments to the boundary Press Apply to see the changes in the 3D viewport Be sure to move the cursor to a different input box after changing a value in the matrix so that the program will pick up the changes You may also want to use the manual registration option under the Manual property tab to translate rotate and scale the boundary geometry See Registration section of the reference manual for more details Press Next to access the Refine menu Under Refine you may select up to 5 levels of mesh refinement operations There are four different types of refinement AlongAllBdy refines along the entire surface boundary of the object The user should input the distance from the surface towards the center of the object that should be refined AlongUserBdy refines along file use the Browse button to from this surface boundary to the WithinClosedBdy refines all the Browse button BasedOnBdySize refines the mesh based on the size of the surface mesh given in the boundary file Distance towards the center of the object may be specified Press Next to continue to the Ouput menu Selecta file for the program to write the volume
9. marker operation and then use Ctrl Mouse Click for Operations Markers can be used to highlight regions of interest and they can be easily used for Marker registration More into detailed marker operations are explained in Lists atlas Applications gt fMRI Module Group tribute Evaluate Group Add Delete Slice Control The Slice Control tool Mark Op Off Create Select Delete displays the current settings of Md 6 04275 3 22875 0 3 da each 2D eraphics M5 Y 3 255 0 3 ME 0 00524986 0 76125 0 3 window The M7 0 00524986 4 80375 0 3 controls are color ME 000524986 1 70625 3 6 coded consistent MI 000524986 2 64875 3 6 t with the graphics MAO 4 704 2 12625 3 6 window color M11 A 746 2 02125 3 6 identifier These slice settings affect the clipping locations displayed in the geometry 4 mM Select All Select Hone Toggle visibility sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 16 application as well f CWBench Prof John Sullivan Copyright 2004 WPI Help File Edit View Applications Analysis MERE The FgSlice Opacity requires that it be turned on and that both Foreground and Slice Control Background images be active If these two conditions are met then sliding sa the control bar modifies the opacity of the foreground image set
10. 35 subject which will be mapped to the other volume image s the Atlas equilateral tetrahedron We demonstrate creating a triangle on one slice the base of the tetrahedron and a single center point on a distant slice the tip of the tetrahedron in the next section 4 Point Fiducial Registration Procedure a Import the images Usually some of the volume images will already be resident in CWBench If not one needs to import them File gt Import gt Image Data then select an image file such as the atlas from your file folder structure Repeat this process and import a subject data set For this example we imported a rat atlas CWBench CWBench20bc 83 bcode Atlas RAT Atlas RAT Atlas eci Ana One Rat brain sdt was already loaded previously from the fMRI Demo fMRI_ Test data folder It is assumed that the user has a minimum of two image sets in memory Under View gt Image Data if one pulls down the menu Active Volume there should be a Rat_ Atlas Ana_ One Rat brain perhaps other images and DefVolume for our example Set the GUI view to be ISEE 41 Wi APL Ta VES enc h T Mei H ua JE Ga Eto a 2004 File dt Yen a ei Todds Help Hide Panel Display Image Cote S Hele geometries z 5 EE Viewparts alla Srientafion Contri Dackground Contes Akozenker P HAHHAA A H EJE e Magnificr Bright Scalar Tye Short He tin a Mac
11. CWBench Release Version 2 0 December 2004 John M Sullivan Jr D E Director of Bioinformatics sullivan wpi edu James Q Zhang Ph D Research Assistant Professor zqy wpi edu Center for Comparative NeuroImaging CCNI Bioengineering Institute WPI 100 Institute Road Worcester MA CWBench CCNI http ccni wpi edu Copyright 2004 WPI File Edit View Applications Analysis Tools Help Slice Control Controls ONE Help FgSlice Opacity Fade a Slice Range ato Manual Tear off From fensa To fensa Pop pallet Table of Contents Val i Oh a a a E ia RT nn 4 NM lean 5 Genie starea Introduction 5 SRO RR I A 6 Notes for CWBench Version 2 0 X X installation for WINDOWS 3_ eee 6 Note for CWBench20 installation for LINUX ieri 7 POR 9 ebbi aa 9 Mb 10 AR ER N NT n n __ _ __ _ ro 11 A A A EAEE 11 A AA 11 A ERE n n n sees cee 11 Ippica 11 A PP dora sea coups ane teen E eae ea EE A E 11 Cleo 11 PP sows eet ne eee gasses ye snc te E E E E E sachs asubesieueiepeamuescacoeasee 11 Pill 12 ROLLS A e e nr i 12 Da A FA 12 LR TT n n 12 RCA ZA A 12 A 13 lb 13 Ss AS Sn E E AE PER N EAE SE E EE AE E 13 A RE 13 Ss SS EEE NE 13 AS eu EI I tee 14 PUM OC CM A IIA 14 AE A E TE OE A E ETE A N S E E E T 14 Pd 14 sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Instit
12. Endian Little Erdi Output Image File Browse Data Type Char Endian Little Endian Big Endian Output Choices Datatype Image Size Parameters Split By Time Split By Slice Endian Little Endian Big Endian The analyses are performed on all selected image volumes However it requires that each volume split By Both Exit Input File Range set has the same Row Column Slice count for anatomy volumes and the same Time count as Output File Range 128 127 well for the functional volumes Only a singe set cn of controls are applied to the entire project If the escale nit collected data vary in these parameters we sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 32 recommend users going to the Reslice tab within fMRI before doing analyses The reslice tool provides users the ability to specify the reference and subject data sets and MRI Module get the resliced subject which is consistent in numbers of rows columns slices and time steps Moreover by Reslice users can reload a resliced subject S S T R in reference space without applying transformation matrix T By default resliced subject has the same row column slice time step counts as reference But users can specify their own image size parameters by checking the box set new reslice parameter I
13. Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 20 View The View menu provides access to two main display operations the Image Data and Geometries Within these submenu selections one can import export image data and geometries clip move and rotate geometries for viewing convenience Hide Panel This View menu also provides the ability to change viewports orientation background or to have a Image Data magnifier window Geometries Viewports Orientation Background AutoCenter Magnifier sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 21 Images The Images application can be used to enhance as well as view image slices When the Image application is chosen the left side of the window displays the Images menu CWBench opens the Images application as default when the program starts The menu has five tabs at the top Display Import Export Other and Help Each tab has a sub menu specific to that function category The Help tab displays useful help information and is available for all the applications Display Active Volume displays which volume set will be modified via the parameters below The Active Volume display is independent of the images displayed in the graphic windows Those images are controlled by the Fg and Bg fore
14. There are three menus to be filled out before the volume mesh files can be generated Input Refine and Output The three buttons that are associated with each menu are located at the top under Settings The Next and Back buttons on each menu will also help you navigate between the menus Under Input select the boundary input file surface mesh using the Browse button or type the address of the file into the input box Use the default internal normalization factor 1 0 and maximum auto refinement limit 0 0 unless these values need to be changed The program is defaulted to select the Ignore Adjacent Elements and Ignore Same Material checkboxes CWBench will automatically detect the size of the bounding box around the mesh object To do so press the Load Bdy button at bottom of the menu and wait for the program to finish loading It will show the dx dy dz and the average boundary patch size values for the bounding box in the respective input fields Choose between either the cube or the deltahedral as the base units for building the block sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI DI At this point it is recommended that you make registration adjustments to the geometry of the surface mesh so that it can be seen clearly in the 3D viewport when the volume mesh is loaded onto the screen Do so by
15. Tutorial with Examples The following tutorial takes you step by step through creating an Image file a Geometry file and a Coupled file that includes both Image and Geometry data This tutorial focuses on getting the data into the CNI format To try out the various options immediately one can load a cni file within the examples folder Starting Up Double click on the CWBench desktop icon to start program A large default window opens displaying 5 black boxes for 2D images 1 green box for 3D geometry and a menu bar on the left hand side for application functions Hover the mouse arrow over most buttons or options to see a brief explanation of the function From here you may alter the layout of the program display x D E a Hi Under the View pull down menu let mouse hover over Viewports A list of display layouts will appear to the right of the menu Click on the layout that you would like to use The program displays the chosen layout Next you might choose to either open an already created cni file which may contain images geometry or both or you can import specific pieces of data to create your own cni file In the following tutorial the viewport with 4 image display windows is generally used It is the checked viewport in the screenshot on the left This option works within a x 1024x768 window If the 4 image display immediately below this selected one is chosen the File Edt View Ape displa
16. Wi PL EWB anchi M5 Wern jua ang Co IOpyriento 2004 Analysis Tools Help A Include whol a ni The user selects the fmr Tree Selection Settings file recently created within saetar imeto creste Recall Save the Merge Registration tab e Cleat Selections von The Run tab color codes each anatomy image TONI anatomy Functional Display according to the VOIs I Display List identified for a fully segmented mask of each slice A series of color coded or segmented files is created They are stored in the same folder as the anatomy files with a map appended to each original anatomy filename Vertice 63826 Tnangles 126612 sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 41 C T Test Analysis The user selects the desired anatomy files A good start location is the CNI file created in the Merge Registration tab The user must manually ADD each functional file to the next window region Frequently one has multiple functional files for the same anatomy Simply add all the functional files and duplicate the anatomy file name such that there 1s a one to one correspondence between anatomy image and functional image If the user performed the ROI VOI component the segmented or masked file entries can default to those linked to the anatomy files In that mode no selections are r
17. a few moments Solution Your hardware acceleration may be on a setting that is too high to run CWBench First close the CWBench you may need to use the task manager to end the task if the program 1s not responding Go to My Computer then Control Panel and Display Under the Settings tab go into the Advanced options Then open the Troubleshooting tab and decrease the Hardware Acceleration down to about 2 notches or less Now apply the changes and open CWBench again You may need to restart the computer if CWBench s initial freeze caused other vital system programs to malfunction Problem When I try to toggle the visibility of image slices on or off so that I can see them displayed inside the geometry model I do not see these slices being displayed Solution First try decreasing the opacity of the geometry model When the model is entirely opaque you cannot see anything inside of it Otherwise Backface Culling may be ON for that particular model Turn it off by right clicking on the model s name under Geometry s display tab If you still do not see slices being displayed you should exit CWBench from the File Menu and restart the program Save any work that 1s important before exiting Problem When I am importing a geometry the detected color of the model on the import menu is not the same as the resulting color of the model after being imported Solution This may be a bug in the software You may go back to the import tab and
18. a volume mesh file in the specified location Auto Load Loads the generated volume mesh file onto the CWBench 3D display view You may choose to output the different material surfaces in which case you should select the Output material surfaces checkbox and type in the list of materials in the input box ex 1 2 3 Press Apply a dialog box will appear to confirm your choice to generate the volume mesh Caution Large mesh generation processes may utilize a substantial portion of the computer s resources and certain tasks may cause the computer to freeze or crash Please make sure that you have made the correct selections on the SpMesh menus before continuing MMC This application is temporarily located under fMRI Module Currently the input file type of Multiple Material Marching Cubes algorithm M3C is sdt spr Other input file formats are scheduled To run M3C you need to select the input sdt spr file specify if you want the output geometry linearized or centered If it 1s a threshold image specify the low and high thresholds as well The default x y spacing and z spacing is 1 which means the cube size is 1 in a certain slice sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 29 and the vertical spacing is the spacing between two adjacent image slices If z spacing is 2 it means the cubes are mar
19. anual is available About CWBench Software logo and release information Help tabs are located within numerous applications and tool ag Menus These Help tabs are active Help E Ed and provide a brief description of the Using Remote Help components specific to that control panel menu Additional help exists on some functions when the mouse cursor hovers over a button or input Internet Phone field A small pop up window F appears next to the cursor with a brief explanation of the feature Request Online Support Provide Online Support About CwBench sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 9 Menu Bar Many functions and features can be accessed and changed using the pull down menus located at the top of the program window These menus can be torn off the menu bar and placed on the desktop by a single left click on the dashed line under each menu The selected menu stays on the desktop and Hide Panel functions as a separate window until closed by clicking on the X in the upper right hand corner of the menu window It can also be minimized maximized and moved like any other program window One can still use the pull down menus in the main program window independent of the tear menu on the desktop f CNI Workbench for Prof John Sullivan
20. bles one to manipulate advanced slice controls over each viewport Each little colored bar represents a different viewport on the window whose color matches it One can select a particular colored set save Record Movie and specify its zoom and slice increment or save the current slice as an image file View Setting sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 17 Opens the View Setting panel wherein one can adjust the pixel size of the 3D mode f CWBench Prof John Sullivan C window only Other view settings are available from this menu selection as well File Edit View Applications Analysis Tools Movie Recordings Annotation The user can create movie files sequences of still images numbered sequentially The start frame number directory and file type are user specified Several 3 party utilities can append the file sequence into an AVI or MOV file QuickTime Pro does a wonderful job of the task Annotation Various methods of annotation may be toggled on or off by depressing the panel buttons When toggled on they will display as appropriate in the viewing Amnotation windows When toggled off they are hidden from view CWBench Prof John Sullivan File Edit View Applications Analysis Tools Visibility Giu Help In CWBench the Help menu at the top of the
21. ching through every two slices When the parameters are set correctly specify the output mesh file name and hit Proceed The file extension vtk is automatically appended to the filename if an extension is absent MRI Module fMRI DATA PREPARATION AND ANALYSIS PRIMER Introduction Complete functional magnetic resonance imaging fMRI is a complicated and iterative analysis This primer walks one through the steps in sequence These steps are not convoluted We present multiple paths to obtain the final result An Examples fMRI Demo data folder in the CWBench main directory contains a variety of data that can be used to run this module Typical Scenarios A group of N subjects is tested for responses to a given stimulus The researcher wants to know several items What were the responses of each individual subject Which areas of the brain were activated Did the stimulation affect different regions of the brain at different times What is the correlation of responses for the N subjects These questions require that the subjects be registered aligned to one another and to a reference atlas The reference atlas alignment facilitates the segmentation color coding of the brain into regions and sub regions The brain activity can then be statistically analyzed and tabulated relative to the regions identified by the user The user must a establish an MRI project folder perform b registration c segmentation and d statis
22. des the inverse of the matrix This feature 1s useful for providing the necessary transformation matrix to modify the non active matrix to the active matrix For this feature to be benefitial one must register only LR jo one image set If so then the inverse matrix can register the non active matrix to the active matrix Manual You may set the registration matrix using manual registration through adjusting 3 translation rotation and scales values The function allows you to choose whether you would like to change the active slice all the slices or the 3D geometry Translation rotation and scale factors may be changed in 3 orientations LR PA and IS Move the sliders under each orientation to see the changes on the active slice s Auto AIR a The Auto AIR function Automatic Image Registration has not yet been implemented yet The A I R product provides automatic registration for contrast based image data sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 26 Mesh Generation The Mesh Generation program is used to create volume mesh objects when given surface mesh data to model It can either create a Script file which can be used as input when running SpMesh or it can automatically run SpMesh within CWBench and load the resulting mesh geometry onto the CWBench display OF Set MHE Settings SpMesh
23. ear correct change the settings in the header tab and reload the images This can be done iteratively The header tab provide data type changes such as char short int float double d File Edit View Applications Analysis Tools Export Images To export image datasets Select the Volume Set that you wish to export ar fa a AE The header tab displayed shows some of the typical information for the images Wa The DICOM tab allows that specific type of medical image format data to be imported to CWBench mE Under the Export Properties tab the option to Apply is available Properties Other The Slider Range for the Width Level Threshold sliders 1s normally automatically set according to the min and max voxel values in the volume If Y ae File Type _tit_ show As 30 volume desired they can be altered explicitly here fess The image properties of all the loaded slices can be modified together Some osa properties allow individual slice modification as well If one imported the images it 1s possible to save the entire import set and all the specific parameter settings as a cni file If the cni file format was selected then subsequent loadings of the cni file will reload Ss hs joo vfoo all initial parameter settings Sagittal L F b Endian Little eig sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Ins
24. eometry data from a variety of format sources It can translate them to other formats as well as our XML driven Filename cni format The CNI file extension is our acronym for Comparative NeuroImaging Image data are generally bitmap pixel data B amp W Grayscale Color and other modes It can exist as an individual file containing a single or sequence of image s Alternately it can be multiple files of 2D image slices which when stacked sequentially represent a 3D image set Geometry data are comprised of nodes or vertices floats etc the node connectivity such as 2D and 3D finite element meshes polygons etc and scalar or vector attributes associated with the geometry A combination of these data types can be supported simultaneously See Basic Tutorial with Examples for more details on how to create these files sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 5 Installation Notes for CWBench Version 2 0 X X installation for WINDOWS System requirements Windows 2000 or XP At least 256Mb RAM To run SPM MATLAB 5 2 or higher is required All CWBench software is stored within the CWBench folder It does not write anything to system folders 1 CWBench uses Tcl8 3 4 2 Unzip all files CWB20BCxxxxxx zip These zip files are 50MB or less in size Each file should be unzipped into the same user specified r
25. equired Alternately each segmented ROI mask file 1s entered in correspondence to the anatomy files IMRI Module MIRI Module MRI Module Project Register Segment Project Register Segment Wore Project Register Segment Update Files ae h Remove X There are only 5 parameters specified by the user the start and stop of the control period the start and stop of the stimulation period and the threshold value sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 42 An output file prefix is specified by the user Fach anatomy file in the list some repeated for different functional tests will have 3 graphics output files one for positive BOLD one for negative BOLD and one for both The file name will contain the prefix perhaps associated with the parameter settings coupled with the anatomy and functional file names and finally the P N or B for the BOLD settings A single time course file will be created for each anatomy Two columns for each ROI will be created positive and negative bold results Composite Graphics file and Time Course file Once we get these modules to perform as stated the composite can be constructed with existing information sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 43 Basic
26. fa T ee eee program is not yet implemented Eventually it will provide access to all the help features CSS i si ee Documentation Opens an online version of this user manual Using Help Reminds one how to find help throughout the program Hover the mouse cursor over a button or input field If available a small yellow box appears next to the cursor with a brief explanation of the feature About CWBench Software logo and release information However each Applications selection has a Help tab within the left control panel Those Help tabs are active and provide a brief description of the components within that application Additionally if the mouse cursor hovers over a button or input field a small pop up window appears next to the cursor with a brief explanation of the feature if available sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 18 Working with Files This section includes information about CWBench s different file types and some file management tips File Types sullivan wpi edu Plain Raw Usually contains one slice of image in single file It uses file extension to number slices a set of files with same file name and numbering file extension e g xxx 001 xxx 002 xxx 00n or xxx 1 xxx 2 xxx n CWBench recognizes the slice range through the file extension within the same folder Raw format doe
27. ferent features on or off Change the opacit ro NCL ge the opacity of the desired feature by clicking and dragging fio LI the bar next to the word or by inputting a numerical value from 0 to 1 0 being sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 48 transparent and being opaque Toggle the feature s visibility on or off by depressing the button with its name on it Right clicking on the names of the geometry features eg Skin vessels ventricles offers more options to you such as altering the color of the feature You may choose to display the figure either rendered using mesh wireframe or smooth surface A mesh rendering of the same geometry shown above looks like this Display Import Export Clip Metive Model Under the Utilities tab you may select a type of movement for the 3D figure in the green box Rotate Spin or Pan Then press the arrow in the direction that you would like the movement to occur The figure in the 3D window will move as desired sullivan wpi edu CWBench Instruction Manual November 2004 Version Zzqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 49 Coupled Both Image amp Geometry Select the Open CNI file option from the File pull down menu Under the browsing window find and click on the file to be opened Brain Regis cn
28. file created Note AIR and CCNI mutual information are not the only two strategies for intra modality registration One can also register the data sets manually by going to Applications gt Registration or by any other mode For the fMRI module to work smoothly one still needs to create Save the final aligned image volumes In this mode the Align button is never used The image volumes are still loaded in the Subject s to align window and a reference image 1s specified in the Standard Volume tab Any image volume not aligned yet can be aligned using tools other than the AIR option The Save button creates the necessary infrastructure to continue the MRI module Inter Modality Registration One of the primary registrations is to align a subject to an atlas That is to translate rotate and scale the subject volume such that it overlays the atlas volume set This form of registration is inter modality since the subject volume is intensity based grayscale whereas the atlas is a segmented or color coded image set We recommend as a 1 attempt the 4 point alignment This strategy can be incredibly fast The down side is that it requires closely matched points and spatial separation of the points The ideal 4 points form an equilateral tetrahedron on one subject the Standard sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI
29. g Active Group to Rat Atlas we create a ge point on slice 104 Two Marker sets have been created Now to align the two image volumes based on these 4 paired points Select Inter R tab within the fMRI application module The graphics at the top of the panel indicate that the Reference selection will be transformed to fit the Subject space There are three fill in windows in the Reference Information area The user selects the Background Image used and the Overlaid Marker Set which was overlaid on this image The third window displays the Number of Points in the selected Marker set A similar selection menu exists for the Subject Information area If more than 4 points exists in the Marker sets the user can specify how many will be used in the transformation determination For this example only 4 points the minimum exist Select Get T Matrix button to determine the transformation Sub T Ref The resultant 4x4 T matrix is displayed in the adjacent window To verify that the transformation was sufficiently accurate one needs to apply the matrix to the Reference Image set Select Apply New Matrix and then sweep through the slices to check alignment The effects of the transform are immediately apparent if the images are visible in the display windows Undo will revert to the previous matrix if selected The marker points still exist If the transformation is acceptable the u
30. i Click on Open to load the file The blue bar at the bottom left of the program window indicates file opening progress You may use both the features under the Image and Geometry applications for this file By toggling both image slices and geometry features on the model gives you a guideline as to where the slices are located in terms of the facial features of a human In order to see what is under the skin of the model it 1s often best to decrease the opacity to a comfortable degree so that the slices within can be easily seen and still compared to the skin The same applies to any opaque ventricles or vessels In Geometry under the Clip property tab you have the option of using the slice planes to act as clipping planes to view inside the model Turn the slice planes on or off and select to clip the portion of the model lying on its positive or its negative side You may change the effect of clipping with multiple planes To clip a particular model you must turn on the clipping attribute for that model by right clicking the model name under the Display tab and selecting clipping or by doing it under the Import tab s Advanced section sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 50 Importing images to create a CNI file After opening CWBench you may import either image data or geometry
31. ical Engineering Department at WPI Expertise Marching cube surface generation and linearization algorithms Multiple material marching cube routine developments and enhancements Praveen K Kulkarni Ph D Candidate Mechanical Engineering Department at WPI Expertise Statistical analysis of functional MRI datasets Murali Murugavel M S Ph D Candidate Mechanical Engineering Department at WPI Expertise Mesh generation segmentation Hongliang Victor Yu Ph D Candidate Mechanical Engineering Department at WPI Expertise Linear and non linear image registration algorithms Shilpa Kinkar M S Graduate Student Computer Science Department at WPI Expertise Image segmentation and ITK utilization Miao Lu M S Computer Science Department WPI Expertise Web development Qiu Autumn Xia M S Computer Science Department WPI Expertise DICOM interface development file utility routine Yingxin Lucy Zhang Undergraduate research assistant sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 4 CNI Workbench Manual Updated December 2004 Getting Started Introduction This software provides an intuitive graphical interface to view and analyze both image and geometry based data The major target is MRI imaging and geometry surface amp volume models constructed from such medical images CWBench can import image and g
32. ions Other property tab Slider range automatic or manual Low High Help tab sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 56 Help information specific to Images Application GEOMETRY Display property tab Rendering screen selection viewRen default Render types wireframe mesh or surface 3D default Visibility Opacity of Any All Geometry Models loaded Drag bar to manipulate opacity of object Select button to toggle visibility of object on or off Right click for additional visibility settings Show all or show none Import property tab Active model selection select any geometry model already loaded Properties basic or advanced mode Basic mode New model file vtk Browse to select file from computer Name Color Visible check box yes or no Opacity for a default setting Apply or Cancel modifications Advanced mode Clipping check box yes or no Each geometry model has the option of being subject to the clip settings for 3D viewing Backface culling yes or no Scalars visible yes or no Labeled relative to a color spectrum Scalar range input low value 0 input high value 100 Optional description enter a description of the imported object Clip property tab color coded slice off clips the positive side of geometry Clipping type union or inter
33. is Scale factor 0 3 dilates image on LR PA or IS axis Mouse action translate or rotate Auto AIR property tab not operational yet sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 59 Help tab Help information specific to Registration Application MESH GENERATION SpMesh property tab Generate tetrahedral mesh on cube or deltahedral building blocks Input Boundary Input File Browse for filename Internal Normalization Factor default at 1 0 Maximum Auto refinement Limit default at 0 Checkboxes Ignore adjacent element Ignore same materials Bounding Box Size dx dy dz amp Average Boundary Size may be manually input or automatically determined by pressing Load Bdy Build Block Cube or Deltahedral Initial Build Block Ratio Size default at 1 0 Radio buttons Ratio to Average or Absolute Size Refine O Choose type of refinement for up to 5 levels Input the distance of refinement from the specified surface towards the center if necessary Select the boundary filename if necessary utput Volume Mesh Output File s Browse for or create new filename Output Format WPI nml or Thayer nod amp elm Element nodal numbering convention Normal towards center normal in or away from the center normal out Output file type ASCII or Binary Check checkbox to use default scrip
34. its the application sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu 11 Center for Comparative NeuroImaging Bioengineering Institute WPI Edit ENT mE a Opens the submenu for creating modifying Regions Of Interest ROI and or Volumes Of Interest VOI Domain Domain Filters Converts frequency spatial complex real domains from one mode to another Qperate i Filters Apply High or Low pass filters to user specified datasets Operate Apply various Boolean cropping options and masks sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 12 View Hide Panel View SEs Toggles the command panel status Hide or Show Heere Image Data Image Data Displays the Images command panel for Display Import Export Help Options This control panel Geometries contains numerous tools including the ability to adjust image properties of all loaded slices import undone slices from file s and alter color and contrast of images This panel is described in a subsequent REA detailed chapter Background dutocenter Viewports DBR Geometries Magnifier Displays the Geometry command panel for Display Import Export Clip Utilities Help Options This control panel contains numerous tools including the display of 3D geometry data the display of scalar vector and tensor solutions onto the geometry surface a
35. le times so that unknown or forgotten parameters can be determined such as big little endian format and signed unsigned short etc Each attempt to load will display the results but they are not entered into the data structure until the user selects Apply within the import options Some other software such as A I R use 1mg as its file extension identifier as well BMP A generic Windows format supported by many software products A BMP file contains image size information Similar to other file formats BMP files can contain an image volume set However the user must fill in some header CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 19 information otherwise the image is assumed to be a single image The BMP missing header information for an image volume are pixel size slice thickness scan order Multiple image slices can exist in sequential formats similar to raw files but the file sequence is identified by the numbers immediately preceding the file extension 1 e xxx001 bmp xxx002 bmp xxx00n bmp or xxx1 bmp xxx2 bmp xxxn bmp Naming Files When CWBench prompts you to type a filename you can use up to 259 characters to create a name for the file If you want to use the CWBench default extensions do not type a or an extension after the filename CWBench automatically adds the appropriate default extension sullivan wpi edu CWBench
36. lting color You may go back to the import tab and select the correct color then press apply again sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 52 To reassign a color press the Color button to find the desired color You may enter RBG codes select from some predefined colors or pick a color from the spectrum at the lower right To define a custom color for the predefined color chart give the selected color a label name ees at i Check or uncheck the visibility box to define if the geometry being imported will be visible Y Opacity 1 1 J visible Manipulate the opacity of the geometry being imported by dragging the pull bar Opacity is given on a scale of 0 1 0 being transparent and 1 being opaque You may input a numerical value on this scale if you wish to have a certain opacity After making the necessary manipulations to the geometries you may save the data as a cni file Press Save CNI as under the file menu and give the file the desired name It will save as a cni file which you may open up from now on using the Open CNI file option sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 53 Troubleshooting Problem The CWBench does not fully open up when I try to open it and the program stops responding after
37. mage space to one of the atlas regions selected via the Tree Browser Analysis Functional files are identified and linked to respective anatomy files The user specifies the control and stimulation time periods A threshold value is set to ignore all pixels with intensities below that percentage value Positive and negative BOLD responses are tabulated A set of images and timelines are created for each functional test In addition a composite model is constructed that represents the average responses of all individual subjects Register Segment Analyze More There are several tabs under the MRI module located in CWBench via Applications gt fMRI The first tab Project recalls or creates a Project Folder Within this folder the system maintains a status file with the same name as the user specified Project Folder name with prj extension Several subfolders are created that are associated with each tab within the fMRI module Data and results are stored within the Project Folder and sub folders One can press the Browse button and select the fMRI Demo sample folder located within the Examples folder of CWBench Then select Recall Alternately one can create a new project folder sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 31 Preliminary Constraints SHORT Datatype CWBench has the ability to im
38. mesh output to You may create a new file by typing its name into the input box Choose the format of the file s to be outputted the entire surface boundary of a separate boundary select the location of the file Define the distance center of it that should be refined the space within the selected boundary file using sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 28 WPI format outputs one file with extension nml Thayer format Dartmouth Thayer School of Engineering outputs two separate files with extensions nod and elm for the node locations and the element information respectively Choose the numbering convention of the element nodes having the normal vector pointing away normal out or towards normal in the center of the object Choose the output file type either ASCII or Binary You may either use the mesh output filename as the name of the script file to be written by keeping the Use default script file name box checked or you may browse for and type in a different name in the input box Before starting the program you may choose to check the Run SpMesh and or the Auto Load boxes No boxes checked Creates a script file that can later be used as input for the SpMesh program run under MSDos mode Run SpMesh In addition to creating a script file also generates
39. mparative NeuroImaging Bioengineering Institute WPI S If you chose to enter the Image headers manually a menu will open to ask you for specifics Enter the header information as desired and press Apply to import the images The blue bar at the bottom shows import progress After any desired manipulations have been made to the images select Save CNI as from the File menu Enter a name for the cni file the file type should automatically be chosen as a cni file Press Save to complete the file save Now you have a complete cni file made from imported image data You may open it from now on using the Open CNI file option Geometry Data Under File hover cursor over Import gt and press Geometries on the menu appearing adjacent to File menu This action will open up the Import tab under the Geometry application You may choose to open up to this tab manually by first choosing Geometries from the View menu if it is not already there and then clicking on the Import tab Press the Browse button to open find the vtk file which contains the geometry data you would like to open example Examples BrainMesh Images Miga composite_vl vtk Press open The program automatically detects the name and color of the file although you may opt to change them if you wish There appears to be a bug here where the default color before pressing apply is different from the resu
40. mport the image volumes into the program The analysis program requires that images of interest are loaded or imported into Help More CWBench To do so one can use the File gt Import gt Images option Although ie CWBench can import a variety of image orientations the AIR registration software is expecting Axial from I S loading Please ensure that this constraint is followed CCNI magnet files on the server have sdt and spr file extensions One can import these images directly from the server location or one can copy them to the fMRI Project folder for a complete self contained project Bottom line these images need to be loaded into CWBench If one uses the fMRI Demo example folder the anatomy files reside in the subfolder data These images can be imported individually or for automated loading a Initial Load cni file has been saved in the fMRI Demo directory Use the File gt Open CNI File and select the file Initial Load cni Home _ None Reslice A Registrations Our GUI offers several modes of registration 4 pt inter modality N pt inter modality Manual linear intra modality and non linear intra modality The recommended first step 1s the Intra Modality Registration to align all subjects to one standard subject That is to shift rotate scale each image to fit one user selected standard image sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy w
41. must simultaneously hold down the ctrl key and perform a left mouse click for each location The Markers do NOT show up on the 2D image sorry They are 3D geometries and their locations and labels are in the 3D window only One can select a 2x2 view and turn on the visibility of the 2D slice in the 3D window to see the location of the 3 points relative to the image Repeat this process for the image set the Ana One Rat brain image set Be sure to create a new label and Add the group then create the SAME 3 locations in the SAME sequence on the appropriate Ana One Rat brain image slice M0 M1 and M2 as shown in the Figure If the sequence was not correct one can move the point locations up and down in the Marker application pallet Ideally one wants the 3 points on the plane to form an equilateral sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 37 triangle that spans the 2D image slice However well identified and matched landmarks on the two image set slices are critical A 4 point NOT in the same plane needs to be identified for both image sets The 4 point is distant from this slice Be sure to have the correct Active Group identified Since we left off with the 3 points on the Ana One Rat brain image set we will continue and create the 4 point We ve selected slice 6 of Ana One Rat brain Switchin
42. nd volume datasets Varieties of clipping operations exist as well as rotations animations pan and zoom tools This panel is described in a subsequent detailed chapter m Viewports Orientation E n cd El p DARI E The various viewports available for 2D and 3D display For 3D Window El characteristics The 2D viewport displays one large 512x512 pixel Front window of a 2D image The 3D viewport defaults to a 768x700 pixel Back Hl window This is the only view that can be resized by the user The 2D Left l display window sizes are fixed since the data are integer pixels Right Remaining viewports are divided as shown each with at least one 2D Top Y window and a 3D window The 3D window is distinguishable by its Bottom default green background A checkmark identifies the currently selected Isometric viewport Axiometric En Orientation Gal Changes the orientation of the 3D window so that the selected direction 1s the full face view on the screen sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 13 Background Changes the background color of the 3D window Default is set as Emerald Other choices include Black Grey Sapphire and User Specified AutoCenter Image Box This function centers and autoscales the image within the display window Geometry This function centers and autoscales the geometry within the display window Mag
43. nifier Opens a new window on the desktop Magnification can be selected via the slide bar at top or a numerical value on a scale of 1 to 10 entered in the box next to the slide bar Applications Detailed explanations of these applications are provided in subsequent chapters CWBench Prof John Sullivan Copyright 2004 WPI Regi stration File Edit View ES Analysis Tools Help Affine transformations of slices translation positioning rn rotations and dilation scaling aa Transformations can be manual via slide bars or keyboard Display FMRI Module entry Direct links to 3 party registration software detive Dataset Def olume Mesh Generation Creation of surface meshes using a multiple material marching cube algorithm Creation of volume meshes using surface mesh data as input MRI Module Complete functional magnetic resonance imaging fMRI is a complicated and iterative analysis This module walks one through the steps in sequence Multiple pathways are presented to obtain the final result The suggested path starts with subject registration alignment to one another and to a reference atlas The reference atlas alignment sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 14 facilitates the segmentation color coding of the brain into regions and sub regions The brain activity can then be statistically
44. ode 5 Launch CWBench by a double click of the Desktop Icon System requirements Windows 2000 or XP Linux Redhat V9 and SuSe V9 tested SGI More than 256Mb RAM Minimum display resolution 1024 x 768 6 Launch CWBench from the Desktop Icon Files with the extension cni and format can be opened directly from the File pull down menu Several of these files already exist in the CW Examples folder Alternate format files need to be Import via the File pull down menu Note for CWBench20 installation for LINUX System requirement Redhat Linux 9 Suse Linux 9 other Linux platforms might work as well More than 128Mb RAM 1 Untar file CWB20BCodexxxxxx tar gz tar xvfz CWBench linux tar gz 2 copy examples to local drive 3 Create a Launcher on Desktop for CWBench right click on desktop select New Launcher sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 7 Name CWBench Command CWBench cwbench Icon CWBench cwb2_83 res Ccn12 1co 4 Get a license key cwb ecl from http ccn1 wp1 edu put the license key under the main directory CWBench cwb2_83 5 Launching CWBench by click the Icon Open the files with extension cni under example directories 6 To run SPM you need MATLAB 5 2 or higher 7 To have native AIR package working properly you should add working path to the AIR directory under CWBench sulli
45. onger time but provides more accurate registration results For both intra modality registration strategies select Ana One Rat brain as the Standard Volume All other images in our example Ana Two Rat brain Ana Six Rat brain in CWBench s memory are automatically loaded in the Subject volume s to align window Any image not to be aligned Project Segment Analyze More rio jee 1 Segment Analyze More sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 34 can be removed Highlight the undesired image and select Remove The user can select two alignment strategies Rigid 6DOF or Affine 9DOF The Rigid 6DOF alignment rotates and translates the Subject Volumes to fit the Standard volume However it does not scale the image set The Affine 9DOF alignment also allows scaling in the 3 coordinates independently An output file is specified to store all the transformations The file extension fmr is automatically appended to the filename if an extension is absent Similarly a second file with the extension cni is created The program uses the fmr file information for internal use The cni file allows the user to resume the process at the same state The Align button performs the registration The subject volumes are distorted to fit the Standard volume A Ty matri
46. ons of the Image application If not select Image Data from the View pull down menu Under the Display property tab are the options to manipulate the opened file sullivan wpi edu CW Bench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 45 SCWRench Me Weihuang Gopynpiio 2004 WPI File Edit View Applications Analysis Tools Help Spi DA f Active Dataset The definition of the images can be manipulated using the drag bar next to Thresholds or by inputting numerical values This action sets the low and or high end of the visibility threshold You can toggle the visibility of the Image slices on or off by using the Slice Control under the Tools pull down menu Next to the slice name whose color code corresponds to that of the menu click the V to turn the visibility of the slice on Press again to turn it off You may select as many slices as you would like to become visible The visible slices are displayed in the 3D box to give you a good idea of where the slice is located and what it looks like in the actual human head sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 46 The image slices may be registered translation and or dilation to fit a certain model by using the Registration application
47. oot directory Ex C Do NOT specify a root directory or path that contains spaces within its path and or name An invalid example would be C Documents and Settings John Sullivan My Documents Some 3rd party links ex AIR require this constraint 3 Add a Shortcut onto Windows Desktop for CWBench a On a blank region of desktop Right click gt New gt Shortcut b Paste the following line into the location of the shortcut target lt User specified root directory gt C WBench C WBench20bc83 bin wish83 exe CWBench tcl where lt User specified root directory gt is that selected by the user such as C c Click on Next button and then rename the shortcut from wish83 exe to CWBench d Click on Finish e Right click on shortcut and select Properties change Start in field to lt User specified root directory gt CWBench C WBench20bc83 bcode f Select Change Icon and Browse to sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 6 lt User specified root directory gt CWBench CWBench20bc83 bcode res CWB _Icon ico g Select OK 4 Get a license key cwb ecl Connect to http ccn1 wp1 edu Follow CWBench gt License Enter required registration information License will be sent as an email attachment Store the license key attachment file within lt User specified root directory gt CWBench C WBench20bc83 bc
48. pi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 33 Intra Modality Registration This component of the fMRI module deals with aligning all subjects to one subject Hopefully it IMRI Module fMRI Module can be done automatically The goal is to align all subjects Subject J to a standard subject That is Std Subject T Subject J In our aa example Subject 1 will be the Standard Subject i Select the Register tab within the MRI module pig Press Intra R button by default this button 1s pressed down when user first enters the Register tab There are two strategies for automatic intra modality registration 1 CCNI mutual information and 2 AIR 1 AIR This strategy uses the AIR registration with several of the parameter options pre selected The code reads the Standard Volume set and defaults the Threshold to 8 of the data range This value can be changed Pixels with intensities below the threshold value are not used in the alignment process The convergence 10 and iteration count 2500 are our recommended values Ana_Two_Rat brain 2 CCNI Mutual Information default strategy pla eral This strategy aligns the subject to the reference image ER i i 7 Ana Five_Rat brain by maximizing the amount of mutual information It RO essentially deforms the subject image based on the transformation constraints to minimize the intensity differences of the two images It takes l
49. port numerous file F Conversion Bo A Conversion Bo formats However the statistical analysis a plit Rescale Merge Endian Conve Split Rescale Merge Endian Conve assumes that the data files anatomy functional and color coded are all SHORT If the data 1s haha fla a not in that format we recommend using the Tools gt Conversion utility This utility Browse Browse ed ud e nati vite ve y Row 256 Column 256 Row 256 Column 256 status split and or merge files rescale data an convert file formats The actions are relatively Slice 18 Timestep 1 Slice 16 Timestep self explanatory from the tcl gui The Rescale cune oa DES Cha option is used frequently especially when one x Char needs to convert a FLOAT or INTEGER toa Endian LittleEn Unsigned Char Input Choices Dal y para SHORT In order not to loose resolution the user Short da Magnitude User Specified Output choices The code will read the input file Int Unsigned Int Float File Suffis 12 2 Double determine the range of data existing within the file and use those values as default for the Input File Range The Output File Range will default to the range of the data type selected by Number stat 1 the user These default values can be changed by the user prior to pressing the Rescale button should select User Specified for the Input and Output Image File seer ett
50. relative to the aa background image set paste cocos JRE Conversion Each set of colored options on the menu represents a different box on the window whose color matches that of the menu There are several features available for each color coded set The colored slide bar can be moved to display different image slices of the dataset The system loads an image set and interpolates all images in different orientations maintaining the same aspect ratio The number box adjacent to the slide bar shows the current image slice displayed One can enter a specific numerical value in this box for direct display of that image Four button controls each with two options exist The smaller square pale colored button affects all windows for that specific function The rectangular color specific button affects the individual colored window only The Orientation button Or sets the orientation There are numerous options for orientation The background Bg and foreground Fg buttons can display separate image sets if desired This feature is helpful when trying to register one image set to another Each fore back ground window can be turned on off using the adjacent buttons to the right of the control buttons The V button is the 3D Visible button If activated the imaged displayed Foo is viewed in the 3D window RE The R button reformats the image in the window Sli p LA 1 The Active Slice Control panel ena
51. rmats are scheduled If geometries are imported one must select Apply before the effects become part of the data structure Again if one saves the file as a cni file all geometries image data sets and their settings are preserved in the cni file Clip The image slice planes can act as clipping planes to view the inside of the model In order to have Clip active the geometry model listed in the Display submenu must have Clipping active in its structure Under Display right click the specific geometry model and verify that Clipping is activated Toggle the slice panes On Off to clip at that slice s position For each slice pane choose whether to clip the portion of the model above or below its the current slice layer status By doing so you are toggling that slice pane ON to be clipped Press OFF if you wish to turn off the clipping for that slice You may change the effect of clipping by toggling multiple planes sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 24 Geometry The Clipping Type determines if the clipping mode is either the Union or Intersections of those J Display Import Clip E J ae 7 activated a gt Press apply to accept changes Utilities The Geometry can be rotated spun or panned using the button option and arrow indicators Select the moving type
52. s distorted to fit the fMRI Module Atlas Merge Registration eliminates Subject 1 as the intermediary Subject o 1 A Subject o J Segment Analyze More Atlas ra Subject o 1 Atlas n CAPA l ce I Subject o J The user recalls the file name saved within the Inter Registration tab for the first Browse button The program goes directly to that location by default Similarly the Intra Registration saved file is recalled for the second Browse button A new file is created that provides alignment of all subjects that is Subject 1 through N to the Atlas 41 Tol asz Apply amp Save sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 40 B Segmentation The user launches the Tree Browser tool Each desired region for analysis is selected The entire shell of the rat brain is always selected Once the desired p or ol Of Interest have been viewed for confirmation the user saves the selections These regions or volumes of j CTE interest will be identified File Edt view Applications on each subject The user MRI Module needs to close the Tree Browser and enter or select _ Rial Sent ES the file just saved from the pr tree browser This is e somewhat redundant but Select ROIfile oreatedin Tre ff Tiza your required currently B fie Edt Siew Options Actor Camera Tree
53. s not include header information The user is responsible for providing correct header information Explicit Raw Has a file extension of raw Photoshop prefers this form This type of raw file can contain a single image but usually includes multiple slices within one file While loading CWBench will put unknown in the last slice and slice range fields to remind the user for input Note that the first slice number index defaults to 0 As with plain raw format the user should provide complete header information even though CWBench has default header settings SDT The native format of STIMULATE SDT format includes two files spr and sdt The spr file contains header information and the sdt file has the image data Both files need the same file name and be in same file path Generally CWBench will extract the header information from the parameter file without user intervention There are some simplified spr files that were generated by utilities other than Stimulate These files only include minimum header information such as image size and number of slices thus the user should fill in the rest of information IMG The native format of Analyze The img file has a separate header file hdr The hdr file contains all of the header information except unfortunately the endian type Sometimes IMG format mixes up signed short and unsigned short both are 16 bits which can cause problems CWBench allows the file to be loaded multip
54. section Apply modifications Utilities property tab sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI Sl Moving type press the directional arrows to move the object in that direction Rotate Spin or Pan select what type of movement the arrows will make Measure Performance inactive Help tab Help information specific to Geometry Application SLICE CONTROL Controls property tab Foreground slice opacity drag bar to manipulate opacity Press button to toggle option on or off Requires an image set in both the foreground and background Slice range automatic or manual From input beginning value to input end value Color coded sections for slices Slide bar indexes through the available slices Adjacent box is an explicit slice number WV if activated makes the image visible in the 3D window R reformats the slice Or Orientation left box applies to entire image set right rectangle applies to specific color coded window Bg Background left box applies to entire window set right box applies to specific color coded window Lb Label Layer identification left box applies to entire image set right rectangle applies to specific color coded window Fg Foreground left box applies to entire window set right box applies to specific color coded window Ac
55. select the correct color and then press apply again sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 54 Application Function Tree IMAGES Display property tab Active volume selection for image parameter modifications Width Level automatic or manual Width Drag bar width of the contrast levels within the data Level Drag bar mid location of the grayscale intensity value Threshold automatic manual or apply Lo Drag bar to determine lower end threshold of image definition Hi Drag bar to determine higher end threshold of image definition Palette color scheme of slices gray iron rainbow natural or label Interpolation On or Off Intensity spectrum distribution of image set Import property tab Properties Basic Header or DICOM First image file press browse to select file from computer Number of last image Slice Range From input slice value to input slice value Time steps from input time value to input time value Image headers automatic or manual Image Data grayscale or label map Name enter name for slice Optional Description input a description of the slice Apply or Cancel modifications Export property tab Select Volume which volume to export Orientation which orientation as primary output Properties o Export Browse button to specif
56. ser supplies a name for this T matrix and selects Save The default name concatenates the two selected marker labels with direction in the current folder i e Reference To Subject or Atlas Markers To Subject Markers for our example N Point Fiducial Registration If the 4 Point Inter Registration results were less than desirable one can perform Manual registration to tweak the alignment This tweak is usually performed within a few minutes Be sure the appropriate matrix is in the Active Matrix window prior to adjusting any of the manual slide bars Alternately one can use more points in the alignment process The Inter Registration module displays the number of markers in each selected data set Adjacent to the Get T Matrix is a user selectable marker count entry It defaults to the lower of the two selected marker counts The user can enter any value between 4 and the default displayed which has a ceiling at 10 markers Adding more fiducial points can enhance the registration The code performs a least squared error analysis on all the paired points The downside is that adding more points takes more time and the sequence must be paired The following CNI files located in the top fMRI demo folder can be useful for rapid reentry into this Inter registration section Step 2a cni sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Ins
57. t file name same name as vol mesh output file with different extension If box 1s unchecked then browse or input a filename Select RunSpMesh to create a volume mesh file in addition to the Script file Select Auto Load to display the volume mesh that was created displays in 3D viewport Check Output material surfaces and input the list of materials to output separated by commas sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 60 Press Apply to begin mesh generation OffSet property tab Offsetting Mesh Generation MMC property tab Multi material Marching Cube Help property tab Find appropriate help documentation about Mesh Generation menus and functions sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 61
58. tical t test analyses in that order Naturally an experienced user can look at a set of slices create a loop and run a t test However in that mode they have a registered the image by mentally picturing the area of interest then they b segmented the area by creating a loop around the region and finally c did the analysis within that loop We present a more formal regimented mode which is summarized as follows sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 30 Registration One subject is selected as the standard volume All other subjects are aligned to this standard subject using an automated intra modality registration The standard subject is then aligned to the atlas using inter modality registration Finally all N subjects are aligned to the Atlas based on the concatenated transformations that aligned each subject to a standard subject and the alignment of the standard subject to the atlas Frequently the automatic registration provides an approximate alignment but not sufficient for the user Several alternate mechanisms exist to tweak the registration Segmentation The interactive 3D brain display Tree Browser is used to select the regions of interest Based on these selections and the registration results a set of IMRI Module anatomy masks segmented images 1s created that classifies each pixel in the subject i
59. titute WPI 23 Geometry The Geometry application can be used to display 3D data simultaneous with image slice information It allows the user to modify visually this geometry data to show specific sections of the object The 3D object in the 3D viewport can be rotated zoomed panned via the left right scroll mouse buttons respectively The user has the option of changing the opacity of the object to see Image and or other geometry data within it Each geometry model is displayed in the control panel list The color and other parameters can be changed by right clicking on the geometry model name The Geometry menu has five tabs at the top Display Import Clip Utilities and Help You can click on any of these tabs to show the sub menu within that topic CNI Workbench File Edit View Applications Analysis Tools Disp lay Geometry T Choose the Rendering Screen where you would like to view the model default and currently only is the green 3D screen Choose the render type to display the model as a Wireframe or Surface model Click the button with the model s name to toggle its visibility and move the slider to change its opacity For additional options right click the model s name File Edit View Applications Analysis Tools You can click on Show All or Show None to toggle all the models on or Geometry off at once Import Currently the only default geometry format is vtk Other geometries fo
60. titute WPI 38 This CNI file Imports the previous images used in the Intra Modality Registration and the Rat Atlas into memory Step 2b cni This CNI file has created 4 markers based on the MRI Module fMRI Module Rat Atlas and Ana One Rat brain images n I The markers are slightly off such that manual Project segment Analyze More Project Segment Analyze More tweaking is required after the Get T Matrix E and Apply buttons pressed The suggested tweaks to the Ana One Rat brain image are 1 2 3 4 5 6 7 8 9 for the 9 manual entries Po in that order Step 2c cni This CNI file has created 4 markers that do align the two images appropriately Further it applied the transform on the Ana One Rat brain image such that it is aligned to the 3 a Rat Atlas image volume This CNI file is the mc L E start point for the next section the Merge Ly Registration wherein all Subjects within the study are aligned to the atlas RAT ias fe Get_T Matrix RAT Alas ja 1 985429 0 0700199 0 011073 0 381737 0 07 s ore fater B ew ne Rat brain To RoT_ Alag sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 39 Merge Registration Two sets of registrations have been performed In Intra Registration all Subjects 2 to N were distorted to fit Subject 1 In Inter Registration Subject 1 wa
61. tive slice color red yellow or green Save active slice Show advanced slice controls Zoom input value 1 0 sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 58 Slice increment input value 1 Close advanced view Help tab Help information specific to Slice Control Application REGISTRATION Matrix property tab Active matrix specifies which dataset is being modified by registration Properties basic or advanced Basic mode Name of the active matrix Matrix the 4x4 matrix in a single string Matrix Definition the 4x4 individual transformation values Apply or Cancel modifications Matrix operation identity or invert Advanced mode Optional description enter a description Get matrix from Volume can recall a different volume set s matrix as initial settings for the current active volume set Type of matrix none RAS gt VTK scaled IJK RAS or RAS gt IJK various right hand rule left hand rule vtk coordinate protocols Apply or Cancel modifications Manual property tab Active matrix specify which matrix will be modified by subsequent changes Render slice All Slices or 3D Generally want transforms to apply to all Translation mm modifies image position LR left right axis PA Posterior anterior axis IS inferior superior axis Rotation deg rotates image on LR PA or IS ax
62. ute WPI 2 RESTO nn 14 Ao MM er ee Rees 14 TEAL Y E A P o e o O II E T E N 14 CO RR II 15 NOUEt Feo A II A 15 PP 15 A 15 ci AA III A 16 LEI RP E E E E E 17 MOVIS R CO e A AA AAEE ea 18 IA 18 A nn P opcode A seae aorsesagie eaaee 18 VUOI AV PORRI 19 scada 21 SAI o E IA PE RO E EEE E AEE OE 22 CRCR REI IZ 05 24 7240 00562100 CREO SARO IR ROGO a E ETA 26 Gn O PP e Oo T EE 26 METIA co A nS re ne Te enn A 2 MREMA Ei I II 30 bacioni ein I al I I ala 44 lmporins macesto crecio a ENT tna 5 NN RR RA 54 APPIA ana OA OI troni 55 VECI ER TNT n n __ 55 GEOMETRY cenctadsctsdendsacoatecposachacsteoessapcinteatesmosdsandesamana E EEE EEEE EEE E EE EROA R EEE ARTERE 57 CEEC ONTROL ul E E A E AE T E T A T 58 REGISTRATI N ci E A E ET 59 MES OP NERATION gt uz 60 sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 3 Acknowledgements The authors add their thanks to the support staff and students that have made contributions to this work Specifically Udo Benz MS Dipl Ing Research Engineer Expertise Image Registration Web Development System Administration Hamid Ghadyani Ph D Candidate Mechanical Engineering Department at WPI Expertise Automatic conversion of atlases into three dimensional segmented atlases suitable for numerical computation automatic mesh generation Wei Huang Ph D Candidate Mechan
63. van wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 3 Program Start amp Exit With CWBench installed and the display drivers functioning correctly CWBench should start by double clicking on the CWBench desktop icon If the program does not start please contact the support staff at http ccni wpi edu The program displays a credits screen which can be closed at any time The default program screen contains a left panel identifying the View status to be Images and the sub tab category of Display To the right of the panel are 6 graphic viewing windows a large 256x256 window with a green background for 3D data display Five smaller 128x128 image windows have a black background They are for display of 2D data Background colors and view layouts can be changed without difficulty A a i CNI Workbench 2 0 search Tool for Medical Image Processing Build 10 20 04 sulliyan wopi edu zgy wpi ed Copyright 2004 WPI To Exit CWBench select Exit in the File pull down menu or perch Pe ovo Salsa Coni 004 WL mouse click on the X in the upper right hand corner of the program window Finding Help In CWBench the Help menu is located at the top of the program menu bar It provides remote access to the cen1 wp1 edu website for interactive help This facility 1s still being developed A PDF file of the m
64. x is created for each subject Typical alignment time ranges are 1 5 minutes per subject for AIR and 7 8 minutes for CCNI mutual infomation These alignments are applied to the image volumes immediately However the user specified output file will not be created until the Save button is pressed Prior to activating the Save option the user should inspect the quality of the alignments for each subject Each subject volume registration matrix was modified to fit the standard The standard volume retains its identity matrix Under Applications gt Registration the user can select Active Matrix and view its 4x4 values The user can select Tools gt Slice Control and specify the background image to be the Standard volume and one of the Subject volumes as the foreground image A variety of viewing tools exist to toggle the images superimpose them and alter the opacity of them These can be used to verify the quality of the registration If the registration s are not acceptable 3 general choices exist in order of preference a manually tweak the results b use the inter registration alternative or c crop the images and do Intra Registration again Once the subject volumes are aligned satisfactorily to the standard volume the user specifies the output fmr file name and selects the Save button This preserves the current status of the system and allows a clean restart of the project if desired via the CNI
65. y is 1280x1024 A E lE Eee e e e o Note for all pull down menus at the top of the window there 1s a dashed line at the very top of the Save CNI As menu You can click on that line to pull the menu out of the program onto the desktop in a small separate window In this mode you have access to all the options under the menu s without Import having to use the main program s pull down options for them Click the X on the upper right EE hand corner of the small window to close it Close Exit sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI 44 1 Opening cni files a Image Select the Open CNI file option from the File pull down menu Open Fale Look ir E BrainMesh 5 Geometry L E Images My Recent C New Folder Documents EX erain cri gt 14 BrainMesh cni El RegisBrainMesh2 cni El RegisBrainMesh cni Desktop My Documents hy Computer My Network File name Brain cri Places Files of type CNI Files cri Cancel _ i a Under the browsing window find and click on the file to be opened Examples BrainMesh Brain cni Click on Open to load the file The blue bar at the bottom left of the program window indicates file opening progress The opened file will be displayed on the screen The menu bar should be automatically displaying the opti
66. y output file name and pathway File Pattern 1 file all images stored in one file Set x 001 each image numbered sequentially with range of 000 999 available Set x 1 each image numbered sequentially without any leading zeros in the file name structure sullivan wpi edu CWBench Instruction Manual November 2004 Version Zqy wpi edu Center for Comparative NeuroImaging Bioengineering Institute WPI DI Number of Slices File Format Type Scalar Type Endian Type or o OriHead subwindow to display orientation and header information prior to export File Pattern 1 file all images stored in one file Set x 001 each image numbered sequentially with range of 000 999 available Set x 1 each image numbered sequentially without any leading zeros in the file name structure File Type Image Width and Height Pixel Width and Height Slice Thickness and Spacing Time Start and Interval Origin X Y and Z location Scalar Type Scan Order Sagittal Left to Right Coronal A gt P etc Headers Size Endian Type First image file press browse to select file from computer Number of last image Slice Range From input slice value to input slice value Time steps from input time value to input time value Image headers automatic or manual Image Data grayscale or label map Name enter name for slice Optional Description input a description of the slice Apply or Cancel modificat

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