guide to BrainVoyager
Contents
1. 13B 3 Correct the GM and WM e On Mesh click vertex mode side bar gt click location of crappiness e On VMR the cursor is now at the source voxel for the crappiness e 3D tools gt segmentation gt check Enable gt SHIFT click to erase CMD click to draw e Continue until the area looks appropriate e Repeat for this section until you ve worked on all the crappy parts e 3D tools gt segmentation gt Prepare e File gt Save as MC1 VMR Manual Correction 13B 4 Make a new mesh e 3D tools gt spatial trans gt Primary VMR e Meshes Create mesh gt Reconstruct makes a new mesh e Meshes Mesh Morphing gt Go smooth s the mesh e Meshes gt Save mesh as gt Append _MC1 to filename to show the version of this mesh e Examine the new mesh for residual crappiness 13B 5 Repeat 14B 3 and 14B 4 as necessary Below fixed a single problem in a single hemisphere left The skull was being detected as white matter middle After erasing all the yellow skull voxels on all axial slices made a new mesh right This single fix took about 15 minutes 14 Granger Causality Mapping Slice time correction and high pass filtering are highly recommended 14 1 Single Subject e Load VMR e Load seed region VOI Analysis gt Region of Interest Analysis gt Load e Load GCM Plugin Plugins RFX Granger Causality Mapping GCM v2 5 13 Brain Voyager 2 4 Abridged Protocol Belyk November 2012 load VTC files for2. e Surface window gt Meshes Spatial Transformation gt mesh gt VMR e Navigate VMR amp ensure segmentation fits white grey matter boundary shown in yellow e To remove WM GM boundary 3D Volume Tools Segmentation gt Reload All 13 8 Inflate Mesh e Open _TAL VMR e Mesh load mesh RECOSM srf step 7 2 e Mesh gt Mesh Morphing check Inflate gt Set NrOfRepetitions gt Go e Repeat as Necessary 13 9 Colour Code e Mesh gt Mesh Surface Functions gt Curvature gt Smoothing e Repeat as necessary X3 e To set colours Mesh gt Material colour 13 10 Overlay Statistics e Open_ VMR amp _ SRF e Load _ VMP to _ VMR Analysis gt Overlay volume maps gt load VMP e Mesh gt Surface Maps gt Create _ SMP e Save _ SMP 13B Fix poor Surface Meshes Meshes will almost always come out crappy on the first try It s generally recommended to work with the fie RECOSM vmr which represents the WM GM boundary It is worth doing anatomical preprocessing before even considering this step 13B 1 Load a peeled VMR and create a mesh 12 Brain Voyager 2 4 Abridged Protocol Belyk November 2012 e Close VMR Load_WM_BL2 BL2 bridge removal algorithm Reload mesh e WMis shown in blue WM GM boundary shown in yellow 13B 2 Show the automatically detected GM and WM e File gt load secondary VMR gt browse for VMR used to produced the mesh e 3D tools gt spatial trans gt check Blend1 or Blend2 and append after current
3. the subject gt browse for VTC Default settings use the whole run all tasks amp rest minus the first last 5 volumes Epoch Selection gt Go gives filename tag RUNCOND interval For task specific analysis check use protocol Epoch Selection gt check use protocol condition per VTC gt choose a task Go Map of effective connectivity is automatically loaded dGCM Map of functional connectivity can be loaded INST Group Analysis Load VMR Load seed region VOI Analysis gt Region of Interest Analysis gt Load Load GCM Plugin Plugins RFX Granger Causality Mapping GCM v2 5 Load from MDM Default settings use the whole run all tasks amp rest minus the first last 5 volumes Epoch Selection gt Go gives filename tag RUNCOND interval For task specific analysis check use protocol Epoch Selection gt check use protocol condition per VTC gt choose a task Go Map of single subject results for effective connectivity is loaded dGCM Map of single subject results for functional connectivity can be loaded INST Perform RFX on the loaded maps Volume Maps gt Advanced gt Combind Maps gt highlight all gt T Test lt G1 gt 0 Group Analysis With Single Subject Seeds Load VMR Load single subject seed region VOls name each as SUBJECT_ROINAME VOI file should contains single subject VOls and an additional VOI consisting of all voxels found in the single subject VOls combined using OR in ROI tools Name this ROI lo
4. Brain Voyager 2 4 Abridged Protocol Belyk November 2012 Before Analysis A Organize A 1 Prepare a word file for analysis notes A 2 Create folders e Project gt Subject gt Scan number amp name SS_scan task_note e NOTE When it comes time to the random effects analysis the vtc file has start with a subject number e g P1 P2 Hence if you don t name you files along the way with a subject number then you need to add it to the vtc file before running the random effects analysis A 3 Create subfolders for DICOM files for each task A 4 Pick a name you like Renaming folders later on will throw everything off A 5 Rename Dicom Files to BV format do this for every scan e File gt Rename Dicom Files gt Browse B Create Stimulation Protocol PRT file B 1 Analysis gt Stimulation Protocol B 2 Add conditions B 3 Change labels and colours of conditions e Select condition and click on Edit Name or Edit Color e Note must click on condition before changing colour or label otherwise BV will crash B 4 Ensure NrofTimePoints Total number of volumes for the scan B 5 Select epochs for each condition e Make sure condition is selected e Then press Show Plot e Expand Time Course Plot window as much as possible B 6 Ensure Time Course Segment Size block length measured in TR s B 7 Assign conditions to blocks e Select a condition e click on appropriate segments of the plot e Press Add to PRT e Repeat for each condit
5. K e Nothing changes visually to the images when you do this 6 7 Leave the VTC linked vmr file open when proceeding to the next step Quality Control Tool new to QX2 4 Confirm that all VTC s are properly aligned e Options verify functional coverage gt browse for all VTC s or an MDM Graphic display showing VTC s with non zero BOLD signal at each spatial location Areas with imperfect overlap will have low power in RFX analyses Can be used for single VTC to check for particular problems Statistical Analyses 7 Single Subject Statistics 7 1 The following steps assume the TAL vmr is open and is linked with the vtc and prt 7 2 Analysis gt General Linear Model Single Study CMD G 7 3 Assign predictors e If PRT was linked to fmr then the design matrix should open up automatically e Right click one coloured block to assign it as a predictor e Hit the HRF button to set hemodynamic response function except for sparse sampling e If there is more than one predictor then do Predictor gt Add Pred and repeat as above e If the design has multiple factors it s important to name the predictors in a systematic manner Brain Voyager 2 4 Abridged Protocol Belyk November 2012 e Add Motion Correction Parameters Add gt browse for _3DMC sdm adds 7 predictors e Save sdm file by pressing Save on the left side of the Single Study GLM box e Hit GO 7 4 Optional Apply a spatial mask to prevent unnecessary tests outside
6. ach box 8 10 If this arrangement applies to multiple scans in an experiment as is the case for Steven s Phonotopy experiment for example then proceed now to steps 9 12 9 16 below to combine the results from the multiple scans In the case of the Phonotopy study 4 pitch levels Low Comfort Mid and High are distributed through 4 scans Pitch1 2 3 and 4 Hence you need to run a multi study GLM to see each pitch across the 4 scans 9 Looking at Contrasts for Multiple Conditions BETWEEN Scans Creating predictors within a scan step 8 above is easy to do because the condition names are listed in the side bar of the Single Study GLM window However creating predictors between scans is much more complicated since you have to type out the name of each predictor and your spelling has to be identical across predictor files Predictor names have to be IDENTICAL across SDM files Otherwise this will not work This procedure follows the logic of creating a design matrix SDM file in step 8 However a new process is introduced called dummy coding If scan 1 contains condition 1 and scan 2 contains condition 2 then when specifying predictor 1 for condition 1 a dummy condition must be reserved for condition 2 9 1 Before starting make sure that all your vtc files begin with the subject number e g P1 P2 Otherwise Brain Voyager will not be able to sort the data by subject 9 2 The following steps assume the TAL vmr is open a
7. ackages e Runa GLM for each task and subject using the model 15 3 as the predictor e Export the residuals from each model R notes here 15 6 Export each residual time course separately e Paste each into text document with the format below e Use file extension RTC FileVersion 2 Type DesignMatrix NrOfPredictors 1 NrOfDataPoints how many TRs Name columns of values here 15 7 Make correlation map in BV e Analysis gt Compute Linear Correlation Maps gt load RTC gt GO e Overlay volume maps gt Save VMP e Repeat for each task and subject 15 8 Perform random effects analysis on saved images 15
8. ally misses peaks 12 1 Set Cluster threshold recommend 15 voxels be sure not to lose peaks of interest e Overlay Volume Maps gt Statistics gt Enable Cluster Threshold 12 2 Set Volumes of Interest VOI s e Options gt Create Volumes of Interest 12 3 Generate Peak Voxel table e VOI Analysis Window Options gt VOI functions gt Map Peak gt Table 12 4 Generate Cluster Size table e VOI Analysis Window gt Options gt VOI functions gt Center of Gravity gt Table 13 Create Display 2D Display 13 1 3D volume tools gt Spatial Transformation gt Export AMR 11 Brain Voyager 2 4 Abridged Protocol Belyk November 2012 e Axial Slices 36 Slice Width 4mm e click MS to make the grid 5 columns by 6 rows 13 2 CMD SHIFT 4 Click amp drag area to screen capture sends to desktop 13 3 Add screen capture to powerpoint template Annotate with appropriate details 3D Inflated brain 13 3 View Mesh e Translation gt Right Click amp drag e Rotation gt Left Click amp drag e Zoom gt Control Left Click amp drag e Slice Mesh e TRA SAG COR cut e 6Alt Left click amp drag 13 4 Cortex Segmentation e 3D Volume Tools gt Sementation gt Auto Segment check grey matter pial boundary e 3D Volume Tools gt Sementation gt Auto Segment check remove bridges 13 5 Align WM GM cutoff between two peaks of histogram gt Go e Image quality will look poor during construction 13 6 load RECOSM SRF step7 4 13 7 Quality Control
9. an or Across Repeats of a Single Type of Scan 9 1 Before starting make sure that all your vtc files begin with the subject number e g P1 P2 Otherwise Brain Voyager will not be able to sort the data by subject 8 1 The following steps assume the TAL vmr is open and is linked with the vtc and prt 8 2 Analysis gt General Linear Model Single Study CMD G 8 3 Click on Add Pred Do this for as many predictors as there are going to be e g click on it 3 times if there are 3 conditions within the scan that you want to contrast 8 4 To select the epochs for a given condition right click on the condition name in the menu on the right hand side of the Single Study GLM window This will add the appropriate name to the predictor It is critical that the conditions are named consistently across scans 8 5 Apply the HRF to it 8 6 Proceed through the predictors one at a time and repeat this for all the conditions in the scan by right clicking on the appropriate condition name in the right hand menu Brain Voyager 2 4 Abridged Protocol Belyk November 2012 8 7 Within the Single Study GLM window click on Save and save an sdm single study design matrix file 8 8 If you press GO now all predictors will be run simultaneously 8 9 To look at each condition independently Analysis gt Overlay General Linear Model CMD V All predictors are present in a list They can be turned on and off independently by toggling the plus sign in e
10. e As gt as anatomical _IIHC vmr 2 6 Peel off Skull and Dura e Volumes gt Segregate Brain from Head wait e Save As gt as anatomical _ peeled Brain Voyager 2 4 Abridged Protocol Belyk November 2012 2 Spatial Normalization 2 1 If not already open open the ISO_SAG vmr 2 2 3D Volume Tools gt Talairach tab gt check Manual 1 Find AC Point Navigate the cursor to the anterior commissure and hit OK HINT Find the AC before hitting the Find AC Point button Use axial amp sagittal views Control A toggles the crosshair on off Make sure this point is indeed in the midsagittal plane and not off to one side Anterior Commissure shown in red 2 3 2 Find AC PC Plane Rotate the brain in 3 dimensions so that both the Anterior amp Posterior commissure are visible The lower row is the modified image The upper row is the original image Make sure to align rotations in all three planes x y and z i Z look at axial view Rotate until vertical line passes between hemispheres ii Y look at coronal view Rotate until vertical line passes between hemispheres iii X look at saggital view Rotate until posterior commissure is visible hit OK Brain Voyager 2 4 Abridged Protocol Belyk November 2012 Posterior Commissure shown in blue 2 4 3 Transform and then GO saves ACPC trf Use default settings cubic spline interpolation 2 5 Set the 8 Talairach proportional grid reference points Ac
11. gical OR Analysis gt Region of Interest Analysis gt Load Load GCM Plugin Plugins RFX Granger Causality Mapping GCM v2 5 Load from MDM Default settings use the whole run all tasks amp rest minus the first last 5 volumes Epoch Selection gt Go gives filename tag RUNCOND interval For task specific analysis check use protocol Epoch Selection gt check use protocol condition per VTC gt choose a task Go 15 Inter regional correlations RFX This section will describe how to perform whole brain correlations with a seed region Importantly we use the residuals from the GLM to avoid looking at simple co activation We look for correlations that are NOT explained by mutual involvement in the task 14 Brain Voyager 2 4 Abridged Protocol Belyk November 2012 15 1 Make a voi for the seed region see previous sections 15 2 Extract time course for the seed region for each Link VTC e VOI window gt Options gt VTC Data gt choose an ROI gt Table e Repeat for all conditins and subjects 15 3 Extract model time course e Single study GLM gt click task of interest gt HRF gt Save 15 4 Combine 15 2 and 15 3 into an excel spreadsheet e Manaully change the file extensions to TXT e Open in excel gt Load file gt Delimited gt check space e Repeat for all files then combine into single spreadsheet e 1columns per task per subject from 15 2 1 for the model from 15 3 15 5 Run GLMs in R or other statistical p
12. ion B 7 Save PRT Brain Voyager 2 4 Abridged Protocol Belyk November 2012 Il Anatomical Processing 1 Create VMR File 1 1 Click on Project Wizard from Menu bar 1 2 Select VMR project 1 3 Select DICOM format 1 4 Name in Subject_Run format 1 5 Select Yes to the question about renaming the DICOM files 1 6 Click on file in Project Source Files window and click OK If not it will not work 1 6 Ensure parameters are correct Clock OK to close Contrasts and Brightness window 1 7 Select Yes to transforming to iso voxel data 1 8 Select Yes to transforming to BV s standard sagittal orientation 1 12 Keep the ISO_SAG vmr open for next step 2 Anatomical Preprocessing QX2 4 or later This step is generally optional but will help with coregistration and automatic Talairaching If the VMR will eventually be used to create a mesh it s worth doing this carefully 2 1 Brightness contrast ballpark it e Volumes gt Brightness amp Contrast 2 3 Manually correct white matter e 3D tools gt segmentation tab gt min 140 max 170 gt grow region cursor in WM e Adjust min max to capture less more intense voxels gt Smooth should capture most WM e If necessary manually draw to capture additional voxels time consuming 2 4 Intensity InHomogeneity Correction IHC e Volumes gt Inhomogeneity Correction V16 tools check mask creation gt Correct IIH 2 5 Save it File gt Save Secondary VMR gt as IIHC vmr File Sav
13. nd is linked with the vtc and prt 9 3 Analysis gt General Linear Model Single Study CMD G 9 4 Click on Add Pred Do this for as many predictors as there are going to be Unlike step 8 above the number of predictors is going to reflect the number of SCANS that are being compared Hence if you are comparing tasks across 4 scans you need to specify 4 predictors 9 5 Create a list of the ordering of the scans that you are going to compare 4 in this case 9 6 Starting in scan 1 go to predictor 1 Now select the epochs of task to be analyzed Apply the HRF to it 9 7 Name that predictor with the name of the scan 9 8 Name the remaining predictors with the remaining scan names But leave them blank don t select any epochs These are the dummy coded predictors for scan 1 They have no task associated with them within scan 1 9 9 Click on Save on the lower left of the Single Study GLM window and name the predictor file 9 9 Repeat this whole procedure for the next scan by linking the vtc file for scan 2 to the anatomical However this time predictor 2 will be the one whose epochs will be selected and HRF d Predictors 1 3 and 4 will be dummy coded NOTE the predictors have to be named identically as within scan 1 Otherwise this will not work 9 11 Repeat this for all of the scans to be compared 9 12 Run Analysis gt General Linear Model Multi Study Multi Subject CTL U Brain Voyager 2 4 Abridged Protocol Belyk N
14. ovember 2012 9 13 Click on Add to List Doing this one at a time enter the vtc for each scan as well as its associated predictor file 9 14 Within the window for General Linear Model Multi Study Multi Subject click on Save and save an mdm multiple study design matrix file 9 15 Run the analysis by clicking on z transform and Separate subject predictors Press GO 9 16 To select individual conditions or to do contrasts between condition click on Analysis gt Overlay General Linear Model CTL V The individual conditions should be listed there You can create contrasts by toggling and for the boxes for each condition 9 17 To run a Conjunction Analysis e Analysis gt Overlay General Linear Model e Click on Add Contrast 1 contrast per condition e Assign one condition per contrast i e 1 0 0 1 e Click the conjunction analysis radio box for each contrast and press OK to run 10 Random Effects Analysis for Multi Subject Results 10 1 Before starting make sure that all your vtc files begin with the subject number e g P1 P2 Other wise Brain Voyager will not be able to sort the data by subject 10 2 Before starting make sure you have an SDM file with the predictors In theory you only need one file since all the scans will use the same design matrix predictors 10 3 Analysis gt General Linear Model Multistudy Multisubject CMD U 10 4 Populate the General Linear Model Multistudy Multis
15. registration tab e Press Select FMR Use the preprocessed fmr created in Step 4 e Press Align gt Fine Tuning Alignment gt Manual Alignment e Press GO This creates the IA trf and FA trf files e Initially things look quite strange The images won t look right until after the alignment step Brain Voyager 2 4 Abridged Protocol Belyk November 2012 5 3 Target display options inspect for proper alignment blend Edges blend Mosaic blend Transparent Edges green should map onto anatomical boundaries 5 4 Check for alignment by traveling through the lateral ventricles in axial and coronal views To do the coronal view use the shift function with the up and down arrows 5 5 If Initial Alignment is bad then manual fixing is a last resort e Adjust translation rotation parameters until coregistration appears subjectively good e Align Fine Tuning Alignment gt Manual Alignment 5 6 Close all windows 6 Create and Link vtc file 6 1 Open vmr in Talairach form anatomical TAL 6 2 Analysis gt Create 3D Aligned Time Course VTC 6 3 Load files from previous steps e fmr pre processed e Autofill the IA trf and FA trf by pressing Auto Fill e Click To Tal e Broese for ACPC trf and ACPC tal in the Anatomical folder 6 4 Click GO e nothing changes visually to the images when you do this 6 5 Link VTC e Analysis gt Link 3D Time Course VTC File CMD K e BV usually directs you to the vtc file when browsing e Click O
16. rotocol Belyk November 2012 10B RFX ANOVA as an alternative to contrasts in GLM 10B 1 Run RFX as in section 10 10B 2 Set up a model for ANOVA e Analysis gt ANCOVA RFX gt Design Set number of factors levels amp covariates gt Go 10B 2 Choose a factors levels to display e Analysis Overlay RFX ANCOVA gt choose a factor or specify a contrast vector 11 Create ROIs 11 1 Define VOI from clusters e Set criterion to desired threshold ie FDR or Bonferonni e Options gt create volumes of interest from map clusters 11 2 Draw an ROI by hand e 3D volume tools gt segmentation gt enable e CMD left click to draw ROI e 3D volume tools gt segmentation gt options gt define ROI 11 3 Analyze ROI s e Analyze gt region of interest analysis CMD R gt options gt VOI GLM gt VOI GLM e Analyze gt region of interest analysis CMD R gt options gt VOI GLM gt table 11 4 Create Mask from ROIs e Select ROI in ROI analysis menu e Volume of Interest Analysis Window gt Options gt VOI Functions gt Use selected Create Mask 11 5 Apply Mask to Single study GLM e Single Study GLM gt Options gt masking Options gt Enable Mask Restriction gt browse for MSK e Load an existing SDM file e g from a previous unmasked GLM gt GO 11 6 Apply Mask to Multi Study GLM e Mutli Study GLM gt Options gt Enable Mask Restriction gt browse for MSK gt Ok e Load existing MDM gt GO Data Displaying 12 Voxel Reports occasion
17. the brain e See section 11 on ROI s for mask creation e In GLM window gt Options gt Masking Options gt Enable Mask restrictions gt browse 7 5 If sdm file is already created load it by pressing Load on the left side 7 6 Statistical Options e Analysis gt Overlay Volume Maps CMD M e Deselect negative activations e Choose multiple comparisons solution FDR or Bonferroni Bonferroni is under Volume Maps gt Map Options e Consider Enabling Cluster Threshold 7 7 Complex Subtractions e Analysis gt Overlay General Linear Model CMD V e conditions e Note It is not recommended to manually specify Rest This is done automatically via baseline 7 8 Save GLM analysis e Analysis gt Overlay Volume Maps CMD M gt Save VMP 7 9 To load a GLM analysis first open the Talairach vmr e Analysis gt Overlay Volume Maps CMD M gt Load VMP 7 10 To save a sliceview of the GLM 3D volume tools gt Spatial Transformation tab Export AMR This automatically saves an amr file Pick 36 slices at 4 mm slice distance When done make this into a 5 column x 6 row matrix Screen capture this using Grab and insert into Powerpoint 7 11 If starting from scratch open up the Talairach vmr and link it to the vtc 7 12 In order to run a new GLM analysis from a different PRT file go to Analysis gt Stimulation protocol and click on Load PRT Select the new PRT to be run 8 Contrasts for Multiple Conditions WITHIN a Single Sc
18. tually the manual says that finding the AC point again is unnecessary Start with the PC One at atime click on each of PC AP PP SP IP RP and LP Once you ve found the relevant point click Set Point Bringing the cross hair on and off by toggling Control A to is very useful at this step Note that pressing the SHIFT key makes the arrows work in the anteroposterior directions Be vigilant about getting the extreme points of each range 2 6 Click on Save TAL and Save this creates the ACPC tal 2 7 Click on ACPC gt TAL and GO this creates the _TAL vmr Use default of Trilinear interpolation 2 8 Close all windows 2B Semi Automatic Spatial Normalization QX2 4 or later Warning this algorithm gives fairly mediocre results It needs to be supervised and corrected manually Best results if Anatomical pre processing has been applied Section1B 2B 1 Detect Midsaggital plane then corpus collosum and finally Anterior and Posterior Commisures e Volumes gt 3D Volumes tool Talairach gt Detect MSP AC PC 2B 2 Uses contrast between grey matter and background intensity to detect bonding box e Volumes 3D Volumes tool Talairach gt Auto Detect 2B 23 Alternatively use the fully automatic method Automatic method Combines 2B 1 and 2B 2 e Volumes3D Volumes tool Talairach gt Auto AC PC TAL Brain Voyager 2 4 Abridged Protocol Belyk November 2012 lll Functional Processing 3 Create fmr Project one for each scan 3 1 Click on Project Wi
19. ubject design matrix e Click on Add to List e Browse fora VTC e Browse for an SDM file this should be common for each scan e Repeat for each scan this goes more quickly if you have an SDM paired with each VTC e NOTE don t confuse the single study design matrix with head motion correction file both are SDM files 10 5 Verify Design matrix MDM window CMD U gt Design Matrix 10 6 Click on RFX GLM radio box before saving 10 7 Save MDM multisubject design matrix If you have a lot of subjects it is best to save this file early on and just keep on using save as to replace the file Otherwise if you make an error you could lose all your work 10 8 Select a type of analysis for the multisubject data e Select RFX GLM box for a random effects analysis to average ACROSS subjects Separate subject predictors will be automatically selected e Fixed effects analysis is used if averaging WITHIN subject To average across scans for a single subject select nothing except the z transform default Select separate study to keep all predictors separate 10 8b If you re comfortable with design matrices you can get a nice sanity check at this stage e Multistudy GLM window gt Design Matrix gt Design Matrix Plot 10 9 Click GO to run the analysis 10 10 In order to save the results go to Analysis gt Overlap General Linear Model CMD V In that window click on Save GLM 10 Brain Voyager 2 4 Abridged P
20. zard from Menu bar 3 2 Project name in format Subject Run NOTE If you do not name the fmr starting with the subject number there will be big problems when running the random effects analysis 3 3 Select source file 3 4 Select Yes to the question about renaming the DICOM files 3 5 Click on file in Project Source Files window and click OK If not it will not work 3 6 Verify parameters slices volumes TR etc e Correct TR if necessary it is often incorrect e Select volumes to skip if necessary e Click Verified box e Inspect data for artifacts Options gt Time Course Movie 3 7 Attach prt file Under Reference protocol PRT file 3 8 Close FMR properties window 3 9 Keep fmr file open for next step 4 Pre process data 4 1 If not already open open the fmr file 4 2 Analysis gt FMR Pre processing e Do NOT select Slice Scan Time Correction Unless you will use Granger Causality Modelling e Select 3D motion correction e Select Spatial Smoothing opportunity 1 e Select Temporal Filtering Advanced gt Temporal Filtering gt Options gt Frequency Space Filter gt Hz gt 0 0078125 Hz 1 128 per S COPY amp PATE cut off value from protocol 4 3 Note maximum movement in any direction e See last page for legend 4 4 Save head motion plot e Right click on plot gt Save snapshot 4 4 When done close all windows 5 Coregister FMR gt VMR in native space 5 1 Open vmr in native space ISO_SAG 5 2 3D volume tools gt Co
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