Magnetic Resonance Imaging Free Surfer Software

fMRI Analysis with the FreeSurfer Functional Analysis Stream (FS-FAST) Preprocessing, First Level Analysis, and Group Analysis

*OverviewAtlas SpacesDirectory StructurePreprocessingSetting up First-Level Analysis and ContrastsGroup AnalysisSetting upCorrection for multiple comparisons

Time-series functional analysisEvent-related, Blocked, Retinotopy, Functional ConnectivityBuilt on FreeSurferSurface-, Volume-, ROI-basedGroup AnalysisHighly AutomatedCommand-line drivenMatlab/Octave, AFNI, and FSL used in the backgroundFSFAST

Respect the inherent geometry of the brain structures (Smoothing and Clustering)Cortex 2DSubcortical 3DRequires that analysis be done in three spaces:Left HemisphereRight HemisphereSubcortical AreasNot simple volumetric-based for all voxels!Philosophy

* FS-FAST Preprocessing1B0 distortion correction not documented yet.2Eventually will be done with CVS.Atlas SpacesMCSTCRaw 3D+TimeSpatialNormalization+ B0 Correction1Masked 2DSmoothingMasked 2DSmoothingMasked 3DSmoothing12 DOFAffine22D+Time2D+Time3D+Time

* FS-FAST AnalysisFirst LevelGLMFirst LevelGLMFirst LevelGLMX1, C1Higher Level GLMHigher Level GLMHigher Level GLMXG, CG2D Multiple ComparisonsCorrection2D MultipleComparisonsCorrection3D Multiple ComparisonsCorrectionFinalCorrectionAtlas SpaceMasked, Smoothed

* Surface MaskingRemove medial wallIntersect with functional brain mask2D Smoothing only inside mask Later individual subjects masks merged (intersection).

* Volume (Subcortical) MaskingAnatomyMaskSubCorProbability(40 Subj)Remove most of cortexRemove some WM and CSFIntersect with functional brain mask3D Smoothing only inside mask Later individual subjects masks merged (intersection).Tip: use compressed NIFTI files (nii.gz)

*Typical Volume-based AnalysisSingle map, activation in both cortical and subcortical GM.fBIRN Group n=18, distractor-vs-fix

*FSFAST AnalysisSubcortical(no cortical) Left HemiRight HemiThree mutually exclusive maps

*Recombining Cortical and SubcorticalVisualization only!!

* Correction for Multiple ComparisonsCluster-basedPerformed separately in each space2D clustering for Left and Right Hemispheres3D clustering for MNI305Cluster table for each individual spaceFinal cluster table is union of individual spaces

Analyze anatomicals in FreeSurferUnpack each subject (dcmunpack,unpacksdcmdir)Create subjectname file.Copy paradigm files into run directoriesConfigure analyses (mkanalysis-sess, mkcontrast-sess)Preprocess (preproc-sess)First Level Analysis (selxavg3-sess)Higher Level Analysis (isxconcat-sess, mri_glmfit )Correction for Multiple Comparisons (mri_glmfit-sim)FSFAST Pipeline Summary*

ProjectSess01Sess02Sess03bold003005006f.nii (raw data)FSFAST Directory Structurebold1. Project2. Session3. FunctionalSubdirectory(FSD, bold)4. Run5. Raw Time-Series DataAutomation Requires Structure!*

Folder where all/most of your data reside (can use symbolic links to data too)Directory where you will run most commandsNOT the same as $SUBJECTS_DIRProject Directory*

All the data collected between the time you put a subject into the scanner until you take him/her out.May include data across breaksAll one subjectData from one subject may be spread over different sessions (eg, longitudinal study)Session does not necessarily equal SubjectFolder name can be anything.Session Directory*

All the data associated with a given paradigmMost people just have one paradigm and so only one FSDUsually called boldDefault is boldFunctional Subdirectory (FSD, bold)*

All the data collected between pressing the Apply button and the end of the scan.Eg, 150 time points (TPs)Raw functional data stored in this folderUsually called f.nii or f.nii.gzRaw data will be in native functional space, eg, 64x64x30, 3.125mm x 3.125mm x 6mmFolder name will be 3-digit, zero-padded number, eg, 002, 014Run Folder/DirectoryProjectSess01bold003f.nii (raw data)*

ProjectSess01Sess02Sess03bold003005006f.nii (raw data)FSFAST Directory Structurebold1. Project2. Session3. FunctionalSubdirectory(FSD, bold)4. Run5. Raw Time-Series DataAutomation Requires Structure!*

Unpack raw data from DICOMAdd paradigm filesAdd subjectname fileSetting Up the Directory StructureThings you need to do before running automated commands:*

unpacksdcmdir Siemens onlydcmunpack Siemens or GE (not sure about Philips)Manually1. Unpacking: Creating the Directory Structure from DICOM FilesGetting help: dcmunpack -help

Get a summary of the scans in a DICOM directory dcmunpack src dicomdir -martinosUnpack: cd ProjectDir dcmunpack src dicomdir -martinos trg sess01 run 3 bold nii f.nii run 5 bold nii f.nii run 6 bold nii f.nii

Sess01bold003005006f.niif.niif.nii*

Codes Stimulus Schedule Simple Text FileManually copy into Run Folder2. Add Paradigm File(s)Sess01bold003005006f.niiodd.even.parf.niiodd.even.parf.niiodd.even.par All have the same name May have different content Different codings have different namesodd.even.par*

Codes Stimulus Schedule (and Weight)Four ColumnsOnset Time (Since Acq of 1st Saved Volume)Stimulus Code (0, 1, 2 ,3 )Stimulus Duration Stimulus Weight (default is 1)Any other columns ignoredSimple Text FileCode 0 Always Fixation/NULLWeight for parametric modulationParadigm File*

3. Add subjectname fileIntegration with FreeSurfer anatomical analysisSubject name is name passed to recon-all, eg,recon-all all subject bert$SUBJECTS_DIR/bertCreate a text file called sess01/subjectname, the content of the file will be, eg, bert (no quotes)Sess01bold003005006f.niiodd.even.parf.niiodd.even.parf.niiodd.even.parsubjectname*

ProjectSess01Sess02Sess03bold003005006FSFAST Directory Structurebold1. Project2. Session3. FunctionalSubdirectory(FSD, bold)4. Run5. Raw Time-Series Dataf.niiodd.even.parf.niiodd.even.parf.niiodd.even.parsubjectnamesubjectnameboldsubjectname*

Congratulations: You are now ready to start running the automated commands but before you do *

*ProjectSess01Sess02Sess03Session Id File (SessId) Text file with a list of sessions to process Easy way to keep track of groups Can have more than one A good way to parallelize

FS-FAST Commands will often take a SessId file as input:selxavg3-sess sf sessid Will run for all sessions found in sessid

Alternatively, selxavg3-sess s Sess01 s Sess02 s Sess03sessidSess01Sess02Sess03

OK, now you are ready to start running the automated commands *

First-Level Analysis Time-series analysis Everything inside of a functional subdir (all runs) Preprocessing GLM AnalysisSess01bold003005006f.niiodd.even.parf.niiodd.even.parf.niiodd.even.parsubjectnameProject*

Preprocessing Registration Template Creation Motion Correction Slice-timing correction (if using) Functional-Anatomical Registration Mask creation Intensity normalization, Part 1 Resampling raw time series to mni305, lh, and rh Spatial smoothing

B0 distortion correction not documented yet*

Preprocessing Command preproc-sess sf sessids surface fsaverage lhrh mni305 fwhm 5 per-runCommand Name Session Id File Surface-based (lh and rh of fsaverage)Volume-based in mni305 (subcort)Smoothing 5mm FWHMRun-wise MC+registrationpreproc-sess -help Preprocess all runs of all sessions Can take a long time!*

Directory Structure after PreprocessingFinal data in atlas space:fmcpr.sm5.fsaverageLots of other intermediate filesLots more boring detailsbold003005f.niiodd.even.partemplate.niitemplate.logfmcpr.niifmcpr.mcdatmcprextregregister.dof6.datglobal.meanval.datfmcpr.sm5.fsaverage.lh.niifmcpr.sm5.fsaverage.rh.niifmcpr.sm5.mni305.2mm.niiSess01Project*

First Level GLM AnalysisSpecify Task ModelEvent-related or BlockedAB-Blocked (Periodic two condition)RetinotopyTask timing (Paradigm file)Hemodynamic Response Function (HRF)ContrastsSpecify Nuisance and Noise ModelsLow frequency driftsTime point exclusionMotion RegressorsOther (Physiology, RETROICOR)Temporal Whitening*

*Example: Odd Even Blocksy = X * bData fromone voxelDesign MatrixRegressors=Raw Time Series

First Level GLM Analysis: WorkflowDo these two steps once regardless of number of sessions:Configure Analysis collection of parameters, mkanalysis-sessCreate Contrasts (mkcontrast-sess)Dont even need data to do thisDo this for each session:Perform Analysis (selxavg3-sess)*

Configure First Level GLM Analysiscd ProjectDirmkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

*

Configuration: Analysis Namemkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

ProjectSess01Sess02oddeven.sm5.lhanalysis.infoAnalysis Name name used toreference this collection of parameters. Use a different name for a different set of parameters.*

Configuration: Preprocessingmkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

Preprocessing options indicate whatthe source time-series file name will be.bold003005fmcpr.sm5.fsaverage.lh.niifmcpr.sm5.fsaverage.rh.niifmcpr.sm5.mni305.2mm.nii*

Configuration: Preprocessingmkanalysis-sess -analysis oddeven.sm5.mni305 -mni305 -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

A different analysis is needed for each space (lh, rh, and mni305)bold003005fmcpr.sm5.fsaverage.lh.niifmcpr.sm5.fsaverage.rh.niifmcpr.sm5.mni305.2mm.nii*

Configuration: Stimulus Timingmkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

bold003005fmcpr.sm5.fsaverage.lh.niifmcpr.sm5.fsaverage.rh.niifmcpr.sm5.mni305.2mm.niioddeven.par*

Configuration: Task Typemkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

Event-related and blocked are the same. Other possibilities are: -abblocked -retinotopy*

Configuration: HRF Modelmkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

Other options: -fslhrf NDerivaties -fir PreStim TotTimeWindow-gammafit 2.25 1.25SPMFSLFSFAST SPM Canonical HRF 0 Derivatives*

Configuration: Reference Event Durationmkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

Just set this to the duration of your event in seconds. *

Configuration: Nuisance Drift Modelingmkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

2nd Order Polynomial. This is the default. 0: mean offset 1: temporal trend 2: quadratic trend

Can also specify a high-pass filter with -hpf CutOffHzwhere CutOffHz is the cut-off frequency in Hz (eg, .01). Careful with this.*

Configuration: Nuisance Motionmkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

Use Motion Correction parameters as nuisance regressors (good idea?). Can specify arbitrary regressor files with nuisreg file N. bold003005f.niiodd.even.partemplate.niitemplate.logfmcpr.niifmcpr.mcdatmcprextreg*

Configuration: Excluding Time Pointsmkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

Skip the 1st 4 time points. Do not need to adjust stimulus timing. Alternative: -tpexclude tpexclude.dat to remove any TP. Good for motion.bold003005f.niiodd.even.partemplate.niitemplate.logfmcpr.niifmcpr.mcdatmcprextregtpexclude.dat*

Configuration: Why TR and NCond?mkanalysis-sess -analysis oddeven.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm oddeven.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run

It could get this from the data and paradigm files, but this command is set up to run without the need of any data, so it needs to know the TR and number of conditions.

Number of conditions is the number of Non-Fixation/Non-NULL conditions.2 = Odd + Even*

*Contrasts: Odd Even Blocksy = X * bData fromone voxelDesign MatrixRegressors=Raw Time Series Two task conditions One nuisance regressor Need weight for each conditionDoes the hemodynamic response amplitude to the Odd stimulus differ from that of Even?g = 1*bOdd -1* bEven C = [+1 -1] Contrast Matrix

Configuration: ContrastsLinear combination of regression coefficients (COPE, CON)Weight for each conditionEmbodies a hypothesis: Does the hemodynamic response amplitude to the Odd stimulus differ from that of Even? C = [+1 -1]

mkcontrast-sess -analysis oddeven.sm5.lh -contrast odd-vs-even -a 1 -c 2

paradigm file*

Configuration: Contrasts-analysis as created by mkanalysis-sess

mkcontrast-sess -analysis oddeven.sm5.lh -contrast odd-vs-even -a 1 -c 0

ProjectSess01oddeven.sm5.lhanalysis.infoodd-vs-even.mat*

Configuration: Contrasts-contrast ContrastNamename used to reference this contrastunique within the given analysisCreates ContrastName.mat (matlab)

mkcontrast-sess -analysis oddeven.sm5.lh -contrast odd-vs-even -a 1 -c 0

ProjectSess01oddeven.sm5.lhanalysis.infoodd-vs-even.mat*

Specifying Contrast WeightsActive positive, Control negativeOdd vs Even means Odd-EvenParadigm File Encoding

mkcontrast-sess -analysis oddeven.sm5.lh -contrast odd-vs-even -a 1 -c 2

paradigm fileConditions with a get +1Conditions with c get -1Contrast Matrix C = [+1 -1]*

Odd vs FixationActive positive, Control implicitOdd vs Fixation means Odd-FixationDo not need Fixation-OddParadigm file coding

mkcontrast-sess -analysis oddeven.sm5.lh -contrast odd-vs-fix -a 1 -c 0

paradigm fileContrast Matrix C = [1 0]Implicit contrast vs Fixation*

Configuration: Three ConditionsHappySadMad

Hypothesis: response to Happy is different than the average response to Sad and Mad (Happy =? (Sad+Mad)/2)

mkcontrast-sess -analysis faces.sm5.lh -contrast happy-vs-sadmad -a 1 -c 2 -c 3C=[1 -0.5 -0.5]Hypothesis: response to Happy is different than that to Mad

mkcontrast-sess -analysis faces.sm5.lh -contrast happy-vs-mad -a 1 -c 3Note: Condition 2 (Sad) not represented (set to 0)C = [1 0 -1]*

Configuration: Summarymkanalysis-sess, mkcontrast-sessNeed configuration for lh, rh, and mni305Specify: Preproc, Task, Nuisance, Noise, ContrastsDoes not do analysis, just creates configurationDo once for each parameter set (space)Do once regardless of number of sessionsShould take a few seconds to run

ProjectSess01oddeven.sm5.lhanalysis.infoodd-vs-fix.mat*

First-Level GLM Analysiscd ProjectDirselxavg3-sess sf sessidfile analysis oddeven.sm5.lh Finds raw data, paradigm file, external regressors, etcConstructs design and contrast matricesCombines runs together using smart concatenation (1st and 2nd level)Performs GLM fit at each voxelTests contrasts at each voxelAll sessions specified in sessid fileMay take a few hours, depending on how many sessionsDoes not re-run if data are up-to-dateWill run preprocessing if not done alreadyRequires matlab or octave*

After First Level AnalysisProjectSess01boldoddeven.sm5.lhodd-vs-evences.niicesvar.niisig.niices - contrast effect size, COPE (FSL), CON (SPM)cesvar - contrast variance VARCOPE (FSL)sig = -log10(p)*

First Level Analysis: VisualizationSurface-based analyses:tksurfer-sess s session analysis oddeven.sm5.lh c odd-vs-fixtksurfer-sess s session a oddeven.sm5.rh c odd-vs-fix

Volume-based analyses (freeview can also be used):tkmedit-sess s session a oddeven.sm5.mni305 c odd-vs-fixOne session at a time (-s session, NOT sf sessidfile)Can specify multiple contrasts, eg, c odd-vs-fix c even-vs-fix c odd-vs-evenOr all contrasts with -call

Note Shortcut: -a instead of -analysis and -c instead of contrast*

First Level Analysis: VisualizationNo activation in medial wall

Individual subject shown on fsaverage anatomyCan show/analyze on individual anatomy.No activation in cortexMasking*fBIRN probe-vs-fix

After First Level AnalysisProjectSess01boldoddeven.sm5.lhodd-vs-evences.niicesvar.niiSess02boldoddeven.sm5.lhodd-vs-evences.niicesvar.niiSess03boldoddeven.sm5.lhodd-vs-evences.niicesvar.nii1. Project2. Session3. FunctionalSubdirectory(FSD, bold)4. Analysis Folder5. Contrast Folder6. Contrast Values*

* FS-FAST AnalysisFirst LevelGLMFirst LevelGLMFirst LevelGLMX1, C1Higher Level GLMHigher Level GLMHigher Level GLMXG, CG2D Multiple ComparisonsCorrection2D MultipleComparisonsCorrection3D Multiple ComparisonsCorrectionFinalCorrectionAtlas SpaceMasked, Smoothed

Group/Higher Level Analysis: Consolidationcd ProjectDirisxconcat-sess -analysis oddeven.sm5.lh-contrast odd-vs-even-sf group1.sessid -o group1ProjectSess01boldoddeven.sm5.lhodd-vs-evences.niicesvar.niiSess02boldoddeven.sm5.lhodd-vs-evences.niicesvar.niiSess03boldoddeven.sm5.lhodd-vs-evences.niicesvar.niigroup1oddeven.sm5.lhodd-vs-evences.niicesvar.niiisxconcat-sess -helpLike mris_preprocin anatomical stream*

ProjectSess01boldoddeven.sm5.lhodd-vs-evences.niiSess02boldoddeven.sm5.lhodd-vs-evences.niiSess03boldoddeven.sm5.lhodd-vs-evences.niigroup1oddeven.sm5.lhodd-vs-evences.niicesvar.niiisxconcat-sess -analysis oddeven.sm5.lh-contrast odd-vs-even-sf group1.sessid -o group1One frame/time point for each sessionOrder is IMPORTANT!!!Order will be as listed in group1.sessidGroup/Higher Level Analysis: Consolidation*

Group/Higher Level AnalysisProjectgroup1oddeven.sm5.lhodd-vs-evences.niicesvar.niicd ProjectDircd group1/oddeven.sm5.lh/odd-vs-even

mri_glmfit --surf fsaverage lh --y ces.nii --wls cesvar.nii --fsgd group1.fsgd --C group.con1.mtx --C group.con2.mtx --glmdir glm.groupSee FreeSurfer Group Analysis, including correction for multiple comparisons.http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysismri_glmfit helpglm.group*

Group/Higher Level Analysismri_glmfit --surf fsaverage lh --y ces.nii --wls cesvar.nii --fsgd group1.fsgd --C group.con1.mtx --C group.con2.mtx --glmdir glm.groupSurface-based analysis on the left hemisphere of fsaverage. For right hemisphere, use surf fsaverage rh.For mni305, so not specify surf.*

Group/Higher Level Analysismri_glmfit --surf fsaverage lh --y ces.nii --wls cesvar.nii --fsgd group1.fsgd --C group.con1.mtx --C group.con2.mtx --glmdir glm.groupLower-level contrast input data, one frame/time point for each subject.*

Group/Higher Level Analysismri_glmfit --surf fsaverage lh --y ces.nii --wls cesvar.nii --fsgd group1.fsgd --C group.con1.mtx --C group.con2.mtx --glmdir glm.groupLower-level contrast variances, one frame/time point for each subject.Performs weighted least squares(Pseudo-Mixed Effects)*

Group/Higher Level Analysismri_glmfit --surf fsaverage lh --y ces.nii --wls cesvar.nii --fsgd group1.fsgd --C group.con1.mtx --C group.con2.mtx --glmdir glm.groupFSGD file must have same orderof sessions as sessidfile used when running isxconcat-sessisxconcat-sess -analysis oddeven.sm5.lh-contrast odd-vs-even-sf group1.sessid -o group1*

Group/Higher Level Analysismri_glmfit --surf fsaverage lh --y ces.nii --wls cesvar.nii --fsgd group1.fsgd --C group.con1.mtx --C group.con2.mtx --glmdir glm.groupHigher Level/Group contrasts. Eg, Normal vs SchizophreniaEasily confused with lower level contrasts (eg, odd-vs-even).Projectgroup1oddeven.sm5.lhodd-vs-evences.niicesvar.niiglm.groupgroup.con1sig.niigroup.con2sig.nii*

Surface-based Correction for Multiple ComparisonsProjectgroup1oddeven.sm5.lhodd-vs-evences.niicesvar.niicd ProjectDircd group1/oddeven.sm5.lh/odd-vs-even

mri_glmfit-sim --glmdir glm.group --cache pos 2 --cwpvalthresh .05 --3spacesglm.groupgroup.con1sig.nii 2D Cluster-based Correction at p < .05Masking*

Surface-based Correction for Multiple ComparisonsProjectgroup1oddeven.sm5.lhodd-vs-evences.niicesvar.niimri_glmfit-sim --glmdir glm.group --cache pos 2 --cwpvalthresh .05 --3spacesglm.groupgroup.con1sig.nii 2D Cluster-based Correction at p < .05*

Surface-based Correction for Multiple Comparisonsmri_glmfit-sim --glmdir glm.group --cache pos 2 --cwpvalthresh .05 --3spaces

2D Cluster-based Correction at p < .05Bonferroni correction across 3 spaces: lh, rh, and subcort*

Correction for Multiple Comparisons Output (Surface)mri_glmfit-sim --glmdir glm.group --cwpvalthresh .05 --cache pos 2 --3spacesglm.groupgroup.con1sig.niicache.th20.pos.sig.cluster.nii map of significance of clusterscache.th20.pos.sig.ocn.annot annotation of significant clusterscache.th20.pos.sig.cluster.summary text file of cluster table (clusters, sizes, MNI305 XYZ, and their significances)*

Projectgroup1oddeven.sm5.lhodd-vs-evences.niicesvar.niiisxconcat-sess -analysis oddeven.sm5.mni305-contrast odd-vs-even-sf group1.sessid -o group1

oddeven.sm5.mni305odd-vs-evences.niicesvar.niiGroup MNI305 Analysisoddeven.sm5.rhodd-vs-evences.niicesvar.nii*

Group Subcortical (MNI305) Analysismri_glmfit --y ces.nii --wls cesvar.nii --fsgd group1.fsgd --C group.con1.mtx --C group.con2.mtx --glmdir glm.group Command-line is very similar to surface No surf fsaverage lhSurface-base commandmri_glmfit --surf fsaverage lh --y ces.nii --wls cesvar.nii --fsgd group1.fsgd --C group.con1.mtx --C group.con2.mtx --glmdir glm.group*

Volume-based Correction for Multiple ComparisonsProjectgroup1oddeven.sm5.mni305odd-vs-evences.niicesvar.niicd ProjectDircd group1/oddeven.sm5.mni305/odd-vs-even

mri_glmfit-sim --glmdir glm.group --grf pos 2 --cwpvalthresh .05 --3spacesglm.groupgroup.con1sig.nii 3D Cluster-based Correction at p < .05Masking*

Volume-based Correction for Multiple ComparisonsProjectgroup1oddeven.sm5.mni305odd-vs-evences.niicesvar.niimri_glmfit-sim --glmdir glm.group --grf pos 2 --cwpvalthresh .05 --3spacesglm.groupgroup.con1sig.nii 3D Cluster-based Correction at p < .05*

Volume-based Correction for Multiple Comparisonsmri_glmfit-sim --glmdir glm.group --grf pos 2 --cwpvalthresh .05 --3spaces 3D Cluster-based Correction at p < .05Bonferroni correction across 3 spaces: lh, rh, and subcort*

Correction for Multiple Comparisons Output (Volume)mri_glmfit-sim --glmdir glm.group --grf pos 2 --cwpvalthresh .05 --3spacesglm.groupgroup.con1sig.niigrf.th2.pos.sig.cluster.nii map of significance of clustersgrf.th2.pos.sig.ocn.nii segmentation of significant clustersgrf.th2.pos.sig.cluster.summary text file of cluster table (clusters, sizes, MNI305 XYZ, and their significances)*

Projectgroup1oddeven.sm5.lhodd-vs-evences.niiFull Group Analysisoddeven.sm5.mni305odd-vs-evences.niioddeven.sm5.rhodd-vs-evences.niiglm.groupglm.groupglm.groupSess01boldoddeven.sm5.lhodd-vs-evences.niicesvar.niisig.nii003f.nii (raw data)oddeven.parsubjectname*

Analyze anatomicals in FreeSurferUnpack each subject (dcmunpack,unpacksdcmdir)Create subjectname file.Copy paradigm files into run directoriesConfigure analyses (mkanalysis-sess, mkcontrast-sess)Preprocess (preproc-sess)First Level Analysis (selxavg3-sess)Higher Level Analysis (isxconcat-sess, mri_glmfit )Correction for Multiple Comparisons (mri_glmfit-sim)Publish (publish-sess )FSFAST Pipeline Summary*

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