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Integrating FreeSurfer and FSL FEAT

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Presentation on theme: "Integrating FreeSurfer and FSL FEAT"— Presentation transcript:

1 Integrating FreeSurfer and FSL FEAT

2 Outline Registering FEAT  FreeSurfer Anatomical Automatic (FLIRT)
Manual (tkregister2) Surface-based Group fMRI Analysis Individual Analysis Viewing FEAT output on Anatomical Sampling FEAT output on the surface Mapping FreeSurfer Segmentations to FEAT

3 Registration Template Functional FreeSurfer Anatomical (orig)
Note: Registering the template functional volume to the anatomical volume is sufficient to register the template to the surface.

4 FreeSurfer Registration
Your Data/Software fMRI (FSL, etc) EEG/MEG DTI … FreeSurfer Subject-Specific Volumes Surfaces Thickness ROIs Registration Registration Matrix Affine 4x4 As many as 12 DOF (usually 6) Text file

5 Automatic Registration
First: analyze your data with FEAT reg-feat2anat –featdir fbert1.feat –subject bert Uses BBR to perform 6DOF registration: fbert1.feat/example_func.nii.gz $SUBJECTS_DIR/bert/mri/brainmask.mgz Creates FreeSurfer registration matrix: fbert1.feat/reg/freesurfer/anat2exf.register.dat Also creates: fbert1.feat/reg/freesurfer/anat2std.register.dat This matrix maps standard space to anatomical space and can be used when combining data within subject across data sets reg-feat2anat --help

6 Manual Registration tkregister2 --help
reg-feat2anat –feat fbert.feat --manual Visually inspect registration Manually edit registration (6 DOF) Cf Manual Talairach registration tkregister2 --help

7 Tips Rigid = 6 DOF = No stretching
Use CSF to get a sense of where the folds are Avoid using B0 distortion regions Avoid using ventricles Warning about “edge” of the brain Same Subject, Left-Right Flips

8 Sampling on the Surface
White/Gray Pial White/Gray Pial Half Way Average Projection Fraction --projfrac 0.5

9 Sampling on the Surface

10 Surface-based fMRI Group Analysis

11 Surface-based fMRI Group Analysis
} Functional COPEs fsaverage S1 R1 Subject 1 S2 R2 Can be compared Voxel-for-voxel Subject 2 S3 R3 Subject 3 … mris_preproc reg-feat2anat recon-all

12 Surface-based fMRI Group Analysis (One Run)
Single Run Analyze with FEAT, No smoothing COPEs are in native functional space Subject1 run1.feat stats cope1.nii

13 Surface-based fMRI Group Analysis (One Run)
run reg-feat2anat Subject1 run1.feat reg stats freesurfer cope1.nii reg-feat2anat anat2exf.register.dat – anatomical–example_func registration

14 Surface-based Group fMRI Analysis (One Run)
mris_preproc --out lh.cope1.nii.gz --target fsaverage --hemi lh --iv bert.feat/stats/cope1.nii.gz bert.feat/reg/freesurfer/anat2exf.register.dat --iv greg.feat/stats/cope1.nii.gz greg.feat/reg/freesurfer/anat2exf.register.dat --iv sally.feat/stats/cope1.nii.gz sally.feat/reg/freesurfer/anat2exf.register.dat --iv pat.feat/stats/cope1.nii.gz pat.feat/reg/freesurfer/anat2exf.register.dat Volumes Registrations lh.cope1.mgh – stack of subjects Can map any functional data, eg, zstat, fzstat, cope, pe, etc fsaverage – defines common space (spherical surface) Group analysis same as with a thickness study: surface smoothing, mri_glmfit, mri_glmfi-sim

15 Surface-based fMRI Group Analysis (>1 Run)
Multiple Runs Analyze each run with FEAT, No smoothing COPEs are in native functional space Subject1 run1.feat run2.feat stats stats cope1.nii cope1.nii

16 Surface-based fMRI Group Analysis (>1 Run)
Merge runs with GFEAT with Fixed Effects GFEAT results are in MNI152 Standard Space Subject1 MNI152 run1.feat run2.feat xrun.gfeat cope1.feat stats stats mean_func.nii stats cope1.nii cope1.nii cope1.nii

17 Surface-based fMRI Group Analysis (>1 Run)
run reg-feat2anat on one run anat2std.register.dat – same across all runs Subject1 MNI152 run1.feat run2.feat xrun.gfeat cope1.feat stats reg mean_func.nii stats cope1.nii freesurfer cope1.nii reg-feat2anat anat2exf.register.dat – anatomical–example_func registration anat2std.register.dat -- anatomical–standard MNI152 space registration

18 Surface-based fMRI Group Analysis (>1 Run)
Verify the registration tkregister2 –mov xrun.gfeat/cope1/mean_func.nii.gz --reg run1.feat/reg/freesurfer/anat2std.register.dat --surf Subject1 MNI152 run1.feat run2.feat xrun.gfeat cope1.feat stats reg mean_func.nii stats cope1.nii freesurfer cope1.nii reg-feat2anat anat2exf.register.dat – anatomical–example_func registration anat2std.register.dat -- anatomical–standard MNI152 space registration

19 Surface-based fMRI Group Analysis (>1 Run)
mris_preproc --out lh.cope1.mgh --target fsaverage --hemi lh --iv bert.gfeat/cope1.feat/stats/cope1.nii.gz bert.feat/reg/freesurfer/anat2std.register.dat --iv greg.gfeat/cope1.feat/stats/cope1.nii.gz greg.feat/reg/freesurfer/anat2std.register.dat --iv sally.feat/cope1.feat/stats/cope1.nii.gz sally.feat/reg/freesurfer/anat2std.register.dat --iv pat.feat/cope1.feat/stats/cope1.nii.gz pat.feat/reg/freesurfer/anat2std.register.dat Volumes Registrations lh.cope1.mgh – stack of subjects Can map any functional data, eg, zstat, fzstat, cope, pe, etc fsaverage – defines common space (spherical surface) Group analysis same as with a thickness study: surface smoothing, mri_glmfit, mri_glmfi-sim

20 Surface-based fMRI Group Analysis
Left Hemi Right Hemi fBIRN Group n=18, working memory, distractor-vs-fix

21 Individual Subject Integration

22 Viewing Functional Activation on the Volume
tkmedit bert orig.mgz -aux brain.mgz -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 –fmax seg aparc+aseg.mgz Visual, Auditory, Motor Thresholds depend on the nature of the data, Eg, for zstat image, 2.3 means z > 2.3 Can be changed with View->Configure->FunctionalOverlay Can display any functional data, eg, zstat, fzstat, cope, pe, etc

23 Volume Viewing Red/Yellow + Blue/Cyan - Seg Opacity ROI Average
ROI Count place holder

24 Viewing FEAT Stats on the Surface
tksurfer bert rh inflated -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 -fmid 3.3 -fslope 1 Visual, Auditory, Motor Can display any functional data, eg, zstat, fzstat, cope, pe, etc

25 Surface Viewing Red/Yellow +,Blue/Cyan - Parcellation Outline
ROI Average ROI Count

26 Mapping Automatic Segmentations
aseg.mgz aparc+aseg.mgz lh.aparc.annot $FREESURFER_HOME/FreeSurferColorsLUT.txt Maps numerical index to ROI name, eg Left-Hippocamus = 17

27 Mapping Automatic Segmentations
aseg2feat --feat fbert.feat –aseg aparc+aseg In the functional FOV, creates: fbert1.feat/reg/freesurfer/aseg+aparc.nii.gz Create Text Summary Table (nvox, mean cope, std cope, etc) mri_segstats --seg fbert1.feat/reg/freesurfer/aparc+aseg.nii.gz --nonempty --ctab-default --in fbert.feat/stats/cope1.nii.gz --sum fbert1.sum.txt Can summarize any functional data, eg, zstat, fzstat, cope, pe, etc

28 Make and View ROI Make a binary mask of the left putamen:
Note: 12 = Left Putamen, see $FREESURFER_HOME/FreeSurferColorsLUT.txt fslmaths ./fbert1.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 12 -uthr 12 ./fbert1.feat/reg/freesurfer/lh.putamen.nii.gz tkmedit bert orig.mgz -aux brain.mgz -overlay ./fbert1.feat/reg/freesurfer/lh.putamen.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh seg aparc+aseg.mgz

29 Practical Data Sensory-motor study
Blocked Design (15sec OFF, 15 sec ON) One subject – “bert” Two runs (TR=3, 85 time points) FEAT has been run on both runs (FWHM=5) Combined with GFEAT FFx One-Sample Group Mean (OSGM) Actually, all analysis steps already performed!

30 Practical Automatic registration (<5 min) Manual registration
View FEAT results on subject’s anatomy (aparc+aseg) View FEAT results with tksurfer Map aparc+aseg to Functional Space Verify GFEAT registration View GFEAT results in volume and on surface “Higher-Level” analysis with mri_glmfit Cross-Run Fixed-Effects (FFX), One-Sample Group Mean (osgm)

31 End of Presentation

32 Sampling on the Surface: Projection Fraction
-0.1 0.0 (white) +0.1 +0.3 +0.5 +0.7 +0.9 +1.0 (pial) +1.1

33 Step 1: Register Anatomical with Surface Atlas (fsaverage)
Native Anatomical Surface Space Surface-based Registration fsaverage Space S recon-all Anatomical Surface in fsaverage Space

34 Step 2: Register fMRI with Anatomical
Native Anatomical Space Native Functional Space Rigid Registration R reg-feat2anat bbregister fMRI in Anatomical Space

35 Step 3: Combine Steps 1 and 2: mris_preproc
Native Anatomical Space Native Functional Space fsaverage Space S R recon-all reg-feat2anat bbregister fMRI in fsaverage Space

36 Within-Subject, Cross-Run Analysis
Analyze each run with FEAT (dataX.feat) Combine runs with GFEAT (standard space) mean_func.nii.gz – avg of example_func in std space Register each run (not .gfeat) with reg-feat2anat. dataX.feat/reg/freesurfer/anat2std.register.dat All runs (X) should be very close Verify the registration tkregister2 –mov data.gfeat/mean_func.nii.gz --reg anat2std.register.dat --surf Use anat2std.register.dat the way you would anat2exf.register.dat

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