Re: [Freesurfer] FMRI Asymmetry Analyses

I don't have any docs set up and ready to use, but here are some instructions that should get you started. doug

------------------------------------------------------------------------------------------------------- Download these files ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz

# Copy surfreg and xhemireg into $FREESURFER_HOME/bin # Untar fsaverage_sym.tar.gz into your $SUBJECTS_DIR cd $SUBJECTS_DIR tar xvfz fsaverage_sym.tar.gz

--------------------------------------------------------- To apply an existing atlas (eg, fsaverage_sym) to an anatomical analysis

# Reg to atlas (1-2 hours per subject) # Creates $subject/xhemi # Creates lh.fsaverage_sym.sphere.reg in $subject and $subject/xhemi foreach subject (subjectlist) surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi end

# Create a stack of subjects mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.mgh \ --s subj1 --s subj2 ...

# Smooth mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5\ --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm05.mgh

# Test mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 \ --osgm --surf fsaverage_sym lh

# View tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh

# Correct for MC (need new version of mri_glmfit-sim) mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 \ --cwpvalthresh .5 --cache 2 abs \ --subject-override fsaverage

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# To apply an existing atlas to an arbitray volume data set:

bbregister --s subject --reg register.dat ... mri_vol2surf --reg register.dat --mov data.nii.gz --hemi lh --o data.lh.nii mri_vol2surf --reg register.dat --mov data.nii.gz --hemi rh --o data.rh.nii

# Map lh data to fsaverage_sym mri_surf2surf --srcsubject subject --srcsurfreg fsaverage_sym.sphere.reg \ --trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval data.lh.nii \ --tval data.lh.fsaverage_sym.nii

# Map rh data to fsaverage_sym. Note: (1) "subject" is subject/xhemi # and (2) The hemi (--hemi lh) is still lh not rh. mri_surf2surf --srcsubject subject/xhemi --srcsurfreg fsaverage_sym.sphere.reg \ --trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval data.rh.nii \ --tval data.rh.fsaverage_sym.nii

data.lh.fsaverage_sym.nii and data.rh.fsaverage_sym.nii are now in voxel-for-voxel registration.

Andy Mayer wrote:

Hello-

     Trying this post again. I would like to directly compare 

asymmetries in FMRI activation in surface space based on the Greve et al poster presented at HBM this year. We would like to register each subject’s T1 data to the contralateral hemisphere of fsaverage and made templates of the contra (?h.con.sphere.reg ) and ipsilateral (?h.sphere.reg ) registrations. Is the following correct for the cross hemisphere registration? Thanks

mris_register -reverse -curv surf/rh.sphere {$FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif surf/rh.CON.sphere.reg

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