Try these instructions. You won't actually need to do the download and install in you're local, but you will need to use the dev env.
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/mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz
# Copy surfreg and xhemireg into $FREESURFER_HOME/bin # Copy mris_preproc into $FREESURFER_HOME/bin after making a backup # 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
# Analyze 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
kelsi wrote:
Hi Freesurfers,
Is there a tool to flip the orientation of surface data to the opposite hemisphere? We are working with stroke patients, and I would like to do analysis of the contralesional hemisphere of all the patients. However, this requires putting them on the same hemisphere for ttests, etc. I saw an earlier thread online about a program for flipping in the works, I was just wondering if this is now possible? Thank you!
Kelsi
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