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 > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
