Hi Anders,
Run mris_preproc twice :
# For the left-lesioned subjects mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out LeftLesionSubjects.lh.lh-rh.thickness.sm00.mgh \ --s Lsubj1 --s Lsubj2 ...
# For the right lesioned subjects mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out RightLesionSubects.lh.lh-rh.thickness.sm00.mgh \ --s Rsubj1 --s Rsubj2 ...
You need to change the sign of the RightLesionSubjects:
fscalc RightLesionSubects.lh.lh-rh.thickness.sm00.mgh mul -1 \ -o RightLesionSubects.lh.rh-lh.thickness.sm00.mgh
Now put them together: mri_concat LeftLesionSubjects.lh.lh-rh.thickness.sm00.mgh \ RightLesionSubects.lh.rh-lh.thickness.sm00.mgh \ -o All.lh.Lesion-Healthy.thickness.sm00.mgh
then proceed replacing lh.lh-rh.thickness.sm00.mgh with All.lh.Lesion-Healthy.thickness.sm00.mgh
doug
On 12/04/2012 12:22 PM, Anders Hougaard wrote:
Dear Doug,
I would like to the same thing that Kelsi (as I read the post) asked about: For patients with a lesion in one hemisphere, I want to compare the hemispheres with lesions to the contralateral hemispheres without lesions.
I think that your answer below is a recipe for comparing right and left hemispheres within subjects. In my case half of the patients have a lesion in the right hemisphere and the other half have a lesion in the left hemisphere.
I guess I should register all of the hemispheres to the left hemisphere of fsaverage_sym, but how do I set up the analysis for doing a paired comparison of hemispheres with lesion vs hemispheres without?
All the best, Anders
2011/11/14 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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