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>

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
greve@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

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