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
-
# 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
>
>
>
>
> ___
> 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
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