Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines.
doug
Alexandru Hanganu wrote:
Dear Freesurfer users,
We have an MNI mask and we want to apply this mask on a group of
subjects for small volume correction.
so we did the following steps:
1. cd $SUBJECTS_DIR/fsaverage/surf
fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg
TT_avg152T1_to_fsaverage.dat
2. cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf --mov /path/to/ROI5.nii --reg
TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest
--hemi lh --out lh.fsaverage.ROI5.mgh
3. cd $SUBJECTS_DIR/subjid/surf
mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval
lh.thickness --tval lh.thickness.fsaverage.mgh
.
.
.
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237
nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits =
2.31875
Saving target data
4. Next step was just for verifying, but we received an error (maybe
it's not so important):
cd $SUBJECTS_DIR/subjid/surf
mri_segstats --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh
--in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt
Loading
/usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh
Loading lh.thickness.fsaverage.mgh
ERROR: dimension mismatch between input volume and seg
We want to determine the statistics only for this mask for the whole
group of subjects (qdec, or mri_glmfit).
If the mapping of our subjects thickness data was good, what should we
do next in order to achieve our goal ?
Thank you.
Best regards,
Dr. Alexandru Hanganu
___________________________________
Department of Neurology,
Schleswig-Holstein University Hospital, Kiel Campus
Arnold-Heller-Str. 3, building no. 41
D-24105 Kiel, Germany.
------------------------------------------------------------------------
_______________________________________________
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
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
