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.