Hello, >From the standard "fsaverage" subject, I'm trying to map a series of labels >(?h.oasis.chubs.*) to a group of my own subjects. My end goal is to create >summary files equivalent to ?h.aparc.stats for each subject. For sample >commands, I've been looking at the "BA label" section of a subject's >recon-all.log
For my test subject, I first ran mris_label2label on each of the seven regions for each hemisphere, and then I visually confirmed that the labels were generated correctly. Here's an example of those commands: mri_label2label --srcsubject fsaverage --srclabel $FREESURFER_HOME/subjects/fsaverage/label/lh.oasis.chubs.ifc.label --trgsubject $subj --trglabel $SUBJECTS_DIR/$subj/label/lh.oasis.chubs.ifc.label --hemi lh --regmethod surface However, I ran into trouble when I tried to combine the labels into an annotation file. This is the command I'm using: cd $subj/label mris_label2annot --s $subj --hemi $hemi --ctab ~/colortable_oasis.chubs.txt --l lh.oasis.chubs.ifc.label --l lh.oasis.chubs.ipc.label --l lh.oasis.chubs.ips.label --l lh.oasis.chubs.lateraltemporal.label --l lh.oasis.chubs.medialpfc.label --l lh.oasis.chubs.mtl.label --l lh.oasis.chubs.retrosplenial.label --l lh.oasis.chubs.tp.label --a oasis.chubs --maxstatwinner --noverbose And these are the contents of colortable_oasis.chubs.txt, which I created by modifying /usr/local/freesurfer/average/colortable_BA.txt: 0 unknown 25 5 25 0 1 oasis.chubs.ifc 0 92 23 0 2 oasis.chubs.ipc 131 148 255 0 3 oasis.chubs.ips 0 0 255 0 4 oasis.chubs.lateraltemporal 255 102 51 0 5 oasis.chubs.medialpfc 196 255 20 0 6 oasis.chubs.mtl 255 51 204 0 7 oasis.chubs.retrosplenial 1 38 153 0 8 oasis.chubs.tp 153 0 38 0 The problem is, when I inspect the annotation file, I'm ending up with the entire brain labeled "unknown". Any ideas what I'm doing wrong? Thanks, Aaron
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