Dear Freesurfer experts,

Is there a way to save out ROIs for all the regions listed in the Freesurfer LUT? I've found posts and tutorials for saving multiple labels from an annotation file, saving an annotation file from multiple labels, and saving rois via the GUI. However, I don't quite understand how Freesurfer comes up with the labels from the LUT. To come up with the annotation file from the LUT, I tried:

(while in Freesurfer/subjects/)

...

mris_label2annot --subject SUBID/ --hemi lh --ctab ../../FreeSurferColorLUT.txt --a test --ldir annot_test

but get the error message:

subject 00303226_1/ hemi lh SUBJECTS_DIR /Applications/fmri_progs/freesurfer/subjects ColorTable annot_test/lh.ctx-lh-unknown.label AnnotName annot_test/lh.ctx-lh-bankssts.label nlables 5003 Loading /Applications/fmri_progs/freesurfer/subjects/00303226_1//surf/lh.orig No such file or directory mris_label2annot: could not open label file annot_test/lh.Unknown.label No such file or directory ERROR: reading annot_test/lh.Unknown.label

Any suggestions would be much appreciated.

Thanks,

Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edumailto:Vy_dinh@rush.edu