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.edu