Hi Doug & Freesurfer experts,

Is there a way to run mri_label2label to copy a label from one subject to another in a different SUBJECTS_DIR, or do the subjects have to be in the same directory for label2label to work (e.g. vs_subject1 in SUBJECTS_DIR_A to subject1_anat in SUBJECTS_DIR_B)? I am having trouble with specifying the source and target registration/white matter files. The subjects in both directories are the same, the only difference being which version of freesurfer the recons were run with and a slight difference in the naming convention.

I tried just copying the file, but when I tried to visualize the label, it looked incorrect. Below are the outputs I got when running mri_label2label. When I do not use the --srcsurfreg & --trgsurfreg flags, I get very similar errors, but with shorter path names that it cannot find.

Thanks for your help!

-Garth

When I try:

setenv SUBJECTS_DIR /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/
cd /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/
mri_label2label --srclabel /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label --srcsubject vs_aric --trglabel /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label --trgsubject aric_anat --regmethod surface --hemi lh --srcsurfreg /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg --trgsurfreg space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg

I get this error:
srclabel = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label
srcsubject = vs_aric
trgsubject = aric_anat
trglabel = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg
trgsurfreg = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0

SUBJECTS_DIR    is /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects
FREESURFER_HOME is /usr/local/freesurfer/stable4
Loading source label.
/space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label
Found 158 points in source label.
Starting surface-based mapping
Reading source registration 
 /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg
MRISread(/autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg): could not open file
No such file or directory
ERROR: could not read /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg
When I try changing the subjects directory:

setenv SUBJECTS_DIR /space/brownie/3/users/gcoombs/SUBJECTS_DIR/
cd $SUBJECTS_DIR
mri_label2label --srclabel /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label --srcsubject vs_aric --trglabel /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label --trgsubject aric_anat --regmethod surface --hemi lh --srcsurfreg /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg --trgsurfreg space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg

I get this error:
srclabel = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label
srcsubject = vs_aric
trgsubject = aric_anat
trglabel = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg
trgsurfreg = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0

SUBJECTS_DIR    is /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR
FREESURFER_HOME is /usr/local/freesurfer/stable4
Loading source label.
/space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label
Found 158 points in source label.
Starting surface-based mapping
Reading source registration 
 /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg
MRISread(/autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg): could not open file
No such file or directory
ERROR: could not read /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg