Hi Garth,
they need to be in the same SUBJECTS_DIR, although it can just be a symlink.
cheers Bruce On Wed, 2 Jun 2010, Garth Coombs wrote:
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