Hi Anita,
I don't believe you have the complete path set to your SUBJECTS_DIR
environmental variable, unless Desktop is in your root dir which I doubt
is the case.
Easy way to set the variable:
cd /path/to/tutorial/data/
setenv SUBJECTS_DIR $PWD
Also, check you have fsaverage symlinked to the SUBJECTS_DIR
cd $SUBJECTS_DIR
ln -s /usr/local/freesurfer/subjects/fsaverage .
That should do the trick.
-Louis
On Tue, 5 Nov 2013, Anita van Loenhoud wrote:
Hi everyone,
I run into an error when I try to do the tutorial on ROI group analysis. I
downloaded the tutorial set, but did not put it into
FREESURFER_HOME/subjects, because my computer doesn't allow it. I made my
own folder and copied everything in there. The error arises when I try to
map a label from the fsaverage subject to a target subject:
mri_label2label \
> --srcsubject fsaverage \
> --srclabel fsaverage/label/lh.BA45.label \
> --trgsubject 004 \
> --trglabel 004/label/lh.BA45.label \
> --hemi lh \
> --regmethod surface
srclabel = fsaverage/label/lh.BA45.label
srcsubject = fsaverage
trgsubject = 004
trglabel = 004/label/lh.BA45.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR
Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/
group_analysis_tutorial
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration
Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/
group_analysis_tutorial/fsaverage/surf/lh.sphere.reg
MRISread(Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutoria
l_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg): could not
open file
No such file or directory
ERROR: could not
readDesktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/g
roup_analysis_tutorial/fsaverage/surf/lh.sphere.reg
In related posts I read that it might have to do with the creation of
symbolic links. I made sure that in my SUBJECTS_DIR, fsaverage is a symbolic
link to my FREESURFER_HOME/subjects directory, in which surf/lh.sphere.reg
etc are stored. What am I doing wrong? Does it still have to do with the
fact that I put the tutorial data in another folder?
Hope you can help me,
Thanks in advance,
Anita
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