Hi,
Thank you for your suggestions Doug and Dan. Moving my subjects directory outside of the freesurfer tree and deleting the symbolic link and then recreating it as per the instructions at www.freesurfer.net/fswiki/FsAverage seem to have sorted the problem.
Best wishes, Clare
________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 21 February 2012 18:03 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsaverage error - too many levels of symbolic links
Hi Clare, try moving your SUBJECTS_DIR outside of the freesurfer tree. doug
Gibbard, Clare wrote:
Hi,
I am running recon-all on several scans, but it is exiting with an error. I think the error is occurring because my symbolic link to fsaverage is self-referential. However, the symbolic link is generated automatically during recon-all so I cannot see how to correct it. I have tried deleting the fsaverage from my subjects directory and re-running recon-all, but this did not work.
I can see that others have had this error before, but I can't see the solution. Are you able to help? I have previously run recon-all without getting this error. Thank you.
ls -l /home/clare/freesurfer/freesurfer/subjects/fsaverage gives this: lrwxrwxrwx 1 clare clare 52 2012-02-17 08:27 /home/clare/freesurfer/freesurfer/subjects/fsaverage -> /home/clare/freesurfer/freesurfer/subjects/fsaverage
Here is the error: #@# BA Labels lh Fri Feb 17 08:27:35 GMT 2012 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject...
cd /home/clare/freesurfer/freesurfer/subjects; ln -s /home/clare/freesurfer/freesurfer/subjects/fsaverage; cd -
mri_label2label --srcsubject fsaverage --srclabel /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject subject_001 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Too many levels of symbolic links mri_label2label: could not open label file /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label
srclabel = /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = subject_001 trglabel = ./lh.BA1.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 /home/clare/freesurfer/freesurfer/subjects FREESURFER_HOME /home/clare/freesurfer/freesurfer Loading source label. Invalid argument ERROR reading /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux clare-OptiPlex-990 2.6.35-32-generic #64-Ubuntu SMP Tue Jan 3 00:47:07 UTC 2012 x86_64 GNU/Linux
recon-all -s subject_001 exited with ERRORS at Fri Feb 17 08:27:35 GMT 2012
Best wishes, Clare
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