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