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