hi,

yes, but it is a link, not sure how is this happen.

///////////////////////////////////
[pom@PomLinux /home/pom]% pwd
/home/pom/Software/freesurfer/subjects
[pom@PomLinux /home/pom]% ls -al
total 10981644
drwxr-xr-x  9 pom pom        4096 2013-07-29 07:24 .
drwxr-xr-x 17 pom pom        4096 2013-07-28 20:07 ..
drwxr-xr-x 12 pom pom        4096 2012-04-21 11:46 bert
drwxr-xr-x  3 pom pom        4096 2012-04-22 06:37 buckner_data
-rw-r--r--  1 pom pom 11245151143 2012-04-21 23:33 buckner_data-tutorial_subjs.tar.gz
lrwxrwxrwx  1 pom pom          48 2013-07-29 07:24 fsaverage -> /home/pom/Software/freesurfer/subjects/fsaverage
drwxr-xr-x 10 pom pom        4096 2012-04-21 15:32 fsavg
drwxr-xr-x 12 pom pom        4096 2011-08-16 11:27 harris
drwxr-xr-x 13 pom pom        4096 2012-04-21 15:13 LarryR
-rw-r--r--  1 pom pom        1512 2011-05-22 08:12 README
drwxr-xr-x 13 pom pom        4096 2013-07-28 20:09 S009002A
drwxr-xr-x  2 pom pom        4096 2012-04-21 15:33 sample
-rw-rw-rw-  1 pom pom         492 2012-04-21 18:43 .xdebug_tkmedit
/////////////////////////////////////////////

I think it linked to itself, should I re-install freesurfer.

thanks
Pom

On Mon, Jul 29, 2013 at 1:09 PM, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote:
Hi Pom,
Does the following path exist?
/home/pom/Software/freesurfer/subjects/fsaverage/label/

if so, do it contain lh.BA1.label?  It probably has something do with the fsaverage symbolic link.  A few lines up in your error log it prints "Too many levels of symbolic links".
-Louis


On Mon, 29 Jul 2013, Pom Sailasuta wrote:

Hi,

I am wondering the errors I got from recon-all is from my FreeSurfer installation, please comments.

Here is my error:
////////////////////////
Reporting on  70 segmentations
/home/pom/Software/freesurfer/subjects/S009002A/label
#--------------------------------------------
#@# BA Labels lh Mon Jul 29 07:24:35 PDT 2013
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

 cd /home/pom/Software/freesurfer/subjects; ln -s /home/pom/Software/freesurfer/subjects/fsaverage;
cd -


 mri_label2label --srcsubject fsaverage --srclabel
/home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject S009002A
--trglabel ./lh.BA1.label --hemi lh --regmethod surface

Too many levels of symbolic links
mri_label2label: could not open label file
/home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label

srclabel = /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = S009002A
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/pom/Software/freesurfer/subjects
FREESURFER_HOME /home/pom/Software/freesurfer
Loading source label.
Invalid argument
ERROR reading /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label
Linux PomLinux 2.6.32-45-generic-pae #104-Ubuntu SMP Tue Feb 19 21:36:53 UTC 2013 i686 GNU/Linux

recon-all -s S009002A exited with ERRORS at Mon Jul 29 07:24:35 PDT 2013

For more details, see the log file
/home/pom/Software/freesurfer/subjects/S009002A/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
//////////////////////////////

thanks

Pom



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