what is fsavg in that same directory? Maybe fsaverage was renamed to fsavg?

You would just need to copy the fsaverage recon folder back into /home/pom/Software/freesurfer/subjects, no need to reinstall. -Louis

On Mon, 29 Jul 2013, Pom Sailasuta wrote:

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Pom