On Mon, Jul 29, 2013 at 1:52 PM, Louis Nicholas Vinke
<vinke@nmr.mgh.harvard.edu> wrote:
You are getting the same error as before? Could you send the log/terminal output?
Are the folders in fsavg symlinks also?
On Mon, 29 Jul 2013, Pom Sailasuta wrote:
So now I got the following in /home/pom/Software/freesurfer/subjects dir and still no lh.BA1.label
per your first email.
[pom@PomLinux /home/pom/Software/freesurfer/subjects]% ls -al
total 10981644
drwxr-xr-x 9 pom pom 4096 2013-07-29 10:39 .
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 17 2013-07-29 10:39 fsaverage -> ./fsavg/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
On Mon, Jul 29, 2013 at 1:37 PM, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote:
ok, that's good. Just make a symlink to the fsaverage dir from your subjects dir
(/home/pom/Software/freesurfer/subjects)
i.e.
cd /home/pom/Software/freesurfer/subjects
ln -s ./fsavg/fsaverage .
-Louis
On Mon, 29 Jul 2013, Pom Sailasuta wrote:
fsavg dir contains several directories.
[pom@PomLinux /home/pom]% cd fsavg
[pom@PomLinux /home/pom]% ls
fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 lh.EC_average
rh.EC_average V1_average
thanks again.
On Mon, Jul 29, 2013 at 1:23 PM, Louis Nicholas Vinke
<vinke@nmr.mgh.harvard.edu> wrote:
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
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