ls -1 $FREESURFER_HOME/subjects
cvs_avg35/
cvs_avg35_inMNI152/
fsaverage/
fsaverage3/
fsaverage4/
fsaverage5/
fsaverage6/
fsaverage_sym/
lh.EC_average/
README
rh.EC_average/
sample-001.mgz
sample-002.mgz
surfer.log
V1_average/
not sure why it thinks it doesn't exist. What are the permissions on
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
can you do an ls on
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf
and post the results? Also do:
ls -l /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
On Wed, 19 Dec 2012, Linda Zhang wrote:
Dear all,
I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I
missed something out. What files should be in the $FREESURFER_HOME/subjects directory?
The error reads as follows:
#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012
INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
ln: creating symbolic link `./lh.EC_average': File exists
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average
lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW.
processing subject lh.EC_average...
MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file
eroding label 1 times before writing
thresholding label stat at 0.400 before writing
No such file or directory
mris_spherical_average: could not read surface file
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg
No such file or directory
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
For more details, see the log file /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Cheers,
Linda
On 14 November 2012 22:29, Linda Zhang <lzhang87@gmail.com> wrote:
Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other
one and try again.
On 14 Nov 2012 22:14, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:
sounds like you are running out of memory. How much ram is in that machine? Are other processes running
at the same time?
On Wed, 14 Nov 2012, Linda Zhang wrote:
Dear all,
After moving my data to a different folder, I've come across a different error when running
recon-all (autorecon2 and 3). The
last few lines are as follows:
0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766
0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766
0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766
0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766
0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766
Killed
ERROR: mri_ca_register with non-zero status 137
but continuing despite the error
#--------------------------------------
#@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012
/home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686
GNU/Linux
recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012
Another set is exiting simply with:
#@# EM Registration Mon Nov 12 17:43:05 HKT 2012
/home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
/home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca
transforms/talairach.lta
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686
GNU/Linux
recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
What's the problem I should be addressing?
Thanks!
Cheers,
Linda
On 2 November 2012 21:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Linda
it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects,
which is where we store our
average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else
cheers
Bruce
On Fri, 2 Nov 2012, Linda Zhang wrote:
Dear all,
I've been running recon-all on my dataset, but all of them are exiting with
the same error.
The command line is:
recon-all -subjid ncpoCCW -autorecon2 -autorecon3
The error reads:
#@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012
INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/subjects; ln -s
/home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label
lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW.
processing subject lh.EC_average...
MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere
.reg): could not open file
eroding label 1 times before writing
thresholding label stat at 0.400 before writing
Too many levels of symbolic links
mris_spherical_average: could not read surface file
/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg
Too many levels of symbolic links
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC
2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012
What should I do? Thanks!
Cheers,
Linda
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