Can you run:
ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
and report the results?
cheers
Bruce
On Thu, 19
Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE)
wrote:
Dear all,
I get the same error when running any subject. I think it may be related to the
step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the
problem is coming from. I thought that it was an issue with my environment,
because there is a double slash in FREESURFER_HOME and all the other
environments:
FREESURFER_HOME /usr/local//freesurfer
FSFAST_HOME /usr/local//freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local//freesurfer/subjects
MNI_DIR /usr/local//freesurfer/mni
but I just saw that this shouldn't be a problem
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860.html).
Could you help me identify this error? I copy-pasted the output of bugr and
other information. You will find attached also the recon-all.log of one of the
subjects.
output of bugr:
---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
---------------------------------------------------------------------
1) subject name:
it happens with any subject
2) the entire command-line executed
recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where:
$g = /path/to/nii/file
and
$subjid = subject ID
3) the error message generated
from the recon-all.log:
SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local//freesurfer
Loading source label.
Invalid argument
ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015
from the recon-all.error:
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/usr/local//freesurfer/bin/recon-all
PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label
CMD mri_label2label --srcsubject fsaverage --srclabel
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject
B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Best regards,
Max
--
Maximilià Bautista-Perpinyà, BSc
Master student at Joint Master in Neuroscience (JMN)
Université de Strasbourg (in partnership with Universität Freiburg and
Universität Basel)
&
Master Intern at Biological and Personality Psychology Laboratory
Department of Psychology, Universität Freiburg
[email protected]
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