that means the FS version you have didn't have those labels. We can get you the entire set of BA labels, but you will need a new version of recon-all. Maybe your best bet is to insteall 6.0 beta and just run the -balabels target from it?
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear Bruce,
# ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label ls: Kein Treffer. (meaning: no match)
# ls /usr/local/freesurfer/subjects/fsaverage ls: Zugriff auf /usr/local/freesurfer/subjects/fsaverage nicht möglich: Zu viele Ebenen aus symbolischen Links (meaning: access to /usr/local/freesurfer/subjects/fsaverage not possible: too many levels of symbolic links)
Best,
Max
On dijous 19 novembre 2015 15:03 CET, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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....). 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
- subject name:
it happens with any subject
- the entire command-line executed
recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid
where: $g = /path/to/nii/file and $subjid = subject ID
- 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
maximila.bautista-perpinya@etu.unistra.fr