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 <[email protected]> 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.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] > > -- 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 (+49) 015759302368 [email protected] [email protected] _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
