Dear Bruce, Thank you, I will try to do that, but I am not so clear about it. I should install the 6.0beta version of FS, but keep the one I have currently (v 1.379.2.73)? Then I should run with the 6.0beta version recon-all -balabels -i /path/to/file -s subjid; and then the complete recon-all with my current version? Is that right?
Best, Max On dijous 19 novembre 2015 15:35 CET, Bruce Fischl <[email protected]> wrote: > 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 > > <[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. 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