Ok, i actually think it would be easier to have only one FS version. How could i get the BA labels (and all the other coontents of fsaverage) again?
Best, Max On dijous 19 novembre 2015 15:51 CET, Bruce Fischl <[email protected]> wrote: > yes, that's pretty much it. Alternatively we could just give you all the > current BA labels and the command lines need to run to map them from > fsaverage to your subjects > > On Thu, 19 Nov 2015, > BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote: > > > 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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