External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run the tractography analyses as described on the Tracula tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), I tried the all pipeline for one subject and it worked. I tried to run in parallel for the rest of the subjects and for three of them I get the following error when I run the trac all -prep command:
#!/bin/bash export FREESURFER_HOME=/opt/freesurfer/6.0; source $FREESURFER_HOME/SetUpFreeSurfer.sh; export SUBJECT_DIR=$/project/3015068.01/ilecam/Reolang/Freesurfer for i in `cat /project/3015068.01/ilecam/Reolang/scripts/list_trac_all_prep2.txt`; do trac-all -prep -c /project/3015068.01/ilecam/Reolang/Freesurfer/${i}/Tracula_out/tracula_config.txt; done
here below the content of trac-all.eror ------------------------------ SUBJECT sub-056 DATE Fri Oct 9 16:18:01 CEST 2020 USER ilecam HOST dccn-c029.dccn.nl PROCESSOR x86_64 OS Linux Linux dccn-c029.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $ /opt/freesurfer/6.0/bin/trac-preproc PWD /project/3015068.01/ilecam/Reolang/scripts CMD /opt/freesurfer/6.0/bin/dmri_train --outdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-056.18934.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni/aparc+aseg_mask.nii.gz --fa /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/dtifit_FA.nii.gz --cptdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/diff --reg /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
I've searched the list and no similar errors have been reported. Please can anyone share their thoughts on how to trouble-shoot this one?
Also, Ive attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer/6.0 build-stamp.txt: Platform: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2) 3) uname -a: Linux dccn-c046.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux) recon-all.log: see attached
thank you in advance
Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618
Hi Ileana - It looks like it fails on the left uncinate. Is there any artifact or missing part of the brain or brain mask, either in the diffusion scan or the T1 scan, in a location that would affect the uncinate?
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Camerino, I.L. (Ileana) i.camerino@psych.ru.nl Sent: Tuesday, October 13, 2020 11:12 AM To: Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] error trac all prep
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run the tractography analyses as described on the Tracula tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), I tried the all pipeline for one subject and it worked. I tried to run in parallel for the rest of the subjects and for three of them I get the following error when I run the trac all -prep command:
#!/bin/bash export FREESURFER_HOME=/opt/freesurfer/6.0; source $FREESURFER_HOME/SetUpFreeSurfer.sh; export SUBJECT_DIR=$/project/3015068.01/ilecam/Reolang/Freesurfer for i in `cat /project/3015068.01/ilecam/Reolang/scripts/list_trac_all_prep2.txt`; do trac-all -prep -c /project/3015068.01/ilecam/Reolang/Freesurfer/${i}/Tracula_out/tracula_config.txt; done
here below the content of trac-all.eror ------------------------------ SUBJECT sub-056 DATE Fri Oct 9 16:18:01 CEST 2020 USER ilecam HOST dccn-c029.dccn.nl PROCESSOR x86_64 OS Linux Linux dccn-c029.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $ /opt/freesurfer/6.0/bin/trac-preproc PWD /project/3015068.01/ilecam/Reolang/scripts CMD /opt/freesurfer/6.0/bin/dmri_train --outdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-056.18934.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni/aparc+aseg_mask.nii.gz --fa /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/dtifit_FA.nii.gz --cptdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/diff --reg /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
I've searched the list and no similar errors have been reported. Please can anyone share their thoughts on how to trouble-shoot this one?
Also, Ive attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer/6.0 build-stamp.txt: Platform: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2) 3) uname -a: Linux dccn-c046.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux) recon-all.log: see attached
thank you in advance
Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618
freesurfer@nmr.mgh.harvard.edu
-
Camerino, I.L. (Ileana) -
Yendiki, Anastasia