Hi Yong-Hwan - Can you please send your entire trac-all.log file? It's possible that something went wrong earlier in the processing even if the other steps didn't fail explicitly.
Thanks, a.y
On Tue, 28 Jan 2014, Yong-Hwan Kim wrote:
Hello, FreeSurfer community, I'm trying to run TRACULA sequentially.
After running, "trac-all -prior -s <subject> -i <input_DWI.nii> -c <tracula_conf.txt>" that shows an error "Segmentation fault (core dumped)" in my server. (Other options, "-corr, -qa, -intra, -inter, -masks, -tensor", were have done without error)
Server was configured as,
- Fedora 13 - 64bit
- FreeSurfer v5.1
- Tracula v5.3 (updated from v5.1)
Can anyone suggest a reason why this would be the case?
Thank you, Yong-Hwan Kim
Captured Shell logs
. . . Loading cortex mask from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/cortex+2mm.nii.gz Processing pathway 1 of 18... Matching streamline ends INFO: Have 4657 non-truncated streamlines (min/mean/max length: 60/99/137) . . . Finding center streamline INFO: Step is 5 voxels Segmentation fault (core dumped) Linux localhost 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 ...
trac-preproc exited with ERRORS at Tue Jan 28 21:30:52 KST 2014
Error Log from <subject>/scripts/trac-all.error
SUBJECT G001 DATE Tue Jan 28 21:30:52 KST 2014 USER user HOST localhost PROCESSOR x86_64 OS Linux Linux localhost 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.46 2013/12/04 17:02:25 ayendiki Exp $ /usr/local/freesurfer/bin/trac-preproc PWD /usr/local/freesurfer/subjects/G001 CMD /usr/local/freesurfer/bin/dmri_train --outdir /usr/local/freesurfer/subjects/G001/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.G001.14153.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 /usr/local/freesurfer/subjects/G001/dlabel/mni/aparc+aseg_mask.nii.gz --fa /usr/local/freesurfer/subjects/G001/dmri/dtifit_FA.nii.gz --cptdir /usr/local/freesurfer/subjects/G001/dlabel/diff --reg /usr/local/freesurfer/subjects/G001/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