Hi Viviana - If you upload this data set I'm happy to look at it.
Also, I strongly recommend getting the updated version of trac-all from
the wiki (I'm guessing from the log file that you're probably not using
that?) See 2012/01/09 update here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
Thanks,
a.y
On Wed, 4 Apr 2012, Viviana Siless wrote:
Hello,
I'm trying to run trac-all prec and I'm getting a segmentation fault error.
Loading streamlines from
/media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk
Loading streamline start ROI from
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
Loading streamline end ROI from
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
Loading streamlines from
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk
INFO: Rejected 0 streamlines for straying off mask
INFO: Rejected 0 streamlines for reversing direction
Segmentation fault
Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11
03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Apr 4 18:24:21 CEST 2012
- When I look at the trak-all.error I see this error:
------------------------------
SUBJECT 000000112288Proc
DATE Wed Apr 4 18:24:21 CEST 2012
USER vivi
HOST vivi-ThinkStation-C20X
PROCESSOR x86_64
OS Linux
Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11
03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
$Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $
/media/vivi/code/freesurfer/bin/trac-preproc
PWD /media/vivi/code/freesurfer
CMD /media/vivi/code/freesurfer/bin/dmri_train --outdir
/media/vivi/images/freesurfer/000000112288Proc/dlabel/mni --out
lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt
rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt
rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt
lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt
rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt
rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt
--slist /tmp/subj33.000000112288Proc.16360.txt --trk
dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk
dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk
dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk
dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk
dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk
dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk
dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk
dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk
dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.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.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz
dlabel/mni/fmajor_PP_roi2.flt.nii.gz
dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz
dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz
dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz
dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
/media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz
--fa
/media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_FA.flt.nii.gz
--ncpts 5 --debug
- If I run that command, I get the same (of course):
INFO: Rejected 0 streamlines for straying off mask
INFO: Rejected 0 streamlines for reversing direction
Segmentation fault
Can anybody give me an idea of the problem? I run recon-all and finished
without errors.
I attach the log file, the error file, and my dmrirc file. Please let me know
if you need anything else.
Thanks in advance!
Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE
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