Hi Anastasia, Here is the data: https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet me know if you have any trouble. I changed to the other track-all, and the error is the same. Please let me know if I'm doing anything wrong! Thank you!
Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE On Thu, Apr 5, 2012 at 7:38 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > 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<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 >> >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
