Hi Anastasia, My mistake with the expiration date. Please try with this link: https://transfert.inria.fr/fichiers/0b1013b5de0fc0cc9e8dd2d6101a054b/testDat...

Thanks!

Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE

On Tue, Apr 17, 2012 at 6:03 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Viviana - I was away from email for some time and it looks like the uploaded file has expired. Could you reupload it? I apologize for the delay.

Thanks, a.y

On Fri, 6 Apr 2012, Viviana Siless wrote:

Hi Anastasia,

...

Here is the data: https://transfert.inria.fr/**fichiers/** 4531ddb4948dff7223febc5a5b4f7e**7d/testData.tar.gzhttps://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 < ayendiki@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/Traculahttp://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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