Hi Viviana - I cannot replicate this on our systems but I think I know what your system may be fussy about and I'll amend it. For now, if you don't get any outputs can you please try running bedpostx directly on /media/vivi/images/freesurfer/000000112288Proc/dmri and see if that works?

Thanks for bringing this to our attention,
a.y

On Mon, 23 Apr 2012, Viviana Siless wrote:

Hello Anastasia,
It fixed the bug. Thank you so much!

Now Im running  trac-all -bedp -c

But it's been running for already 3 days, and it just printed that:

> trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example
INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer
INFO: Diffusion root is /media/vivi/images/freesurfer
Actual FREESURFER_HOME /media/vivi/code/freesurfer
ln -sf 
/media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/anat_brain_mask.flt.nii.gz
/media/vivi/images/freesurfer/000000112288Proc/dmri/nodif_brain_mask.nii.gz
ln -sf /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi.nii.gz 
/media/vivi/images/freesurfer/000000112288Proc/dmri/data.nii.gz
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_seychelles /media/vivi/images/freesurfer/000000112288Proc/dmri
subjectdir is /media/vivi/images/freesurfer/000000112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
Queuing parallel processing stage


Is it normal?
Thanks for your help!  (let me know if I should create another thread)

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


On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki 
<ayend...@nmr.mgh.harvard.edu> wrote:

      Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI 
template brain, and our atlas was built using the 1mm one. From your
      dmrirc file:

      # MNI template (the only option for inter-subject registration in this 
version)
      # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
      #
      #set mnitemp = /path/to/mni_template.nii.gz
      set mnitemp = /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz

      Can you please try changing the above from 2mm to 1mm and see if it 
works? If so, I'll make sure this is handled more elegantly in the next
      version.

      Hope this helps,
      a.y

      On Fri, 6 Apr 2012, Viviana Siless wrote:

            Hi Anastasia,
            Here is the data: 
https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gz
 Let 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

                 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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