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 <ayendiki@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 <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/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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