Hi Viviana - Does it die at that point or does it keep running? If it's
the latter it doesn't look wrong. For your first problem you should make
sure that your path includes the bin/ directory under the FSL
distribution.
a.y
On Wed, 25 Apr 2012, Viviana Siless wrote:
Hi Anastasia,
I ran:
- bedpostx /media/vivi/images/freesurfer/000000112288Proc/dmri
and got the following output:
subjectdir is /media/vivi/images/freesurfer/000000112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
But before it told me that /bin/fsl_sub was mising, so i copied from where
i had it to there, and then it arrived at the same place than before
then I ran
- fsl4.1-bedpostx /media/vivi/images/freesurfer/000000112288Proc/dmri
I made symbolic link from fsl4.1-whatever to whatever.
Im working in ubuntu 11.04 and I installed fsl from the package manager.
and I got this:
subjectdir is /media/vivi/images/freesurfer/000000112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed
What should I do?
Thanks!
Viviana
On Wed, Apr 25, 2012 at 12:52 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
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/testDa
ta.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.n
ii.gz
Loading streamline end ROI
from/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.n
ii.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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