Hi Keith - This seems to be a different problem here, since all the
bedpostx outputs are there and are loaded in without a problem. The error
occurs after that. What's the size of your images? Does the mask file look
normal?
Thanks,
a.y
On Thu, 26 Jul 2012, Keith Yoder wrote:
Hi,
Was there any resolution to this issue? I'm having a similar problem
running trac-all on a Linux cluster.
I think bedpostx works if I call it directly from the command line twice.
The first time, bedpostx_postproc.sh doesn't seem to work and the
*samples.nii.gz files are only created if I rerun bedpostx. However,
trac-all...-path fails. I've attached the trac-all-path output and pasted
the relevant section below:
Creating output
directory/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dpath/lh.cst_AS_av
g33_mni_flt
Loading DWIs from
/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/dwi.nii.gz
Loading mask
from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/diff/aparc+
aseg_mask.flt.nii.gz
Loading BEDPOST parameter samples from
/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri.bedpostX
Loading segmentation map
from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/mni/aparc+a
seg.nii.gz
Loading b-values from
/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvals
Loading gradients from
/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvecs
Segmentation fault (core dumped)
Here are the contents of the subjects bedpostX directory:
bvals
bvecs
commands.txt
diff_slices
dyads1_dispersion.nii.gz
dyads1.nii.gz
dyads2_dispersion.nii.gz
dyads2.nii.gz
logs
mean_dsamples.nii.gz
mean_f1samples.nii.gz
mean_f2samples.nii.gz
mean_ph1samples.nii.gz
mean_ph2samples.nii.gz
mean_S0samples.nii.gz
mean_th1samples.nii.gz
mean_th2samples.nii.gz
merged_f1samples.nii.gz
merged_f2samples.nii.gz
merged_ph1samples.nii.gz
merged_ph2samples.nii.gz
merged_th1samples.nii.gz
merged_th2samples.nii.gz
monitor
nodif_brain_mask.nii.gz
xfms
Also, I'm attaching the bvals, bvecs, dmrirc.local, trac-all.error, and
trac-all.log for the subject. Let me know if there is any other information
you need.
Thanks in advance,
Keith
--
Keith YoderPhD Candidate, Integrative Neuroscience
Social Cognitive Neuroscience Laboratory
The University of Chicago
5846 S. University Avenue, Kelly 312
Chicago, IL 60637
Phone: 574-215-9678
kjyo...@uchicago.edu
On Fri, Oct 7, 2011 at 10:04 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Judit,
1. If you can run bedpostx directly then you should do:
bedpostx /usr/local/freesurfer/subjects/C001/dmri
Note that this dmri directory and the one you tried to run
bedpostx_single_slice.sh on are different, so I'm not sure which
location is the right one where your data is, but in any case
you don't need to run bedpostx_single_slice.sh.
2. The error seems to occur either when it's reading the bvecs
file, or right after that when it's accessing the bedpostx
outputs. So I'd try to look those for that subject and see if
everything is ok.
Hope this helps,
a.y
On Fri, 7 Oct 2011, Judit Haasz wrote:
Hi,
I ran into 2 problems related to tracula.
1. trac-all -bedp command exits with following
message.
WARN: Running FSL's bedbost locally - this might
take a while
>> > WARN: It is recommended to run this step on a
cluster
>> > bedpostx_seychelles
/usr/local/freesurfer/subjects/C001/dmri
>> > subjectdir is
/usr/local/freesurfer/subjects/C001/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
>> > [: 223: NONE: unexpected operator
>> > [: 327: xbedpostx: unexpected operator
>> > [: 486: x53: unexpected operator
>> > 0 slices processed
>> > Queuing post processing stage
>> > [: 223: NONE: unexpected operator
>> > [: 314: NONE: unexpected operator
>> > [: 327: xbedpostx_post: unexpected operator
>> > [: 486: x: unexpected operator
>> > [: 486: -le: argument expected
>> >
This problem has been posted in May and June.
bedpostx from command line
runs perfectly and that is how I have been running
it so far. One of u
suggested to try the following:
/usr/local/fsl/bin/bedpostx_single_slice.sh/disks/open/judit/subjects/diffu
sion_tutorial/dtisubjects2005/subj_523/dmri
2 1 1000 1250 25 1 0
then I got:
** ERROR (nifti_image_read): failed to find header
filefor'/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/
dmr
i/data_slice_0000'
**ERROR:nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisub
jects2
005/subj_523/dmri/data_slice_0000): bad header info
ERROR: failed to
openfile/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/
dmri
/data_slice_0000
ERROR: Could not
openimage/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523
/dmri
/data_slice_0000
Image Exception : #22 :: Failed to
readvolume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_52
3/dmri
/data_slice_0000
An exception has been thrown
Failed to
readvolume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_52
3/dmri
/data_slice_0000Trace: read_volume4DROI.
Done
Can u suggest a reason behind all this? This happens
on Linux machine
(2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM
Version: Java
1.6.0_17-b04 with Sun Microsystems Inc. Java
HotSpot(TM) 64-Bit Server VM
mixed mode).
On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz
6-core Intel Xeon
processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp
runs well.
My other question is:
trac-all -path exists with error (in case of a
single subject):
Loading
DWIsfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/
dmri
/dwi.nii.gz
Loading
maskfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/
dlab
el/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter
samplesfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/
dmri
.bedpostX
Loading segmentation
mapfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/
dlab
el/mni/aparc+aseg.nii.gz
Loading
b-valuesfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/
dmri
/bvals
Loading
gradientsfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/
dmri
/bvecs
Segmentation fault
Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar
18 18:42:20 UTC 2011
x86_64 GNU/Linux
trac-paths exited with ERRORS at Fri Oct 7 10:21:20
CEST 2011
thanks for help.
Judit
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