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/diffusion_tutorial/dtisubjects2005/subj_523/dmri
2 1 1000 1250 25 1 0
then I got:
** ERROR (nifti_image_read): failed to find header file
for'/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmr
i/data_slice_0000'
**
ERROR:nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2
005/subj_523/dmri/data_slice_0000): bad header info
ERROR: failed to open
file/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri
/data_slice_0000
ERROR: Could not open
image/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri
/data_slice_0000
Image Exception : #22 :: Failed to read
volume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri
/data_slice_0000
An exception has been thrown
Failed to read
volume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/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 DWIs
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri
/dwi.nii.gz
Loading mask
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlab
el/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri
.bedpostX
Loading segmentation map
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlab
el/mni/aparc+aseg.nii.gz
Loading b-values
from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri
/bvals
Loading gradients
from/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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