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/dmri/data_slice_0000'
** ERROR:
nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/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/dlabel/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/dlabel/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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