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