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