Dear Priti

The bedpostx works fine on the data if I run it outside of tracula.

The command "/home/kutato12/freesurfer/bin/fsl_sub_seychelles -T 60 -m a -N bedpostx_pre -l /home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh /home/kutato12/freesurfer/subjects/my_subject/dmri"

gives the following error:

[: 224: NONE: unexpected operator
[: 315: NONE: unexpected operator
[: 328: xbedpostx_pre: unexpected operator
[: 487: x: unexpected operator
[: 487: -le: argument expected

But "/usr/lib/fsl/4.1/fsl_sub -T 60 -m a -N bedpostx_pre -l /home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh /home/kutato12/freesurfer/subjects/my_subject/dmri"

works.

So I think there is a problem with fsl_sub_seychelles. Any idea how to solve this thing?

Thanks,
Gabor

2012/5/24 Priti Srinivasan <rspriti@nmr.mgh.harvard.edu>
Hi Gabor,

If you run bedpostX on the data outside of tracula using the default
options, do you get the same error?

Priti

> Dear all,
>
> I've the following error right after starting trac-all -bedp -c
> configuration_file:
>
> 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
> 0 slices processed
> [: 327: xbedpostx: unexpected operator
> [: 486: x70: unexpected operator
> 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
>
>>From the created files it seems that the first error occurs at
> "preprocid=`${BPDIR}/fsl_sub_seychelles -T 60 -m a -N bedpostx_pre -l
> ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`"
>
> Any idea how to fix this error?
>
> Trac-all -prep finished without error.
> I've Freesurfer 5.1.0, Ubuntu 11.04 and FSL 4.1.8 installed using
> Neurodebian and I don't use SGE.
>
> I'd appreciate an early answer.
>
> Thanks,
> Gabor
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