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 ${FSLDIR}/bin/bedpostx_preproc.sh /home/kutato12/freesurfer/subjects/my_subject/dmri"
works.
So I think there is a problem with fsl_sub_seychelles. Any idea how to solve this thing?
Thanks,
Gabor
Hi Gabor,
If you run bedpostX on the data outside of tracula using the default
options, do you get the same error?
Priti
> _______________________________________________
> Dear all,
>
> I've the following error right after starting trac-all -bedp -c
> configuration_file:
>
> Making bedpostx directory structure
> Queuing preprocessing stages
> [: 223: NONE: unexpected operator
> [: 314: NONE: unexpected operator
> [: 327: xbedpostx_pre: unexpected operator
> [: 486: x: unexpected operator
> [: 486: -le: argument expected
> Queuing parallel processing stage
> [: 223: NONE: unexpected operator
> 0 slices processed
> [: 327: xbedpostx: unexpected operator
> [: 486: x70: unexpected operator
> Queuing post processing stage
> [: 223: NONE: unexpected operator
> [: 314: NONE: unexpected operator
> [: 327: xbedpostx_post: unexpected operator
> [: 486: x: unexpected operator
> [: 486: -le: argument expected
>
>>From the created files it seems that the first error occurs at
> "preprocid=`${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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> Freesurfer@nmr.mgh.harvard.edu
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