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
${FSLDIR}/bin/bedpostx_preproc.sh
/home/kutato12/freesurfer/subjects/my_subject/dmri"
works.
So I think there is a problem with fsl_sub_seychelles. Any idea how to
solve this thing?
Thanks,
Gabor
2012/5/24 Priti Srinivasan <rspr...@nmr.mgh.harvard.edu>
> Hi Gabor,
>
> If you run bedpostX on the data outside of tracula using the default
> options, do you get the same error?
>
> Priti
>
> > Dear all,
> >
> > I've the following error right after starting trac-all -bedp -c
> > configuration_file:
> >
> > Making bedpostx directory structure
> > Queuing preprocessing stages
> > [: 223: NONE: unexpected operator
> > [: 314: NONE: unexpected operator
> > [: 327: xbedpostx_pre: unexpected operator
> > [: 486: x: unexpected operator
> > [: 486: -le: argument expected
> > Queuing parallel processing stage
> > [: 223: NONE: unexpected operator
> > 0 slices processed
> > [: 327: xbedpostx: unexpected operator
> > [: 486: x70: unexpected operator
> > Queuing post processing stage
> > [: 223: NONE: unexpected operator
> > [: 314: NONE: unexpected operator
> > [: 327: xbedpostx_post: unexpected operator
> > [: 486: x: unexpected operator
> > [: 486: -le: argument expected
> >
> >>From the created files it seems that the first error occurs at
> > "preprocid=`${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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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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