This is going to be updated in the next version of freesurfer. There have
been some compatibility issues with the latest version of bedpostx that
we've had to fix. For now please run bedpostx by itself. Thanks!
On Fri, 25 May 2012, Gabor Perlaki wrote:
> 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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