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 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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