Is it possible that FNIRT is asking for too much RAM for your system?
On 9 Mar 2009, at 18:19, Mahinda Yogarajah wrote:
> Dear List,
>
> I wonder whether anyone can offer some advice regarding the SGE and
> tbss_2_reg. Our SGE works with older versions of fsl and had
> previously run
> tbss_2_reg without any problems (eg. 4.0.1). Currently we are
> trying to use
> fsl 4.1.2 - the 1st tbss script runs fine. With tbss_2_reg (using -T
> option), a couple of things happen - all jobs are passed to the SGE
> and an
> appropriate commands file is generated. However the registration
> seems to
> take too short a time, and indeed when one looks at the resulting
> files
> there are
> a) empty msf files and no _FA_to_target_warp.nii.gz files for most
> subjects
> b) a lot of "core.12345"gedit co files generated
> c) 4 of the 20 or so subjects do get fully processed such that we
> have a
> _FA_to_target.mat file, _FA_to_target_warp.msf and
> _FA_to_target_warp.nii.gz
> file
>
> It seems as if the SGE is dropping some of the processing commands
> that have
> been sent to it. Any help anyone can offer would be greatly
> appreciated.
>
> Thanks.
>
> Mahinda
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
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