Hi,
I'm guessing that tbss_skeleton is running out of RAM. This means
either you are running out of RAM or swap, or that the 32-bit maximum
process size is being reached. If you can run instead on a 64-bit
machine that should fix it.
Cheers.
On 30 Aug 2007, at 10:05, Michael Such wrote:
> Dear all,
>
> I am currently trying to use TBSS on some MD data using the
> tbss_non_FA
> script in fsl 3.3. It seems to generate the all_MD image ok, but
> fails to
> generate the skeletonised image, aborting with the following error:
>
> line 43: 17433 Aborted ${FSLDIR}/bin/tbss_skeleton -i
> mean_FA -p $thresh mean_FA_skeleton_mask_dst
> ${FSLDIR}/etc/standard/lower-cingulum all_FA all_${ALTIM}
> _skeletonised -a
> all_$ALTIM
>
> Trying to run tbss_skeleton independently confirms this is where
> the fault lies.
>
> Some extra information if this helps:
> 1. The all_MD image has the correct number of volumes
>
> 2. The scaling of the FAi images is 0:9967. In the original MD
> images some
> of the voxels were negative, as per the list I used avwmaths -max 0 to
> correct this, then scalled up.
>
> 3. The threshold being used was 2000
>
> 4. I've checked and all the files being put into tbss_skeleton are
> there.
>
> 5. I'm using the unpatched version of the script (i.e. I had to change
> all_L2 to all_$ALTIM manually), were there any other important fixes?
>
> Any help appreciated,
> Thanks,
> Michael
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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)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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