Hi,
On 24 Nov 2008, at 19:34, SUBSCRIBE FSL Anonymous wrote:
> I'm new to this message system, so my apologies if this is posted
> twice.
>
> I am running TBSS on a large number of subjects (N = 75), everything
> works
> smoothly for the FA analysis, but I get the following error when I run
> TBSS_non_FA (MD):
>
> projecting all_MD onto mean FA skeleton
> /home/ssorg/fsl4/fsl/bin/tbss_non_FA: line 104: 7038 Killed
> ${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh
> mean_FA_skeleton_mask_dst
> ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_${ALTIM}_sk
> eletonised
> -a all_$ALTIM
>
> So, it creates the all_MD image fine, but stops short of creating
> all_MD_skeletonized... bummer.
>
> I've noticed that the suggested solution is to get more ram or
> increase
> swap. I'm running on 2 gb of ram and 4gb of swap currently. I am
> wondering
> if there is an alternative solution?
Are you definitely running on 64-bit hardware and OS? 4GB isn't a lot
- you should increase this to 10GB for example in any case.
> Is it possible to split the all_FA and all_MD 4D images into
> individual
> subject images and run tbss_skeleton for each subject in a loop and
> then
> merge the files to create all_MD_skeletonized?
>
> tbss_skeleton -i mean_FA.nii.gz 2000 mean_FA_skeleton_mask_dst.nii.gz
> ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA0000.nii.gz
> MD_skeletonized_0000 -a all_MD0000.nii.gz
>
> I've seen this posted as a solution to memory shortages for
> generating the
> FA skeletons, but haven't seen it posted for non_FA.
Hi - yes, this solution would be fine for this scenario too.
Cheers.
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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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