Indeed!
The solution however, is quite simple, do not merge the subjects into a single file, but rather process it on subject by subject basis.
pk
________________________________
From: FSL - FMRIB's Software Library on behalf of Steve Smith
Sent: Thu 6/26/2008 6:25 PM
To: [log in to unmask]
Subject: Re: [FSL] need help to run TBSS on large sample
Hi , please see the FAQ:
http://www.fmrib.ox.ac.uk/fslfaq/#general_ram
Cheers.
On 27 Jun 2008, at 08:03, Jane Zhang wrote:
> Dear FSL experts,
> I process DTI data of 184 subjects with TBSS recently. When I ran
> the 3rd step "tbss_3_postreg -S" in /brodmann4/dti/conte/tbss/all,
> the following error message showed up.
> ----------------------------------------------------------------------------------------
> merging all upsampled FA images into single 4D image
> creating valid mask and mean FA
> /usr/local/fsl/bin/tbss_3_postreg: line 177: 20665
> Killed $FSLDIR/bin/fslmaths all_FA -max 0 -Tmin -
> bin mean_FA_mask -odt char
> /usr/local/fsl/bin/tbss_3_postreg: line 178: 20838
> Killed $FSLDIR/bin/fslmaths all_FA -mas
> mean_FA_mask all_FA
> /usr/local/fsl/bin/tbss_3_postreg: line 179: 20918
> Killed $FSLDIR/bin/fslmaths all_FA -Tmean mean_FA
> ----------------------------------------------------------------------------------------
>
> Thus, I ran the following commands separately:
>
> ---------------------------------------------------------------------------------------
> fslmaths all_FA -max 0 -bin mean_FA_mask -odt char
> fslmaths all_FA -Tmean mean_FA
>
> ---------------------------------------------------------------------------------------
> However, both commands could not be run and were killed.
>
> Then, I reduced the sample size to 69 subjects. It worked for step
> 3 "tbss_3_postreg -S", but not for step 4 "tbss_4_prestats 2000".
> The error message was as follows:
>
> "creating skeleton mask using threshold 2000
> creating skeleton distancemap (for use in projection search)
> projecting all FA data onto skeleton
> /usr/local/fsl/bin/tbss_4_prestats: line 99: 11940
> Killed ${FSLDIR}/bin/tbss_skeleton -i mean_FA -p
> $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/
> LowerCingulum_1mm all_FA all_FA_skeletonised"
>
> Any idea why? Is it because of the computer? The computer running
> this program is a 64-bit machine with 32G disk space.
>
> I once ran tbss on a smaller sample of 51 subjects in April and it
> worked well. From the literature, some groups can run tbss on large
> samples (n>=70). I really have no clue why tbss can not be run on
> n=69 sample in our computer system.
> I'm wondering--Is it possible to run tbss on a n=184 sample with
> regular PC 64-bit computers? Or, shall I give up? Please help.
> Very frustrated,
> Jane
>
>
>
>
>
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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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