Hi, hopefully the image format doesn't make any difference here.

This sounds like the same problem that has cropped up a few times on  
the list now: you are probably running out of RAM or swap space or  
just going over the 64-bit limit, presumably because you have quite a  
lot of subjects.

If the problem is not RAm/swap, the best solution is to run on a 64- 
bit machine if you have access to one. Otherwise you could use avwroi  
to cut down the FOV in:
mean_FA_skeleton
mean_FA
all_FA
images which may solve things when you rerun tbss_4_prestats

Cheers.



On 31 Jan 2007, at 15:48, Suzanna Laycock wrote:

> Hi,
>
> Sorry I should have noticed this first: when I run tbss_4_prestats,  
> I get
> the following error, which explains why there's no all_FA_skeletonised
> image.  Tbss_3_postreg seems to have run okay, and has generated  
> the files
> it says it should on the webpage, although some are in analyze and  
> some in
> nifti format.  I've been working in analyze format.
>
> Suzanna@suzanna ~/FSL_DATA/tbss
> $ tbss_4_prestats
> 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 23:  5852 Aborted
> (core
>  dumped) ${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh
> mean_FA_skeleton_mask
> _dst ${FSLDIR}/etc/standard/lower-cingulum all_FA all_FA_skeletonised
> now run stats - for example:
> randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d
> design.mat
> -t design.con -n 5000 -c 3 -V
> (after generating design.mat and design.con)
>
>
> Suzanna
>
>
>
> Hi,
> Where is your all_FA_skeletonised image? What happens if you
> type: avwinfo all_FA_skeletonised Cheers, Andreas
>
> -----Ursprüngliche Nachricht-----
> Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> Im Auftrag von Suzanna Laycock
> Gesendet: Dienstag, 30. Januar 2007 13:55
> An: [log in to unmask]
> Betreff: [FSL] Randomise
>
> Hi,
>
> I'm trying to use randomise. I've followed all the steps on the
> TBSS web page, and so far everything has been sucessful, but
> when I run randomise I get the following error message. The
> design.con and design.mat are below.  I have two groups of 6 subjects.
>
> All advice gratefully received.
> Suzanna
>
> ---------------
> Suzanna@suzanna ~/FSL_DATA/tbss/stats
> $ randomise -i all_FA_skeletonised -o tbss -m
> mean_FA_skeleton_mask -d design.m at -t design.con -n 5000 -c 3
> -V 924 permutations required for exhaustive test
> ** ERROR: nifti_image_read(all_FA_skeletonised): can't open header  
> file
> ** ERROR: nifti_image_open(all_FA_skeletonised): bad header info
> Error: failed to open file all_FA_skeletonised
> ERROR: Could not open image all_FA_skeletonised Image Exception
> : #22 :: Failed to read volume all_FA_skeletonised Aborted (core  
> dumped)
> --------------
> /NumWaves 2
> /NumContrasts 2
> /PPheights 1 1
> /Matrix
> 1 -1
> -1 1
> ----------------
> /NumWaves 2
> /NumPoints 12
> /~/FSL_DATA/stats/t-test
> /~/FSL_DATA/stats/t-test
> /PPheights 1 1
> /Matrix
> 1 0
> 1 0
> 1 0
> 1 0
> 1 0
> 1 0
> 0 1
> 0 1
> 0 1
> 0 1
> 0 1
> 0 1


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