Hi Matthew,
Thanks very much - I've uploaded slicetimer_test.tgz file, reference number 880981. I re-tested just before creating the archive, and got the following results (I've not included fmri_odd_down.img or fmri_odd.img in the archive):
MD5 File Note
c12dd270820de65a6fb58f6937b7fb69 fmri.img raw data
7abdb7216a76981a222e2acd9cb06440 fmri_odd_down.img slicetimer -i fmri.img -o fmri_odd_down.img -r 2.68 --odd --down
7abdb7216a76981a222e2acd9cb06440 fmri_odd.img slicetimer -i fmri.img -o fmri_odd_down.img -r 2.68 --odd
Also in the archive is an image, fsl.png, containing raw (red) and corrected (blue) time series plots for voxel (32,32) at every slice; I included it, as I was still confused about whether, by default, slicetimer assumes that odd slices are captured before even slices. In the end, I realised that I was confusing myself with regard to 0- and 1- indexing (and thus the definition of 'even' and 'odd'), so you can safely ignore this file. If you do look at it, in the image, the slices are laid out as follows:
1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16
This is not a big deal for me, by the way; I can get correct behaviour for my data set by using a custom timing (--tcustom) file; I am just curious as to what is going on.
Thanks again,
Paul
P.S. My system information:
> paulmccarthy@macbook:~/Projects/st$ slicetimer
> ***************************************************
> The following COMPULSORY options have not been set:
> -i,--in filename of input timeseries
> ***************************************************
>
> Part of FSL (build 416)
> slicetimer (Version 1.8)
> FMRIB's Interpolation for Slice Timing
> Copyright(c) 2001-2002, University of Oxford
> paulmccarthy@macbook:~/Projects/st$ cat /etc/lsb-release
> DISTRIB_ID=Ubuntu
> DISTRIB_RELEASE=10.10
> DISTRIB_CODENAME=maverick
> DISTRIB_DESCRIPTION="Ubuntu 10.10"
> paulmccarthy@macbook:~/Projects/st$ dpkg-query -l fsl
> +++-==============-==============-=========
> ii fsl 4.1.6-1 analysis tools for FMRI, MRI and DTI brain i
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