Hi Rick, this doesn't sound like anything obvious/familiar wrt bugs or
design mistakes - so I suspect that this is something unusual in the data.
If you go into the .gfeat directory and load in the cope1.hdr 4D file (ie
the input to the higher-level analysis) into FSLView and look around at
the timeseries it should be quite easy to see if this is due to some weird
outlier in one of the lower level analyses. If this doesn't help, then
feel free to make the whole .gfeat directory available as a compressed
tarfile on a web/ftp site and we can easily take a look.
Cheers, Steve.
On Tue, 20 Jul 2004, Rick Hoge wrote:
> We've been analyzing some block design data using FEAT, and have encounted a strange negative
> bias in the Z and T images generated for our groups by FLAME. We do see a set of positive foci in
> plausible locations, but these appear against a background of a consistently negative Z score of
> around -5. This would suggest there's either something wrong with our data (but these look ok
> from what we can tell) or, more likely, that we are setting up the analysis incorrectly.
>
> I am wondering if this symptom calls to mind any kind of obvious misconfiguration, or if anyone
> has advice on how to debug this sort of thing. We did look at the cope images, and these also
> appear to have the negative bias in much of the brain.
>
> The design contains three stimulus types (EV's) in non-overlapping blocks, and the problem is
> appearing in the general contrast testing for presence of response to all three stim types. The F
> images show a global background of abnormally high value, and you can see the zero crossing
> separating most of the brain (negative) from the isolated positive foci.
>
> Any advice on how to resolve this would be much appreciated - I can provide all or part of the .fsf
> file or output images if needed.
>
> Rick
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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