Hi Rick - thanks for sending the data.
The group-level analysis looks fine (though it would normally be hard to
find mixed-effects activation with only 4 lower-level analyses - but your
activation is huge). I checked with OLS as well as FLAME and you still get
the negative background values.
The first-level analyses also look fine, in the sense that it's not
artefacts in the data causing the problem (note that MELODIC PICA analysis
did show a few spikes still left in btw, but I don't think that's the
problem).
I'm pretty sure I know what the problem is - though without the original
data I can't check to be certain. You have used intensity normalisation,
which is normally turned off by default, for various reasons including
this one: your data is so lovely, and the activation so huge, that
intensity normalisation is interacting with the strong activation to
produce "negative activation" in the background (nonactivated) voxels, for
obvious reasons. I'm pretty sure this is what's going on - you can easily
re-run without intnorm and see if the problem improves.
A much less likely possibility is that structured noise (eg resting state
networks) is causing the problem, but I'd try the above first.
Let us know how you get on! 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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