Dear Jon,

> The data were acquired with a block design, 15 seconds OFF,
> 15 seconds on, etc, etc. Did the method Richard proposed require
> some re-ordering of the data? Basically I'm not too sure about
> how to specify the required model.

You don't need to reorder the data. What I think Richard was suggesting was
that instead of specifying two conditions in a boxcar design (active and
rest), you instead specify four conditions (active_early, active_late,
rest_early, rest_late). Take the onsets for _early from blocks acquired in
the first half of scanning, _late from the second half. Then you can use a
the contrast he suggested to test for a difference between activation and
rest that is greater during the first half, compared to the second half, of
your scanning run. 

I was suggesting a related but different approach; specify just one
condition, but then use the 'parametric modulation' button to create a
modulation of that boxcar by some function of time. I'd be happy to help you
set this up but it may be easier done off-list.

> Also, considering modification of BOLD signal due to scanner
> 'variation' - does SPM detrend the time course data? If so
> wouldn't a time dependent reduction in BOLD signal be physiological
> rather than artifactual?

That was what Richard & I were debating I think. I was arguing that
artefactual differences due to the scanner would affect each condition
equally, so could not account for differences between active and rest that
varied over time (activation x condition interaction).

Richard was arguing (correct me Richard if I am misrepresenting your
argument !!), on the other hand, that he could envisage sources of
artefactual variability that could differentially affect 'active' conditions
(in essence affecting the gain of the BOLD response to neural activity,
rather than just adding a constant offset). So Richard wanted (ideally) to
identify not just an activation-by-time interaction, but also show that this
putative correlate of learning could be reset by a psychological
manipulation at the end of the session (thus ruling out artefactual causes).

Hope this helps,

best wishes,

Dr. Geraint Rees
Wellcome Advanced Fellow,                       Lecturer,
Division of Biology 139-74,                     Institute of Neurology,
California Institute of Technology,             University College London,
Pasadena CA 91125                               London WC1N 3BG

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