On Tue, 26 Oct 2004, Dost Ongur wrote:
> - Our design involves 5 conditions, each presented twice for 30 seconds.
> All conditions are modelled (including crosshair). So the model is:
> CH A B C D A B C D CH.
This is a little confusing - in a block design like this you should not
generally model _all_ conditions - there will normally be one condition
which you can consider "baseline" (I'm guessing CH in this case) which you
should not model. This is because (at first level) the data gets demeaned.
So you should probably only have EVs for A,B,C,D and use appropriate
contrasts to ask whatever questions you want.
> - All 5 PEs we specified in our design matrix (block design) are negative
> in our ROI. Thinking that our ROI may have a lower blood flow level than
> the brain overall as Joe Devlin mentioned, we ran avwstats on a couple
> filtered_func_img and get a mean of about 9900. But the raw data in our
> ROIs are typically around 11000-13000!
I'm guessing that getting -ve PEs is a result of the design being close to
rank deficient for the reasons above. Contrasts would still be well
conditioned, but PEs on their own would not be. I suspect this is what's
> Part of our study is repeating an earlier study of the hippocampus done
> with healthy subjects, analyzed using SPM. In this study, we get the
> expected results with FSL for new healthy subjects. We don't see the
> predicted group differences between patients and controls and we are
> trying to understand our data better.
> So given a task that seems to work in a complex contrast, we have trouble
> understanding how all PEs that were modeled are negative in value.
Ok - try the above and see if things make more sense - let us know how you
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