Dear Tommy,
> The fMRI model that I am attempting to create is based upon the following
> experimental design:
> TR = 2; total images = 105; 2 trial blocks of 35 images each; Block 1
> prefaced by roughly 13-14 scans of rest; Block 2 prefaced by roughly 13-14
> scans of rest, and followed by roughly 8 scans of rest. (I say roughly
> because each subjects model is different)
>
> I am in the process of redoing our data using the SPM99b model. A problem
> that arose, is that there are discrepancies between our X, Y, Z pixel
> coordinates.
I'm not sure what you mean by 'discrepancies' - perhaps you could clarify?
Are you just comparing SPM96 & SPM99 analyses on the same raw data, or have
you repeated the realignment, normalisation and so on in SPM99. If the
latter, then the most likely cause of any differences between analyses is in
these preprocessing routines, which have been substantially improved and use
slightly different algorithms.
> Due to the fact that this new version inherently includes rest
> into the model, we believe this may be part of the problem when creating our
> contrast. Please clarify how to establish the contrast for this new model.
Karl outlined the (minor) differences between statistical inference in SPM96
and SPM99 in the email earlier today. I don't think these differences are
likely to account for your problems. Modelling rest implicitly is something
that is a feature of the design matrix, not the SPM version, and can be done
in SPM96 also. However you are right that a different design matrix can lead
to different results!
If you could give a little more detail both on what the problem is, and how
you specified the design matrix then I'm sure it would be possible to give
some more specific advice!
Best wishes,
Geraint
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Dr. Geraint Rees
Wellcome Advanced Fellow, Lecturer,
Mailstop 139-74, Institute of Neurology,
California Institute of Technology, University College London,
Pasadena, 12 Queen Square,
CA 91125 London WC1N 3BG
voice (626) 395-2880
fax (626) 796-8876
web http://www.klab.caltech.edu/~geraint
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