Dear Jon, Karl and others
>
> Dear Jon,
>
> > I have recently been experimenting with a random effects analysis of
> > several trials in an fMRI study. I have 18 subjects, so I guess this is
> > the right analysis to use. Basically, I was wondering whether I should
> > use a corrected height threshold in the generation of the SPMs? If I do
> > I get no supra-threshold clusters.
> >
> > Is it appropriate to use an uncorrected p, given that the random
> > effects analysis is quite stringent? Is there any general consensus on
> > the best approach to choosing p-levels in this situation?
>
> I am afraid exactly the same inference criteria apply to first and
> second level analyses. I would think about any anatomical priors that
> could be used to provede small volume correction to the p values. One
> point you might want to take forward is that inter-subject differences
> may include anatomical variations in the response profile. Increasing
> the smoothing (of the con??? or beta???.img) prior to the 2nd level
> analysis might improve your sensitivity (e.g. 8mm FWHM).
>
> I hope this helps - Karl
I hope that the following proposition won't seems to odd !
Let say that you have no clear idea of which cortical region should activate
except that you are looking for cortical activation only.
Why not using a mask constructed on the basis of gray matter segmentation for
corrected p ?
You will just have to choose a threshold from your gray matter segmentation map
in order to put the above values to 1 and the others to 0. Than you could
eliminate the basal ganglia by a logical routine setting to 0 every voxel
between a certain coordinate.
I tried this approach once just for testing the feasibility, and it allowed me
to use less conservative threshold (although the gain was not proportional to
the volume loss - see Matthew's pages on SVC for reasons to that).
Does this sounds reasonable ? Did anyone else tried this, and what difficulty
did they have to cope with ? The most critical point I faced was the threshold
do use (as far as I remember, 200 seems to be resonable). Any advice on that
point ?
Since I did try this at the time of SPM99 beta and using Matthew's SVC routines
(that gave the uncorrected p to use for equivalent corrected p), I faced a
problem of representation : how to display the only activation falling within
the mask (except by removing them 'by hand' from the T.img using the same mask
- I haven't tried that) ?
Thanks for any input
Sincerely
Jack
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