Anusha,
> I have a question regarding FDR probability.
>
> Inorder to study the FA value differences between two groups I perform
> two-sample t-test under basic models in SPM2. The tmaps look good but non of
> the clusters were significat at FDR/FWE < 0.05. So to reduce the multiple
> comparisons,
>
> 1. I generate t map with Puncorr < 0.05 and k = 50 and save it as an image.
> 2. I re-do the basic model-two-sample ttest, with the t-image generated as
> explicit mask.
>
> The tmap and the t/z values are exactly the same as before and the FDR/FWE
> have lower probality values, as expected. My question is;
>
> 1. using a mask as in (1) is it acceptable ? My reason for using such
> a mask is that I am only interested in testing those volxels with
> Puncor < 0.05.
No, I'm afraid it's totally invalid. You are in essense throwing away
all the data w/ Pucorr<0.05 and pretending like it never existed. Put
another way, you are using your statistic image itself to define what
regions to make inference on, which is a no-no; by assessing the
Puncorrs you have gone and done many tests and you have to account for
this.
> 2. all clusters listed obtained with explicit mask as in (1) have
> same FDR values. why is this?
I would have thought they changed some; do they not change a bit, even
if you increase your Puncorr thresh? (Say to 0.001)?
That they didn't change at all could be attributed to FDR's
adaptiveness; FDR inferences are determined by the emperical
distribution of P-values; by throwing out big P-values you've
truncated the distribution but possibly haven't changed the shape of
the tail of the distribution that much.
However, it is possible that you've found a bug. If you see
absolutely no change in FDR P-values with ever smaller masks, then
there would appear to be a problem. Let me know if that seems to be
the case.
-Tom
-- Thomas Nichols -------------------- Department of Biostatistics
http://www.sph.umich.edu/~nichols University of Michigan
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-------------------------------------- Ann Arbor, MI 48109-2029
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