as you've noticed, SPM8's default is to report topological FDR results
(peak- and cluster-FDR). This is described in:
False discovery rate revisited: FDR and topological inference using
Gaussian random fields. J. Chumbley and K.J. Friston, NeuroImage,
44(1):62-70, 2009. http://dx.doi.org/10.1016/j.neuroimage.2008.05.021
and in another manuscript under revision.
The height threshold you define during the Results procedure is the
feature-inducing threshold (used to define local maxima and clusters).
For topological FDR, I would typically choose "none" and a small
T-value, for example 3.
The MIP will display all voxels whose T-value is above 3 and the Results
table will display all local maxima whose T-value is above 3 (actually,
at most 3 local maxima per cluster, more than 8mm apart) and the
corresponding FWE p-values and FDR q-values for peaks and clusters.
If you want to threshold the MIP to a particular significance level, go
through the Results procedure again and enter the corresponding height
and extent thresholds (the 0.05 critical thresholds are indicated at the
bottom left of the Results table):
(height) FWEp and FDRp for peak-FWE and -FDR.
(extent) FWEc amd FDRc for cluster-FWE and -FDR.
I hope this helps,
Claus Lamm wrote:
> Dear SPM8 developers,
> I just started using SPM8 to check out the topological FDR option, but I
> didn't find it other than via the FDR-values listed in the results table. Is
> there an option to threshold using topoFDR (in the way it used to be
> possible in SPM5), i.e. via a button used during the Results procedure?
> Thanks a lot,
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG