> How can I see images with a threshold at the cluster-level instead of the peak level with the graphical user interface?
I'm not aware of a way to set a cluster-level threshold when running
results the first time (i.e., "show everything that is cluster-level
corrected p < .05"). What I would do is this:
1) Run results using some voxelwise threshold. This threshold defines
your clusters, and it's fine to use an uncorrected threshold (e.g., p
< .001, uncorrected).
2) In the results table, for each cluster you will see the cluster
extent (i.e. how many voxels) and the cluster-corrected p value. In
SPM8 you will see 2 cluster-corrected p values, one for topological
FDR (Chumbley & Friston, 2009), one for random field theory (labeled
FWE). You can then look at the size of those clusters, and figure out
the cluster extent that divides p < .05 from the others. For
example, if a cluster of 300 voxels is p = .10, and a cluster of 400
voxels is p = .04, then you know that any cluster 400 voxels or larger
would be p < .05.
3) Re-run the results, selecting the same voxelwise threshold. But
now, in the minimum cluster extent, specify the cluster size you just
figured out—in the above example, you could specify 400.
4) Now all of the displayed results should be cluster-level corrected.
5) If you want to save this thresholded image for displaying with
another program, just click the "save" button, and you can write out a
thresholded t map as a nifti file.
In practice this is actually fairly quick to do once you've done it a
couple of times.
Hope this helps!
Chumbley JR, Friston KJ (2009) False discovery rate revisited: FDR and
topological inference using Gaussian random fields. NeuroImage
Dr. Jonathan Peelle
Department of Neurology
University of Pennsylvania
3 West Gates
3400 Spruce Street
Philadelphia, PA 19104