Hi Donald,
thanks! You write that "they are almost all significant if you've
properly used alphasim", so, can I infer that it is not problematic if
some p-values are not significant at cluster-level? Can I still report
them? Or have we done something wrong with alphasim?
10.07.2015, 18:17, MCLAREN, Donald kirjoitti:
> If you have used alphasim, you don't need to report the cluster
> p-values. They are almost all significant if you've properly used
> alphasim. In Alphasim/3dclustim, make sure that you use the smoothness
> of the data and not the smoothing kernel size.
>
> Best Regards, Donald McLaren
> =================
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General
> Hospital and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> <http://www.martinos.org/%7Emclaren>
> Office: (773) 406-2464
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> On Fri, Jul 10, 2015 at 10:59 AM, MRI Study
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Thanks Helmut and Donald for your very helpful and quick replies!
>
> I just have one more question; so we've performed an "alphasim"
> correction for the data and thus gotten the cluster size. Do I
> still report the cluster level pFWE correction, or can I use
> cluster level p-uncorr data?
>
> Best regards!
>
>
> 10.07.2015, 16:35, H. Nebl wrote:
>
> Oh yes, and the "& extent threshold {voxels}" doesn't perform
> any statistical test, you can enter any arbitrary number if
> you want to. However, if you go with the default "0" you can
> then look at the bottom of the results table, FWEc tells you
> the size of the smallest, still sig. cluster, e.g. 112 voxels.
> You can then reload the SPM.mat, take the same uncorrected
> voxel threshold (e.g. .001), followed by "112" for "& extent
> threshold {voxels}". This way only sig. clusters are displayed
> in the glassbrain and reported in the results table.
>
> If you go with correction on voxel/peak level there's no need
> for an additional correction on cluster level, but often,
> people go with an arbitrary extent threshold of a few voxels
> (e.g. 5, 10, 20) nonetheless. Their implicit assumption is
> that while the voxels are significant by itself (due to
> surviving the voxel threshold), they are only relevant if they
> form a "cluster" of several connected voxels.
>
> For the statistical concepts behind voxel and cluster
> thresholds I'd suggest to look at the corresponding
> literature, but e.g. these sites
> http://mindhive.mit.edu/book/export/html/90 and
> http://support.brainvoyager.com/functional-analysis-statistics/40-cluster-tresholding/87-users-guide-the-multiple-comparisons-problem.html
> might give a first overview.
>
>
