There is no reason why you shouldn't be able to get the cut-off size from monte carlo simulations. It just depends on the program you use to do it. For example, AFNI's AlphaSim gives cluster sizes as a function of corrected p-value.
By the way, monte carlo simulations are a waste of time. Keith Worsley's "Random Field Theory" method (http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m) can be used to directly (in seconds) estimate the cluster size thresholds given: total surface area number of vertices fwhm smoothness
I've found (Hagler et al., Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data, NeuroImage, 2006) that RFT and monte carlo simulations give practically identical results.
See the attached matlab script for a wrapper around Worsley's code to calculate the cluster size thresholds using RFT.
From: Robert Levy levy@nmr.mgh.harvard.edu To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] determining sizes of clusters at given CWP cutoff Date: Fri, 03 Aug 2007 11:44:33 -0400
Hi,
I was trying to figure out if there is any way to determine the exact size at which clusters becomes significant given a specified significance, and it appeared from the mc-corrected overlay that in this overlay the clusters do not continously change in size but appear discretely at a given threshold and are the same size at higher thresholds in an all-or-nother sort of way. I take this to mean that because the monte carlo simulation was performed at a given threshold, the clusters at that threshold size are corrected for mutiple comparisons based on the probability distribution of the chance data (though I don't know the details). Because it is done in this way, it seems I would either have to run several monte carlo simulations, at successively higher minimum thresholds, in order to arrive at the critical cutoff sizes for significance. This is impractical, so I guess my question is, does the way in which the monte carlo simulations are done preclude the possibility of getting the cluster sizes at which they will have a certain CWP value, or is there some way of doing this?
Thanks, Rob
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Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy@nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078
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