Sorry, I have not used this toolbox much. Maybe Don can chime in.
doug
On Fri, 3 Apr 2009, Zhong Jidan wrote:
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 on the surface data.
Then i found there is a subject talking about this: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.ht...
In that talk,Don Hagler mentioned 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. function [cluster_threshold,peak_threshold] = fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval); *> % alpha: corrected p-value *>* % {default = 0.05} *>* % pval: uncorrected p-value *>* % {default = 0.001}
*I tried this function, and it does give me a cluster size with mm^2, say 100 mm^2. But I don't know whether this is the right thing to do.
As I'm doing some statistical analysis using GLM, so I also try the method from Keith Worsley's statistical toolbox, then I can get the cluster's No. of vertices and the corrected p-value(alpha=0.05) for the cluster.
Here is one example:
clusid nverts resels P
1 2205 18.2781 2.1299e-06 2 208 1.42105 0.013359 3 127 1.15533 0.026747 4 58 1.0443 0.036658 5 5 0.519762 0.20884 6 105 0.464429 0.2571
The thing I don't understand is , if we are looking for a cluster size threshold, then we can say that, the clusters above that threshold size is what we want to keep. And also, the p-value of the clusters above that threshold size should be below alpha we set, say 0.05. But when checking the tale above, the first four clusters' p- value is smaller than 0.05, then we should keep it. But according to the no. of vertices, we can caculate the cluster size in mm^2. Then the 4th cluster size is obviously below 100mm^2, the threshold we found using the function fs_calc_cluster_thresh. Oppositely, the 6th cluster has a large no. of vertices and its cluster size is above 100mm^2, while it's not kept because its p value is above 0.05.
I know what happened here is because of the 'resels', but it really confuse me which one is the right one. Since you said we can use the function, then why is the result conflicted with each other?
Could you tell me what's wrong here or what did I miss ?
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.htmlThanks a lot,
Jidan