Ray,
About your question on the Corrected Cluster Size threshold script
( http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0504&L=spm&P=R14014&I=-1 )
...
> I read your recent contribution to the spm list and I wondered if you
> could help me out (I am quite new to spm). Does the script you kindly
> posted allow inferences to be based on cluster size rather than on voxel
> based statistics (either corrected or uncorrected).
That's precisely what it does; it tells you the critical cluster
size threshold, corrected for searching over the whole brain.
> I guess what I am asking is does it change the behaviour of spm such
> that MIPs are shown based on cluster extent?
Well, in as much as this script lives totally outside of the SPM
GUI, it has absolutely no impact on the behaviour SPM results.
But the very purpose of the script is what you suggest in your question:
What "Spatial Extent" threshold should I tell SPM Results to use? By
using the script I posted, you can find out the threshold that
will exclude any clusters not significant at (say) 0.05 corrected.
> Is this something like the cluster stats implemented in FSL?
That's right; if you select cluster-based significance in FSL, it
filters out all blobs that aren't significant.
> Finally, I would really appreciate it if you could let me know how to
> implement the script. Where do i place the file CorrClusTh.m and what
> is the call up in matlab.
Put it in your local matlab directory where you put all scripts
(e.g. /usr/local/spm/spm2_local, or c:\spm\spm2_local, and make sure
that directory is on your matlab path) or put it in the current directory
where you are working. Then just type CorrClusTh.
Hope this helps.
-Tom
-- Thomas Nichols -------------------- Department of Biostatistics
http://www.sph.umich.edu/~nichols University of Michigan
[log in to unmask] 1420 Washington Heights
-------------------------------------- Ann Arbor, MI 48109-2029
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