June 03, 2010

SPM2 Gem 13: Corrected cluster size threshold

This is a script that will tell you the corrected cluster size threshold for given cluster-defining threshold: corrclusth.m

The usage is pretty self explanatory:

 Find the corrected cluster size threshold for a given alpha
 function [k,Pc] =CorrClusTh(SPM,u,alpha,guess)
 SPM   - SPM data structure
 u     - Cluster defining threshold
         If less than zero, u is taken to be uncorrected P-value
 alpha - FWE-corrected level (defaults to 0.05)
 guess - Set to NaN to use a Newton-Rhapson search (default)
         Or provide a explicit list (e.g. 1:1000) of cluster sizes to
         search over.
         If guess is a (non-NaN) scalar nothing happens, except the the
         corrected P-value of guess is printed. 

 Finds the corrected cluster size (spatial extent) threshold for a given
 cluster defining threshold u and FWE-corrected level alpha. 
  

To find the 0.05 (default alpha) corrected cluster size threshold for a 0.01 cluster-defining threshold:

>> load SPM
>> CorrClusTh(SPM,0.01)
  For a cluster-defining threshold of 2.4671 the level 0.05 corrected
  cluster size threshold is 7860 and has size (corrected P-value) 0.0499926
  

Notice that, due to the discreteness of cluster sizes you cannot get an exact 0.05 threshold.

The function uses an automated search which may sometimes fail. If you specify a 4th argument you can manually specify the cluster sizes to search over:

>> CorrClusTh(SPM,0.01,0.05,6000:7000)

  WARNING: Within the range of cluster sizes searched (6000...7000)
  a corrected P-value <= alpha was not found (smallest P: 0.0819589)

  Try increasing the range or an automatic search.

Ooops... bad range.

Lastly, you can use it as a look up for a specific cluster size threshold. For example, how much over the 0.05 level would a cluster size of 7859 be?

>> CorrClusTh(SPM,0.01,0.05,7859)
  For a cluster-defining threshold of 2.4671 a cluster size threshold of
  7859 has corrected P-value 0.050021

Just a pinch!


- No comments


Add a comment

Name
Email
Anti-Spam Question
My t-shirt is red. What colour is my t-shirt?
Anti-Spam Answer
Comment


Your IP address will be recorded. -

You can not use HTML, but you can use our special markup -

Search this blog

Tags

Most recent comments

  • Hi, Folks, conversion to HTML still works for PPT 2011 under OS 10.10 (as on my computer), with coup… by Andrew Fisher on this entry
  • HTML pages are different from PPT. It is possible to convert PPT in HTML page but it will create a p… by Ramjas on this entry
  • Hi This doesn't really address the issue at hand (powerpoint to html), but an alternative and very e… by Rose on this entry
  • @Michael. You are a SAINT. BLESS. by emma riley on this entry
  • I look this up every couple of years, and always struggle with it, so here are some notes for improv… by johann beda on this entry

Blog archive

Loading…
Not signed in
Sign in

Powered by BlogBuilder
© MMXIX