## June 03, 2010

### SPM5 Gem 6: Corrected cluster size threshold

This is SPM5 version of SPM2 Gem 13.

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)

Try increasing the range or an automatic search.
```

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!

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