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SPM for programmers » Extent threshold
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Code Martin Pyka on 28 May 2010 04:50 pm

Extent threshold

The “extent threshold” function deletes all clusters in a given contrast image that consist of less than k voxels. The corresponding matlab code can be found in spm_getSPM.m (line 674f). In case you would like to use this code manually for other imaging data, here is a matlab-function called extentThreshold that allows you to apply the extent threshold on a 3d volume of your choice.

The function can be used in the following way: if data is a 3d-matrix (of let’s say voxel values) and you want to display clusters with voxels that are greater than zero and with a cluster size of at least 20, write:

indices = find(data>0);
newdata = extentThreshold(data, indices, 20);

newdata includes only the elements of data that are greater than zero and that belong to a cluster with at least 20 other elements exceeding this threshold.

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