afni.nimh.nih.gov

Another alternative is the Threshold plugin, which uses a simpler algorithm for brain
extraction than 3dIntracranial does. (Sometimes KISS is a win.) If you try this and it works well for your application, please let me know.

Note that the current version of the Threshold plugin (listed at the bottom of the help page) is 1.1. Version 1.0 had some problems with Siemens data sets (and perhaps others).