We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
The script does the skullstripping based on the alignment of the brain to a template instead of the usual method in 3dSkullStrip. The output is a skullstripped brain. Presumably, you would apply the same transformation to the EPI dataset. The "BASE" refers to the template in this case.