Hi Ben,
Thanks there are a few places in the help that need to be updated.
The original default of 1 made more sense a long time ago, when we used to actually mask the EPI data in orig space. But for years now, we have not. So that mask now is used not so much for removing non-brain voxels, but for doing computations (besides the final regression) over voxels where we think valid brain data is. Some computations are thrown off a bit by having non-brain voxels included (TSNR average, smoothness, correlation volumes, etc).
So it seemed much better to make that a tighter and more accurate mask, at least by default. Users can always ask to make it bigger.
Thanks again, I will make some updates to the help.
- rick