Hello AFNI gurus,
A minor question and observation. Why did the default EPI masking in afni_proc.py change from applying 3dAutomask with dilation of 1 voxel to using no dilation? I noticed this while comparing coverage maps from two different datasets, one processed with a more recent version of AFNI in which the dilation is not applied, and just want to be consistent (easy enough to rerun 3dAutomask). Just curious, what is the justification for this change? Also, wanted to point out that the afni_proc help doc (https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html) still says that a dilation of 1 voxel is applied by default.
Thank you for your support!
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.
Gotcha, that makes sense. Thank you Rick!