We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
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.
If you plan to do an ROI analysis, then assuming the ROIs are actually inside the brain masks, then applying the brain mask won't make any difference.
Both the scaling and regress steps use a mask to decide which voxels to zero out. Other voxels are unaffected. That is why you need not apply a mask, it only hides results. One would usually prefer to see more results.