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.
The coordinates in the AFNI GUI are actually
irrelevant, as they are given in a "standard"
orientation (either RAI or LPI, say). That is
so that a brain looks like a brain, and those
coordinates mean the same thing across
subjects and datasets per subject.
Your slices are left to right, so that is what
3dmaskave would use with the -slices option.
So you were planning to class 3dmaskave
repeatedly, once for each slice? That should
work.