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 continue to struggle, you may need to try doing some hand alignment first before allowing 3dAllineate/align_epi_anat.py to work their magic. I've written up some instructions here. It closely follows the methods we used to perform with ANTs, just with AFNI tools.