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.
You can try align_epi_anat.py with the -partial_xxxx options (maybe partial_coronal for your case). The -AddEdge option allows you to examine the alignment closely in the AFNI GUI. The deobliquing can be done together with the alignment by the same program. See the help for align_epi_anat.py for more details.