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 problem is your partial coronal data was not partial enough for 3dAllineate's center of mass correction to apply it correctly. The solution is pretty simple though; instead of specifying "-partial_coverage", use "-partial_coronal" or leave it out completely. Both seem to work well for this dataset.