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.
That's a longstanding issue: align_epi_anat.py doesn't like NIfTI files (it can't deal with the .nii or .nii.gz file names, only +???.HEAD/BRIK file names).
As Daniel mentioned, a workaround is to use 3dcopy to convert the files into AFNI file format.