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.
Use an AFNI format as intermediate file. The 3drefit command is meant to work only on AFNI format datasets and not NIFTI files, the format of your input dataset. Copy the input dataset to AFNI format with the 3dcopy command, and then 3drefit to change the orientation and deoblique.