afni.nimh.nih.gov

align_epi_anat.py has -partial_... options that might help. Still, it can be difficult depending on how much spatial structure there is in the anatomical datasets. It's usually best to acquire partial coverage datasets with a full brain dataset, and then use alignment of that full brain dataset to pull the partial one as a kind of follower dataset.

There was a recent thread here too on the available manual tools:
[neurostars.org]