afni.nimh.nih.gov

How far in the analysis did it get? You don't give the full output of the program, so it's hard to say, but it looks like the program failed when creating the output dataset in memory at some point.

Are you using align_epi_anat.py or 3dAllineate directly? The former is to be preferred.

Are you aligning the structural to the EPI or vice-versa? Which one is -master and which one is -base?