afni.nimh.nih.gov

Quote
dbliss
Fair enough, but the call to cat_matvec is described as catenating the volreg and epi2anat transformation, but it is catenating the anat2epi transformation with the volreg one.

Adding the -I option after an input in cat_matvec will invert the transformation matrix. So while the file is the anat2epi transform, the inverse is the correct epi2anat transform.

You can (and should) always check the alignment using AFNI or @AddEdge.