afni.nimh.nih.gov

Maybe I am missing something, but sub002.warp.mat.1D
(the source of warnings from 3dAllineate) does not look
like what would be created by your cat_matvec command.

Instead of sub002.warp.mat.1D, it looks like you are writing
something like sub002_01.warp.mat.1D, which has the run
number in it.

- rick