Hi-
I don't think that the file after the "-1Dmatrix_apply" argument is correct. I ran your initial align_epi_anat.py command on my computer with BRIK/HEAD files, and the matrix didn't have the "+orig" part in that file name. Can you tell me what the output of this is?
\ls Q08.DLPFC.T1.Pre*_al_keep_mat.aff12.1D
I am assuming that it will be:
Q08.DLPFC.T1.Pre_al_keep_mat.aff12.1D
If that's the case, then does this 3dAllineate command work for you?
3dAllineate -source Q08.DLPFC.T1.Pre+orig -master Q08.DLPFC.T1.Pre_al_keep+orig -final wsinc5 -1Dmatrix_apply Q08.DLPFC.T1.Pre_al_keep_mat.aff12.1D -prefix anat_w_skull_warped
--pt
