Yes, the matrix comes out as one of the 1D files. In your case, based on your previous logs, the file should be named refvol.lpcreg_al_mat.aff12.1D. That file will contain the elements corresponding to the 12 parameter matrix on each row. Each matrix combines the obliquity (s-form type matrix) with the motion correction matrix and the epi to anat transformations.

You don't really have to think too much about that (unless you really want) because there is an option (-master_epi) that takes SOURCE, BASE, MIN_DXYZ, n.nn (a cubic dimension) or the grid of another specified dataset.

This is from the hlep of align_epi_anat.py that's relevant:

-master_epi nnn : master grid resolution for aligned epi output
-master_tlrc nnn : master grid resolution for epi+tlrc output
-master_anat nnn : master grid resolution for aligned anatomical data output
(SOURCE/BASE/MIN_DXYZ/dsetname/n.nn)
Each of the 'master' options can be set to SOURCE,BASE,
a specific master dataset, MIN_DXYZ or a specified cubic
voxel size in mm.

MIN_DXYZ uses the smallest voxel dimension as the basis
for cubic output voxel resolution within the bounding box
of the BASE dataset.

SOURCE and BASE are used as in 3dAllineate help.

The default value for master_epi and master_anat is SOURCE,
that is the output resolution and coordinates should be
the same as the input. This is appropriate for small
movements.

For cases where either dataset is oblique (and larger
rotations can occur), the default becomes MIN_DXYZ.

The default value for master_tlrc is MIN_DXYZ.



You can let the script do this for you, or call 3dAllineate directly with the 1dmatrix_apply option and the 1D matrix file to apply and the -master option to give output grid options.