I'm not sure from that description if they are looking for an affine transformation matrix or for the list of parameters. For the affine transformation matrix, our format for the 1D file saved by align_epi_anat.py/3dAllineate defines xyz->xyz both in RAI coordinates. The translations are every 4th number (the last column if laid out as 4 columns by 3 rows), so that might be "a b c j d e f k g h i l" as the one row in the text file.

cat m3d_ns_al2epi0_mat.aff12.1D
# 3dAllineate matrices (DICOM-to-DICOM, row-by-row):
0.995758 0.0152865 0.0198008 2.90661 -0.0164348 0.941894 0.347633 -13.4597 -0.00749007 -0.353944 0.946086 -41.2396

cat_matvec anat_ns_al2epi0_mat.aff12.1D
0.995758 0.0152865 0.0198008 2.90661
-0.0164348 0.941894 0.347633 -13.4597
-0.00749007 -0.353944 0.946086 -41.2396

On the other hand, if you need the list of parameters, these can be saved during alignment by adding "-1dparam_save" to the 3dAllineate options or by extracting an attribute for each sub-brick of the aligned dataset:

3dAttribute -name ALLINEATE_PARAMS_000000 anat_ns_al2epi0+orig
ALLINEATE_PARAMS_000000 = 2.906609 -13.45973 -41.23965 1.299778 20.24949 -1.2141 0.996072 1.004121 1.010128 0.004955 0.005911 -0.004357

In this case, the parameters are listed in order of translation, rotation, scale and shear (x,y,z for each, RAI). Rotation is about the center of the dataset. Translation units are in mm, and rotation is in degrees.