In order to align a session's anatomical scan to the first volume in the first EPI run, I'm issuing the following command:

align_epi_anat.py -anat 8391-T1+orig -epi pb01.8391.r01.tshift+orig -epi_base 0 -volreg off -tshift off

This caused a file I wasn't expecting to be created:

8391-T1_al_e2a_only_mat.aff12.1D

I can't find any description of this file in the align_epi_anat.py or 3dAllineate documentation, but I traced it to the following commands, called within align_epi_anat.py:

3dAllineate -lpc -wtprefix __tt_8391-T1_ns_ob_al_wtal -weight ./__tt_pb01.8391.r01.tshift_ts_rs_ns_wt+orig -source ./__tt_8391-T1_ns_ob+orig -prefix __tt_8391-T1_ns_ob_temp_al -base ./__tt_pb01.8391.r01.tshift_ts_rs_ns+orig -nocmass -1Dmatrix_save 8391-T1_al_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass

cat_matvec -ONELINE 8391-T1_al_e2a_only_mat.aff12.1D __tt_8391-T1_ns_obla2e_mat.1D -I > 8391-T1_al_mat.aff12.1D

It looks like this transform is being concatenated with another one to create the final matrix that transforms the anatomical scan to be aligned with the EPI one. But what exactly is 8391-T1_al_e2a_only_mat.aff12.1D, and why doesn't align_epi_anat.py treat it like the other temporary intermediate files, and delete it before completing?

Many thanks,
Dan