Howdy-
I ran:
@SUMA_AlignToExperiment \
-exp_anat FT_anat+orig. \
-surf_anat ~/REF_TEMPLATES/MNI_avg152T1+tlrc. \
-wd \
-align_centers
... and got "MNI_avg152T1_Alnd_Exp.A2E.1D" (-> which is the mat_MNI_to_anat).
And I ran:
align_epi_anat.py \
-dset1 short_epi+orig. \
-dset2 FT_anat+orig. \
-dset1to2 \
-partial_axial \
-dset1_strip None \
-dset2_strip None \
-edge \
-cost lpa
... getting "short_epi_al_mat.aff12.1D" (-> mat_EPI_to_anat). Note that in this step, the whole EPI time series was selected---is that really what you want? Normally we use 3dvolreg for across-EPI motion correction, and just select a single volume from the EPI time series to align to the anatomical. (It will take a much longer time to have the whole EPI aligned in the way currently coded here; in your case, it sounds like you should already have a processed/motion-corrected EPI time series, anyways?)
I can then run:
cat_matvec \
-ONELINE \
MNI_avg152T1_Alnd_Exp.A2E.1D \
short_epi_al_mat.aff12.1D -I \
> mat_MNI_to_EPI.aff12.1D
... with no error. (Note the use of ">" to redirect the output---that was missing from your command, above, and would create a "missing" file error, but it would be a different filename than what you had input.)
Note that I don't think I would use @SUMA_AlignToExperiment in this way, if I were wanting to bring a volumetric ROI dataset from one space to another. It should be OK, but I would probably use 3dAllineate if I only wanted affine, and (as noted above) a nonlinear program for closer alignment.
--pt