Are there some things missing from that command? I don’t see an “-epi …” input, for example, and there are an odd number of double-quotes.
As an example, this is an example of align_epi_anat.py generated by afni_proc.py from the Bootcamp example in “AFNI_data6/FT/FT_analysis/”:
# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, FT_anat_ns+orig)
align_epi_anat.py -anat2epi -anat FT_anat+orig \
-save_skullstrip -suffix _al_junk \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-cost lpc+ZZ -giant_move -check_flip \
-volreg off -tshift off
… though perhaps you have based your own command on this?
That being, said, you mention that a “1D file” is output— I had interpreted this as a “1D text file” of alignment parameters, but perhaps you mean a “3D volume” gets output, which is should with the specified suffix, because you juxtapose it with getting a 4D volumetric output? Could you please list the outputs you do get?
Note that EPI-anatomical alignment is a 3D volume to 3D volume procedure: one EPI volume gets picked out. Typically the “whole time series being aligned” procedure comes from 3dvolreg, aligning each EPI volume to a particular EPI volume (called the “base EPI” volume, chosen using a nice minimum-outlier criterion within afni_proc.py).
The 3dvolreg command is run separately, as is anatomical-to-template alignment, and all the alignment procedure outputs are concatenated before applying them as a single transform to the original EPI dset. A lot more about this procedure and these considerations are described in the AFNI Bootcamp videos on alignment:
Note that afni_proc.py handles a lot of this concatenation/etc. under the hood, and it is a really useful tool for designing a processing pipeline.
Please let me know if I have misunderstood the question here and waffled on needlessly (which is a distinct possibility…).