We're using align_epi_anat.py to perform coregistration on resting state MRI data. The script does work but it doesn't give us the desired output. As input we're giving a .nii.gz anatomical file and a functional .nii.gz file with about 98 volumes. Align_epi_anat.py gives us a 1D file as output, which makes sense when looking at the docs, but we're wondering if it's possible to receive a 4D file with more than one volume. For further preprocessing steps it wouldn't make any sense to continu on with a 1D file.

Is there an option in align_epi_anat.py or are there different programs with Afni?

Thanks in advance.