I am applying the align_epi_anat.py function and would like to know what the default number of degrees of freedom is. I am not using the rigid_body or rigid_equiv flags, and I cannot find on the documentation what the default number is. I am assuming it is 12, but I could be totally wrong. Please let me know.
It is 12 degrees of freedom: 3 rotation + 3 translation + 3 shear + 3 scale. These will be stored in an output *.aff12.1D file. You can ask for fewer degrees of freedom, with some of the options you noted.
You might be interested in the AFNI Academy playlist about alignment.
The relevant handout about it is:
afni_open -aw afni14_alignment.pdf
esp. slide 14.
--pt
Thank you!! That resource was very helpful