Hello,
I wanted to ask if I understand the help correctly and not missing something.
In afni_proc.py I want to use a -volreg_base_dset that is different from -align_epi_ext_dset: MIN_OUTLIER vs. epi[0], the latter is otherwise removed by -tcat_remove_first_trs. As all epi volumes are aligned to MIN_OUTLIER, but epi[0] is used as a basis of anat alignment, any difference between epi[0] and MIN_OUTLIER should be included in the pipeline as another transform, correct? Do I have to explicitly do that in any way? Or, as I am inferring from the help, this is handled internally by afni_proc?
