Hi there,
Thanks for your response.
The command we're running is:
align_epi_anat.py -anat2epi -anat " + functional_dir + " -save_skullstrip -suffix "
"al_junk -epi " + input_name_coregistration + " -epi_base 0 -epi_strip 3dAutomask -giant_move -volreg off -tshift off"
Where the functional_dir is a .nii.gz with more than one volume and the input_name_coregistration is a anatomical.nii.gz with only 1 volume.
This is in Python with string concatenation, the input files are saved in a variable because we're running it in a pipeline.
I am using Afni version AFNI_21.0.12 'Titus' on MacOS Big Sur.
Thanks,
Eric
