afni.nimh.nih.gov

Sure! You can tell afni_proc to just do the mask and regress steps and then feed it the motion file (that you'll have to modify from fMRIprep).

Here's a related tutorial about running afni_proc to do different analysis pipelines for just regression that may be helpful. I can type it out more if it's not clear.

[blog.cogneurostats.com]