Is there the option to specify custom atlases in ASLPrep?
That’s not currently supported behavior, but if the atlases are in the same space as your chosen output-space, you can use something like Nilearn’s NiftiLabelsMasker.
If this is a feature you think we should add, please open an issue in the ASLPrep repo requesting it: Issues · PennLINC/aslprep · GitHub. I can’t guarantee that we’ll implement it, but we will definitely discuss it in the issue.