Hello,
I am hoping to run the denoising pipeline in subject space. However, I've noticed that during the denoising step, the MNI atlas is used to mask the data. Obviously this is not ideal - I have GM,WM and CSF masks in subject space to use for any sort of tissue prior needs. How can I make it so the MNI brain is not masking the denoised data? 

I've attached the MNI brain over my GM outline. My functional data looks exactly like the MNI brain and the functional data overlap, so its clear that its being masked.