Dear Alfonso,
Thank you so much for this answer! It worked great. I have another question- we want to stay in the subject volumetric space (not a surface). Our preprocessing output has a u*.nii file name, and is still in the native space. The problem is that after denoising the du*.nii file is no longer in the original resolution ans space, but in the mni space. That said, it seems that the brain itself did not go through the normalization process but only been resliced, probably due to our need to use the denoising step of csf\WM\GM regressors. 

Is there a way to recieve the du*.nii output in both the original space and resolution of the subject?

Thank you!
Inbar