Co-registration ROI with structural data

Hello,

I am a new user of Conn, and I have a question regarding ROI.
I want to process data with brain lesions. In order to do so, I wanted to add a ROI with a mask of the entire brain without the lesion.
These ROIs are not in the MNI space.
Should I co-register these ROIs (drawn on the original MPR T1) with the initial data, or after the pre-processing steps?
If I need to co-register the pre-processed data with my ROIs, where is the pre-processed MPR T1 saved?

Thanks a lot for your help!
Best,
Mickael