Preprocessing of MRI anatomical images

I am using ABIDE dataset for Structural MRI analysis. I am willing to run CNN for it. Can someone guide me on the preprocessing of the anatomical(structural ) .nii images. I am confused as to what tools to use and what each step means.

If you know now, can you help me. What are the steps?

It’s not clear to me what you’re asking. What specifically do you want to do?

How to apply simple CNN on neuroimaging data (where data is in format .nii AND .dcm)?