Patrick -- Thank you for your question to the ADNI MRI Core.
Since your question is with co-registering the images, and not the masks themselves, the analysis team would recommend you get in touch with the team that developed the MINC toolkit for assistance navigating their software, or utilize a different program altogether. The analysis team at CIND primarily uses of SPM8 for co-registration, which has a fairly user-friendly interface. There is other software one can use for mask overlay, such as MIPAV, but if the images need to be moved into the same space for analysis.
Thank you
ADNI MRI Core