Hi,
I suggest you to check elastix (https://elastix.lumc.nl/, manual: https://elastix.lumc.nl/download/elastix-5.0.0-manual.pdf, examples of parameters files: http://elastix.bigr.nl/wiki/index.php/Parameter_file_database). They also have an extension based on SimpleITK (http://simpleelastix.github.io/). Your registration task gets much simpler as you may just need to define your fixed image (the 3T I guess), your moving image, and the correct parameters. The only thing I find weird is that you mention that your images only have a binary mask on one slice (only zeros and values with 255). It feels to me that you have masks that someone draw in images with more intensity values. If that is the case, you may need first to get those original images. Those are the ones you will be registering, and then you can apply the transformation between the moving image and the fixed image to these masks that you have. There’s plenty documentation regarding these registration steps that you may find on internet. You can also check the ITK Software Guide or ANTs documentation.
Good look with that,
RaC