Registering MNI image to template using mrregister

Hello MRtrix community,

I am encountering challenges with registering and transforming MNI images to a template space using MRtrix. Here’s a breakdown of my issue:

  1. Problem Overview:

    • I used the mrregister command to register each ROI to the template mask (template_maskPS1.mif) using an affine transformation. However, the registration did not succeed as expected. Only 6 out of 8 ROIs had output files generated, and they were incorrect.
  2. Questions:

    • How should I structure my mrregister command to ensure proper output?
    • After a successful registration, how should I structure the mrtransform command to correctly transform the files to the template space?
    • Are there specific parameters or settings I should adjust in mrregister or mrtransform for better alignment results?
  3. Data and Checks:

    • I have verified the compatibility of my ROI files (CC.nii.gz, etc.) and the template mask (template_maskPS1.mif). They appear to be correctly formatted and aligned spatially.
  4. Overall goal:

    • I want to use various ROIs defined by an MNI atlas to extract FBA based metrics (the template space i am trying to register to).

Any insights or guidance on troubleshooting or improving this registration and transformation process would be greatly appreciated.

Thank you for your assistance.

Best regards,
Paige Spencer