I work on bovine brains and am trying to fully segment pre and postoperative MRIs, then register them to compute the difference in brain tissue between the two sets of MRIs. I have put plastic fiducials to help with registration but am facing a few difficulties.
- Because of the amount of brain deformation during image acquisition, I have trouble doing a rigid registration before applying affine registration. Is there a way to designate whole structures as fiducials on 3D slicer before registration?
- What format should I save my segmentations in to do registration of segmentations? I am trying to register 2 whole brain segmentations.