Whole bovine brain segmentation/registration

Hi,

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.

Thank you.

Dan

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