# Whole bovine brain segmentation/registration **URL:** \ **Category:** Support\ **Tags:** registration, segmentation\ **Created:** [December 30, 2019, 3:04pm UTC](https://discourse.slicer.org/t/whole-bovine-brain-segmentation-registration/9662 "2019-12-30T15:04:27Z")\ **Posts on this page:** 3\ **Page:** 1

**Author:** ![DanTran](https://avatars.discourse-cdn.com/v4/letter/d/c6cbf5/32.png) [@DanTran](https://discourse.slicer.org/u/DanTran)\ **Post date:** [December 30, 2019, 3:04pm UTC](https://discourse.slicer.org/t/whole-bovine-brain-segmentation-registration/9662/1 "2019-12-30T15:04:27Z")

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 ---

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\ **Post date:** [December 30, 2019, 4:36pm UTC](https://discourse.slicer.org/t/whole-bovine-brain-segmentation-registration/9662/2 "2019-12-30T16:36:56Z")

A post was merged into an existing topic: [Whole brain segmentation registration](https://discourse.slicer.org/t/whole-brain-segmentation-registration/9663) ---