Register uCT scans with conventional CT scan

I am trying to register a microCT scan of an implant with a conv. CT of the same implant within the jaw.

I transformed the microCT scan to the correct position however the final 3d-3d registration fails. Even when I resample the microCT image to the same voxel sizes (which means a significant reduction of the visualization of the implant).

I also tried elastix modul.
So my question is, whether there is a chance at all to automatically register them or is manual the best I can achieve?
I uploaded an example of the manual transformation outcome…

Kind regards

How can I remove the rest of the unsegmented area?
I am only interested in the segmented implant and want to remove all other grey values!

The mask tool lets me only fill the voxels with a different intensity…

Shape of an image array is always a box and you need to set some value in each voxel of the array.

What would you like to achieve with the registration?
Does the registration need to recover rotation around the long axis of the implant?

Yes the registration would need to recover the rotation around the long axis of the implant.

  1. I want to register the uCT scan of the implant with the same implant in a jaw from a conventional CT scan. For the registration I need to mask out everything except the implant, which seems to work with the mask tool.

  2. After the registration, I want to transfer the implant position to a CT scan from a jaw without any implants, i.e. fuse 2 scalar volumes using add scalar volumes.
    I tried substract scalar vol (because faster compared to add) which results in a “black” implant in the ct scan of the jaw, however I get deteriorated voxels around the “black” implant in the extent of a box which I want to avoid.

Is there an option for “transparent” voxels, so that the voxels of the other CT scan are not changed around the “blanked out” implant.
Finally, I would prefer the add scalar vol option as I would need the implant in the CT scan to be as in uCT.

There is no need for “transparent” voxels, just set voxel values outside the implant to 0. Adding/subtracting 0 will not alter the volume.

You can use Threshold scalar volume to set values outside a chosen intensity range to 0.

If you want to fine-tune what happens at the implant’s boundary then you can use Segment Editor’s Mask volume effect (provided by SegmentEditorExtraEffects extension).