Registration of head CT and MRI of sheep

Hi all,

Goal: accurately registering head CT (bone) and T1 MRI from ovine subject - to be used for surgical planning.

Problem: unable to apply general registration (BRAINS)

I am new to using 3D slicer for registration. I am currently attempting to register CT bone and T1 weighted MRI scans (head). The resulting registration will be used to plan neurosurgeries.

So far, I have manually transformed the CT scan to align with the MRI (both have been centred). I have attempted to then use general registration (BRAINS), however the resulting output is grey squares.

See google drive link for the DICOM images being used.

Any help or guidance would be greatly appreciated!


Default parameters of “General registration (BRAINS)” module work for human brain registration but you need to tune the parameters to work for other cases.

“General registration (Elastix”) module (provided by SlicerElastix extension) is much more robust. Its default parameter set works well for most registration tasks, as long as the two images approximately contain the same region.

Fully automatic registration of your data set took 2 minutes on my laptop using Elastix, using default parameter set, and the result looks almost perfect: