Registration - lining up fiducials into the same plane

I am registering histology and MRI images by using fiducials in the Markups module then performing initial rigid landmark registration, then going to the transforms module. I am having difficulty after transforming when aligning the 2 images (MRI and histology) so that they are in the same plane. I’ve succeeded by manually moving the 3D images but I am finding this to be very tedious, and very difficult at times. Is there anything that can automatically align the fiducials into one plane?

I’ve attached some sample images. The first image is one where I was able to manually align everything but case 2 I am still having difficulty and the fiducials are not all in one plane with the MRI and histology overlaying each other.

Case 1 (good):

Case 2 (having problems!! bad!!):

Hi -

Sounds like an interesting use case and a workflow that would be nice to support. If you are able to share a sample dataset and instructions for replicating the issue then I’ll bet there are some simple python commands that would help, like projecting the fiducials to a best fit plane.

Hi Steve -

I’ve uploaded a sample dataset you will be able to access here:

I’ve done everything prior to projecting the fiducials all into one plane, so you don’t need to worry about that. :slight_smile:

After loading the dataset into Slicer, double-check that ALSP_5_F_01_Biels is loaded as the foreground and 05_F_N4ITK is loaded as the background in the red slice view.

Thanks so much for your help and let me know if you need anything else!

Hi @uwo27 -

Thanks for sharing the data - I finally had a chance to look at it and I am able to load it (looks like your Case 2 screenshot above). But I’m not really sure what I am looking at and what you need next.

In particular what is the 05_F_ALGN volume? It looks like different slabs of brain stacked at random? Maybe it would help to start if you could list out the nodes in the scene with a brief summary of what the data is and how you need to use it.