Then I use the transform module to check if the registration has been correctly. I have started off with both geometries and tried different orders of the transformation (in combination with hardening transform) but the two geometries do not seem to overlap. My question is whether the registration has taken all three listed transforms into account and if my method of checking the registration using transform module is correct? Any help/suggestions would be appreciated.

I am fairly certain that the transformations are independent, i.e. the BSpline deformable and the affine transform are not related, but can be set independently. This means that if you set the Deformable Transform to the moving volume / segmentation, then the result should be applied correctly.

It’s another question if the result is good or not. You can debug where it went wrong by checking the Keep intermediate nodes checkbox and visualizing the results. There are two distance map images that are generated from the two segments on the geometry of the input images (that’s why you need to also specify the volumes that the segmentations correspond to!), and are registered using different methods (i.e. the affine and deformable BSpline). Try to show these distance maps on top of each other (set the moving one as foreground and set opacity to 0.5), and apply the result transformation on the moving one. We can go from here.

@cpinter sorry but I do not understand when you say visualising distance maps. Where do I do this from? I can visualise the intermediate geometries and also apply the transform to the moving model.

If you turn on the option I mentioned then a lot of extra objects show up in the Data module. Two modules there will be the distance maps. You can identify them by name

The registration approach implemented in the Segmentation Registration Module involves several steps (hence you will see several intermediate results generated). You might want to take a look at the code to understand the approach better

The last step uses the distance map based registration implementation in SlicerProstate extension

Hi @cpinter, I can see the two distance maps (volume) under data but cant visualise them in the 3d viewer. I only see a set of geometries presumably including the one at intermediate step.

I could visualise the distance map (both fixed and moving) volume using volume rendering but for some reason it seems the scale of the two distance maps are off by quite a lot. Is this expected?