Segment registration

I am trying to compare the coordinates of a geometry before and after deformation in order to compute displacements in x,y and z direction. I am using segment registration feature from 3D slicer to register the two segments. However, when I press perform registration, it just loads but does not do anything. Just wanted to know if I am doing it wrong or if this usually takes very long time. I have attached a pic of my segments and the setup used.

Could you try if registration works if you select a fixed and moving image? You can probably use a labelmap volume exported from the segmentation (by right-clicking on the segmentation in Data module).

Hi Andras,

Thank you for your prompt reply. I created the segments from stl files. When you refer to labelmap volume from the segmentation, do you mean to say exporting as binary labelmap? (screenshot attached)

When I do this and retry registration, i still cannot select anything from the image i.e the volume dropdown.


Probably it expects a scalar volume and not labelmap volume. Go to Volumes module’s Information section to convert the labelmap volumes to scalar volumes.

Hi Andras,

My overall aim is to determine how the coordinates of test3 changes as it moves to the configuration of test4 (see pic below)

The segment registration does seem to complete when i use the scalar volume as input. However, i still do not understand how I can use the end result to fulfil my aim and if indeed the registration has been done correctly (attached the results i can view after registration) .

From my understanding, in the surface registration module, the initial configuration actually transforms to the desired configuration and this way I could export both the initial and transformed coordinates and find the change in X,Y ,Z. Since this module only works for rigid motions, I am using the segment registration instead but I cant see the transformation happening in this module.