Can you make a difference overlay of two scalar overlays?

Support
1

If I have two scalar overlays for the same model, is there a way to create a new overlay that gives me the difference between overlay 1 and overlay 2?

Operating system: Windows 10
Slicer version: 4.8.1

2

If by “scalar overlay” you mean scalar data associated with points or cells of a mesh of model node, then it is really easy to do using numpy, since you can get the values as an array, and do any operation, and then create a new array or update an existing one with the result. For example, you can store difference of two arrays in one of the arrays like this:

a1 = slicer.util.arrayFromModelPointData(modelNode, 'SomeArray')
a2 = slicer.util.arrayFromModelPointData(modelNode, 'SomeOtherArray')
a1[:] = a1-a2
slicer.util.arrayFromModelPointsModified(modelNode)

In Slicer-4.8.1, some of these convenience methods may not have been added yet, so you can either use a recent nightly, or add these methods to your code (see for example here: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/util.py#L773-L783).

3

Thank you!

I had been given two different FreeSurfer thickness maps from two populations and wanted to show the difference between the two. I loaded them in as scalar volumes and then subtracted the volumes and reloaded them as scalar overlays to visualize on the surface model. Would that do the same thing?

4

Slicer can read FreeSurfer geometry and thickness scalar overlay maps and create MRML model nodes. The model node has a function called Composite Scalars that can combine two scalar overlays that are associated with a single model to show the differences between one designated as background and one as foreground.

Nicole

5

That looks like it would be perfect! Can you give me any information on how to implement this? I apologize for my lack of familiarity.

6

It’s not exposed via the GUI, you’ll have to do some coding to call it. Assuming you’ve loaded a left hemisphere model and two thickness maps as scalar overlays (in my case thickness and area) you can do the following in the python console:

lh = slicer.util.getNode(‘lh’)
lh.CompositeScalars(‘surf/lh.thickness’, ‘surf/lh.area’, 0.0, 1.0, 0, 1, 0)

It creates a new scalar overlay called [name1]+[name2] and sets it active. You’ll need to adjust the numerical parameters to get the compositing you want.
You can see the scalar range of the overlays in the Models module, Display, Scalars section.

Nicole

1 Like
7

That’s great! Thank you so much!

I notice that it only displays positive numbers. Is this just giving me the absolute difference? Is there any way to specify that I want the foreground subtracted from the background?

8

The compositing of the scalars doesn’t do addition or subtraction, it’s a logical operation showing either the one overlay or the other depending on a comparison of values (this was a specific function I included years ago for FreeSurfer overlay display for a project). Check the code comments in the link above for implementation details. If you need mathematical operations, Andras’s method will be necessary.

Nicole