Using a GP to model scalar value variance on a tetrahedral mesh of a humerus bone

[Michael Lennon]

Dear Scalismo team,

I have a high level question that I am hoping you can provide some guidance on.  I have been able to use Scalismo to create a set of images that were discretised using a tetrahedral mesh of the humerus bone.  All images shapes are identical size (after warping the different images to a reference image using ANTs) and the only variation between the discretized humerus tetrahedral meshes now is the scalar value which is the image intensity.  I could then save them as Scalar tetrahedral mesh fields using the UI.  My question is whether Scalismo currently has the methods to create a point distribution model where changing the alphas of the model would vary that scalar value on the fixed tetrahedral mesh?  I suspect this is a hopeful task but I notice that there is a method to create a DataCollection from s ScalarVolumeMesh3DSequence.  I am familiar with creating a data collection from triangle and tetrahedral meshes and then simply building a model with a datacollection using PointDistributionModel.createUsingPCA(dc).  I have also noticed that to create a Datacollection from ScalarVolumeMesh3DSequence  only takes one argument (vs 2 used for the other data collection types).  You can see my code below that I hopefully tried working with this and maybe magically your code would produce a model.  Unfortunately not  :( as you can see from the type mismatch error below.  

Note I am using the latest testing version of Scalismo off maven central as recently directed to by Marcel. As always thank you in advance for any feedback you have.  My research objective is to model bone density with a gaussian process and it would be great if Scalismo provides a way to do that using my training images. Otherwise it is a challenge I will persist with and thankfully so far Scalismo and this forum have been extremely helpful to me.

Regards,,

Michael

[Marcel Luethi]

Dear Michael,

What you try to do is possible, but sadly still really poorly documented. You were almost there with your implementation, I hope it was not too much pain to get there.

You can find a working example here:

https://gist.github.com/marcelluethi/22047059d67526a32f140e0e4d18890f

Unfortunately, we don't yet have the nice visualization of the model in ScalismoUI, where you could explore the intensity variations using sliders. To show the intensity variation, you will have to obtain random samples from the model (which are ScalarVolumeMeshFields) and visualize them manually using ui.show.

I hope this helps to get you unstuck.

Best wishes

Marcel

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