SPHARM-PDM alignment

Community SlicerSALT
#1

Hello, Beatriz, Martin, and others. My name is Ikhsan and I would like to ask a few things regarding SPHARM-PDM.

Firstly, I have looked at the tutorial and worked on the hippocampus example dataset. It functions properly on my laptop and I got the same output with those mentioned in the tutorial, except for the *SPHARM_procalign.vtk file which appears to be missing. My questions are:

  1. How do I get the *SPHARM_procalign.vtk file? I have exactly followed the tutorial (using the hippocampus dataset provided) and tried to use my dataset as well but it doesn’t shows up.

  2. Can I use the mean shape that I got from the ShapeVariationAnalyzer as a template for Rigid Procrustes alignment? Or do you have any recommendation which file should I use for the registration template?

Thank you in advance.

Regards,
Ikhsan

#2

Hi Ikhsan,

Thank you for using SPHARM-PDM!

How do I get the *SPHARM_procalign.vtk file? I have exactly followed the tutorial (using the hippocampus dataset provided) and tried to use my dataset as well but it doesn’t shows up.

You will need a previously computed spharm model and to use it as registration template

Screen Shot 2021-02-12 at 3.01.05 PM

Can I use the mean shape that I got from the ShapeVariationAnalyzer as a template for Rigid Procrustes alignment? Or do you have any recommendation which file should I use for the registration template?

That is definitely an option, but it does not need to be.

I hope that helps!!
Thanks,

Bea

#3

Hello Bea,

Thank you for the answer, I have now successfully generated the *procalign.vtk file.

If I may ask once again, I have read in some articles that mentioned about the scaling normalization for the head size (intracranial volume) after the rigid-body Procrustes alignment. Can I perform this step on the SPHARM-PDM module, or should I use another module on the SlicerSALT?

I am currently exploring other modules as well, but so far I couldn’t find it on the SPHARM-PDM tutorial.

Thank you once again for your response, I really appreciate it.

Best regards,
Ikhsan

#4

Hi Ikhsan,

Great to hear that you were able to get your procrustes aligned models!

Currently we still do not have a SlicerSALT module to do procrustes alignment (with and without scaling). There is however, a C++ CLI in SPHARM-PDM that does this, it is called MeshMath..

We will definitely look into incorporating this functionality in SlicerSALT soon.
Thank you!

Bea

#5

Hi Bea,

Thank you so much for the quick response. I will try to look deeper into MeshMath while continuing my shape analysis.

Many thanks,
Ikhsan