Acquisition of coordinates post SPHARM/Procrustes for analysis

Good morning!

I have a dataset of 51 different vertebrae I am analyzing for shape variation. I’ve utilized the population analysis module to export the PCA data in the json format and acquired the first two PCs from the table in the Data Module. However, I am unable to figure out what my PC values are in the json (or they do not seem to match up) with the Population analysis PC values.

I have attempted to also export the coordinates from my aligned vtk’s using the python interactor into an array and run the analysis through geomorph in Rstudio. I am also acquiring PC results very different from the Population analysis results.

First, I am wondering what the workflow is for acquiring PC values in the Population Analysis module. Second, I’d like to be able to acquire the coordinates of my vtk’s after SPHARM-PDM and Procrustes registration to be able to conduct further statistical analysis in R rather than in Slicer itself. I may also be missing something big, I’d love to have a second opinion!

Thanks so much.


Hi @Hoai-Nam_Bui

If you are referring to the 3D point coordinate, you can simply upload into Paraview software your aligned vtks that you used for PCA (after using correspondence improvement module & Procrustes alignment module). Paraview will show you clear information about the point coordinates when you open the vtk file in their spreadsheet.

Regarding the PCA score/value, you are correct. Unfortunately, still, the PCA scores shown in the interface - do not match the information listed in the (.json) file. To overcome this issue, and until they address this technical issue, my only approach to obtain clear information about the PC score [beyond the first two PC] was to extract the ‘number of PC score shown on the screen’ - using Microsoft PowerToys tool. The tool should allow you to extract the number - then past it into your external sheet.

Hopefully they fix this issue soon - to make our life easier.

All the best,