Covariate Significance Testing User Tutorial

Authors: Mahmoud Mostapha, Jared Vicory, Chao Huang, Martin Styner, Beatriz Paniagua

Collaborators:

Covariate Significance Testing Description

This module provides the following functions:
- Model Fitting & Hypothesis Testing
- Visualize Statistical Results

Important note: If you are downloading this module as part of the Slicer Extension mechanism then it will be named multivariate functional shape data analysis (MFSDA)

Covariate Significance Testing provides an interface for MFSDA (Multivariate Functional Shape Data Analysis) method, which is a Python based tool for statistical shape analysis. A multivariate varying coefficient model is introduced to build the association between the multivariate shape measurements and demographic information and other clinical variables. Statistical inference, i.e., hypothesis testing, is also included in this tool, which can be used in investigating whether some covariates of interest are significantly associated with the shape information. The hypothesis testing results are further used in clustering based analysis, i.e., significant suregion detection.

The Covariate Significance Testing tool has of the following structure:

Covariate Significance Testing Installation on SlicerSALT

Download the SlicerSALT packages for your respective operating system from the SlicerSALT website and install it. Covariate Significance Testing will be ready to use as a module.

MFSDA Installation on 3D Slicer

Download 3D Slicer packages for your respective operating system on the 3D Slicer website and install it.

In 3D Slicer, open the Extension Manager

In the Install Extension tab, select MFSDA under Categories . Under MFSDA , select the Install button and restart Slicer when prompted

Covariate Significance Testing Module

In SlicerSALT, select _Covariate Significance Testing Module _ (in Slicer, select MFSDA ) from the Modules drop-down menu ( Category: Shape Analysis) or on the Search bar

Setting up Input Files

For Input CSV File , select the csv file which contains the location of input surface meshes (*.vtk) and corresponding covariates

In the CSV file the first column contains the location of input surface vtk files and each additional column represent a covariate to be tested, which can be categorical or continuous. Below is an example of an input CSV file with one categorical covariate.

Input Surface Meshes Visualization

Shape Population Viewer can be used to check the input surface meshes, where the same CSV file as its input

Setting up Input Files

For Input Spherical Template , select the vtk file which provides a common coordinates for the of input surface meshes

Below there is an example of an input spherical template file, which can be an average surface or one of the input surfaces

Setting up Input Files

For Input Shape for p-values , select the vtk file which will be used to visualize the fitted model parameters and the resulted p-values

Below there is an example of an input shape for p-values file, which can be an average surface or one of the input surfaces

Setting up Output Directory

For Output Files Directory , select the folder where the module will store the output files

Running Covariate Significance Testing Module

Click on the Run button, to run the MFSDA_run & MFSDA_createShapes CLIs on the provided inputs files

SlicerSALT Error Log can also be used for debugging if the module was completed with errors.

The outputs files for the Covariate Significance Testing Module are stored in the output folder specified by the user: and they include fitted model parameters, shape template with Scalars, hypothesis testing p-values and the output files generated by running Covariate Significance Testing

Output Shape Template Visualization

Shape Population Viewer can be used also to visualize the output shape template with fitted model parameters and p-values as scalars

Acknowledgements - Resources - Questions

The MSFDA developers gratefully acknowledge funding for this project provided by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the Slicer community.
Github repository:

Forums:

For other remarks or questions, please email: beatriz.paniagua@kitware.com