OTFeatures - Optimal Transport Features

This is a repository for an R package to compute optimal transport features for brain morphometry.

The package contains only the optimal transport feature extraction step and can be used to integrate optimal transport features with existing morphometry approaches.

Install

library(devtools)
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = "true")
devtools::install_github("samuelgerber/OTFeatures")

Example

library(OTFeatures)
data(brains)
otf = extract.otf.image.3d(brain1, brain2)
par(mfrow=c(2,2))
image(brain1[,,2])
title("From")
image(brain2[,,2])
title("To")
image(brain1[,,2] - brain2[,,2])
title("Difference Per Voxel")
image(otf$difference.from[,,2])
title("Mass Allocation in From")

References

The optimal transport based morphometry approach was first described in:

Gerber S, Niethammer M, Styner M, Aylward S. Exploratory Population Analysis with Unbalanced Optimal Transport. Med Image Comput Comput Assist Interv. 2018
Pubmed Link

A journal article with improvements and additions to the method is in progress.