ModelArray

ModelArray is an R package for statistical analysis of fixel-wise data and beyond. Its features include:

• Easy to use: set up your statistical analysis with just several lines of code;
• Supporting linear and nonlinear modeling, and extensible to more models:
  • At present, ModelArray supports linear models as well as generalized additive models (GAMs) with and without penalized splines, which are particularly useful for studying nonlinear effects in lifespan data. ModelArray is also extensible to diverse models available in R;
• Scalable for large-scale datasets;
• Compatible with fixel-wise data, voxel-wise data, and greyordinate-wise data.

Please cite our NeuroImage paper if you use ModelArray:

Zhao, C., Tapera, T. M., Bagautdinova, J., Bourque, J., Covitz, S., Gur, R. E., Gur, R. C., Larsen, B., Mehta, K., Meisler, S. L., Murtha, K., Muschelli, J., Roalf, D. R., Sydnor, V. J., Valcarcel, A. M., Shinohara, R. T., Cieslak, M. & Satterthwaite, T. D. (2023). ModelArray: an R package for statistical analysis of fixel-wise data. NeuroImage, 271, 120037. https://doi.org/10.1016/j.neuroimage.2023.120037

Overview

ModelArray is packaged with the companion software ConFixel for converting fixel-wise data, voxel-wise data or greyordinate-wise data to the expected file format that ModelArray uses. Specifically, ConFixel is Python-based command-line interface software, and it converts between the original image format (.mif for fixel-wise data, NIfTI for voxel-wise data, CIFTI-2 for greyordinate-wise data) and the HDF5 file format (.h5) used for ModelArray.

Installation

Please refer to webpage Installation for a full guidance of installation of ModelArray and its companion python package ConFixel. The most important steps for installing ModelArray are:

• Make sure you have necessary libraries for HDF5 - see this section
• Install ModelArray from GitHub - see this section

Additionally, we also provide a container image that includes ModelArray and ConFixel. With this container image, there is no need for the user to install ModelArray, ConFixel, and dependent R and Python packages. Please see this webpage for how to use this container image.

How to use

Load the ModelArray package into R via:

library(ModelArray)

We provide a walkthrough here with example fixel-wise data. For additional notes on application to voxel-wise data, please refer to here.

For documentation of ModelArray functions, you can:

• Either go to this webpage;
• Or in R console, type: help(<function_name>). For example: help(ModelArray.lm)

Full documentation of ModelArray can be found here.

Source code of ModelArray can be found here.