ciftiTools: A package for reading, writing, visualizing and manipulating CIFTI files in R

Surface-based analysis of MR data has well-recognized advantages, including improved whole-cortex visualization, the ability to perform surface smoothing to avoid issues associated with volumetric smoothing, improved inter-subject alignment, and reduced dimensionality. The CIFTI ``grayordinate'' file format introduced by the Human Connectome Project further advances surface-based analysis by combining left and right hemispheric surface metric data with subcortical and cerebellar gray matter data into a single file. Analyses performed in grayordinates space are well-suited to leverage information shared across the brain and across subjects through both traditional analysis techniques and more advanced Bayesian statistical methods. The R statistical environment facilitates the latter given its wealth of advanced statistical techniques for Bayesian computation and spatial modeling. Yet little support for grayordinates analysis has been previously available in R, and few comprehensive programmatic tools for working with CIFTI files have been available in any language. Here, we present the ciftiTools R package, which provides a unified environment for reading, writing, visualizing and manipulating CIFTI and related data formats. We illustrate ciftiTools' convenient and user-friendly suite of tools for working with grayordinates and surface geometry data in R, and we describe how ciftiTools is being utilized to advance the statistical analysis of grayordinates-based functional MRI data.