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

There is significant interest in adopting surface- and grayordinate-based analysis of MR data for a number of reasons, 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 grayordinate-based analysis by combining gray matter data from the left and right cortical hemispheres with gray matter data from the subcortex and cerebellum into a single file. Analyses performed in grayordinate space are well-suited to leverage information shared across the brain and across subjects through both traditional analysis techniques and more advanced statistical methods, including Bayesian methods. The R statistical environment facilitates use of advanced statistical techniques, yet little support for grayordinates analysis has been previously available in R Indeed, 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 files 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 grayordinate-based functional MRI data.