Radtools: R utilities for smooth navigation of medical image data

Abstract

The radiology community has adopted several widely used standards for medical image files, including the popular DICOM (Digital Imaging and Communication in Medicine) and NIfTI (Neuroimaging Informatics Technology Initiative) standards. These file formats include image intensities as well as potentially extensive metadata. The NIfTI standard specifies a particular set of header fields describing the image and minimal information about the scan. DICOM headers can include any of over 4,000 available metadata attributes spanning a variety of topics. NIfTI files contain all slices for an image series, while DICOM files capture single slices and image series are typically organized into a directory. Each DICOM file contains metadata for the image series as well as the individual image slice.\n\nThe programming environment R is popular for data analysis due to its free and open code, active ecosystem of tools and users, and excellent system of contributed packages. Currently, many published radiological image analyses are performed with proprietary software or custom unpublished scripts. However, R is increasing in popularity in this area due to several packages for processing and analysis of image files. While these R packages handle image import and processing, no existing package makes image metadata conveniently accessible. Extracting image metadata, combining across slices, and converting to useful formats can be prohibitively cumbersome, especially for DICOM files.\n\nWe present radtools, an R package for smooth navigation of medical image data. Radtools makes the problem of extracting image metadata trivially simple, providing simple functions to explore and return information in familiar R data structures. Radtools also facilitates extraction of image data and viewing of image slices. The package is freely available under the MIT license at https://github.com/pamelarussell/radtools and is easily installable from the Comprehensive R Archive Network (https://cran.r-project.org/package=radtools).