Working with the DICOM and NIfTI Data Standards in R

Abstract

Two packages, oro.dicom and oro.nifti, are provided for the interaction with and manipulation of medical imaging data that conform to the DICOM standard or ANALYZE/NIfTI formats. DICOM data, from a single file or directory tree, may be uploaded into R using basic data structures: a data frame for the header information and a matrix for the image data. A list structure is used to organize multiple DICOM files. The S4 class framework is used to develop basic ANALYZE and NIfTI classes, where NIfTI extensions may be used to extend the fixed-byte NIfTI header. One example of this, that has been implemented, is an XML-based “audit trail” tracking the history of operations applied to a data set. The conversion from DICOM to ANALYZE/NIfTI is straightforward using the capabilities of both packages. The S4 classes have been developed to provide a userfriendly interface to the ANALYZE/NIfTI data formats; allowing easy data input, data output, image processing and visualization.