CRAN Task View: Medical Image Analysis

Maintainer:Brandon Whitcher
Contact:bwhitcher at

Data Input/Output


The industry standard format, for data coming off a clinical imaging device, is DICOM (Digital Imaging and Communications in Medicine). The DICOM "standard" is very broad and very complicated. Roughly speaking each DICOM-compliant file is a collection of fields organized into two four-byte sequences (group,element) that are represented as hexadecimal numbers and form a tag . The (group,element) combination announces what type of information is coming next. There is no fixed number of bytes for a DICOM header. The final (group,element) tag should be the "data" tag (7FE0,0010), such that all subsequent information is related to the image(s).


Although the industry standard for medical imaging data is DICOM, another format has come to be heavily used in the image analysis community. The ANALYZE format was originally developed in conjunction with an image processing system (of the same name) at the Mayo Foundation. An Anlayze (7.5) format image is comprised of two files, the "hdr" and "img" files, that contain information about the acquisition and the acquisition itself, respectively. A more recent adaption of this format is known as NIfTI-1 and is a product of the Data Format Working Group (DFWG) from the Neuroimaging Informatics Technology Initiative (NIfTI). The NIfTI-1 data format is almost identical to the ANALYZE format, but offers a few improvements: merging of the header and image information into one file (.nii), re-organization of the 348-byte fixed header into more relevant categories and the possibility of extending the header information.

Magnetic Resonance Imaging (MRI)

Diffusion Tensor Imaging (DTI)

Dynamic Contrast-Enhanced MRI (DCE-MRI)

Functional Connectivity

Functional MRI

Structural MRI



General Image Processing

Positron Emission Tomography (PET)

Electroencephalography (EEG)

CRAN packages:

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