Last updated on 2020-02-03
by Brandon Whitcher
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).
ANALYZE and NIfTI
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)
- The tractor.base package (part of the tractor project)
consists of functions for reading, writing and visualising MRI
images. Images may be stored in ANALYZE, NIfTI or DICOM file
formats, and can be visualised slice-by-slice or in projection.
It also provides functions for common image manipulation tasks,
such as masking and thresholding; and for applying arbitrary
functions to image data. The package is written in pure R.
- Diffusion anisotropy has been used to characterize white
matter neuronal pathways in the human brain, and infer global
connectivity in the central nervous system. The
gdimap package implements algorithms to estimate and
visualize the orientation of neuronal pathways using model-free
methods (q-space imaging methods). The estimation of fibre
orientation has been implemented using (1) by extracting local
maxima or (2) directional statistical clustering of the ODF
Dynamic Contrast-Enhanced MRI (DCE-MRI)
- The dcemriS4 package contains a collection of
functions to perform quantitative analysis from a DCE-MRI (or
diffusion-weighted MRI) acquisition on a voxel-by-voxel basis
and depends on the S4 implementation of the NIfTI and ANALYZE
classes in oro.nifti. Data management capabilities
include: read/write for NIfTI extensions, full audit trail,
improved visualization, etc. The steps to quantify DCE-MRI are
as follows: motion correction and/or co-registration, T1
estimation, conversion of signal intensity to gadolinium
contrast-agent concentration and kinetic parameter estimation.
Parametric estimation of the kinetic parameters, from a
single-compartment (Kety or extended Kety) model, is performed
via Levenburg-Marquardt optimization or Bayesian estimation.
Semi-parametric estimation of the kinetic parameters is also
possible via Bayesian P-splines.
- The brainwaver package provides basic wavelet
analysis of multivariate time series with a visualisation and
parametrisation using graph theory. It computes the correlation
matrix for each scale of a wavelet decomposition, via
waveslim. Hypothesis testing is applied to each
entry of one matrix in order to construct an adjacency matrix of
a graph. The graph obtained is finally analysed using
small-world theory and, with efficient computation techniques,
tested using simulated attacks. The brainwaver project is
complementary to the CamBA project
for brain image data processing. A collection of scripts (with
a makefile) is available to download
along with the brainwaver package.
- adaptsmoFMRI contains R functions for estimating the blood oxygenation level dependent (BOLD) effect by using functional magnetic resonance imaging (fMRI) data, based on adaptive Gauss Markov random fields, for real as well as simulated data. Inference of the underlying models is performed by efficient Markov Chain Monte Carlo simulation, with the Metropolis Hastings algorithm for the non-approximate case and the Gibbs sampler for the approximate case. When comparing the results of approximate to the non-approximate version the outcome is in favour of the former, as the gain of accuracy in estimation, when not approximating, is minimal and the computational burden becomes less cumbersome.
- AnalyzeFMRI is a package originally written for
the processing and analysis of large structural and functional
MRI data sets under the ANALYZE format. It has been updated to
include new functionality: complete NIfTI input/output,
cross-platform visualization based on Tcl/Tk components, and
spatial/temporal ICA (Independent Components Analysis)
via a graphical user interface (GUI).
- The package arf3DS4 applied the active region
fitting (ARF) algorithm for the analysis of functional magnetic
resonance imaging (fMRI) data. ARF uses Gaussian shape spatial
models to parameterize active brain regions.
- The R package fmri provides tools for the
analysis of functional MRI data. The core is the implementation
of a new class of adaptive smoothing methods. These methods
allow for a significant signal enhancement and reduction of
false positive detections without, in contrast to traditional
non-adaptive smoothing methods, reducing the effective spatial
resolution. This property is especially of interest in the
analysis of high-resolution functional MRI. The package
includes functions for input/output of some standard imaging
formats (ANALYZE, NIfTI, AFNI, DICOM) as well as for linear
modelling the data and signal detection using Random Field Theory.
It also includes ICA and NGCA (non-Gaussian Components Analysis)
based methods and hence has some overlap with
- Neuroimage is an R package (currently only available within
the neuroim project on R-Forge) that provides
data structures and input/output routines for functional brain
imaging data. It reads and writes NIfTI-1 data and provides S4
classes for handling multi-dimensional images.
- The package mritc provides tools for MRI tissue
classification using normal mixture models and (partial volume,
higher resolution) hidden Markov normal mixture models fitted by
various methods. Functions to obtain initial values and spatial
parameters are available. Facilities for visualization and
evaluation of classification results are provided. To improve
the speed, table lookup methods are used in various places,
vectorization is used to take advantage of conditional
independence, and some computations are performed by embedded C
- The package brainR includes functions for creating
three-dimensional (3D) and four-dimensional (4D) images using
- Morpho is a collection of tools for statistical shape analysis and visualization of point based shape representations (landmarks, meshes). Apart from the core functions such as General Procrustes Analysis and sliding of semi-landmarks, Morpho is sporting a variety of statistical procedures to assess group differences and asymmetry, most of them based on permutation/bootstrapping methods. For registration purposes there are functions to calculate landmark transforms (rigid, similarity, affine and thin-plate spline) as well as iterative closest point registration and automated alignment exploiting the shapes' principal axes. To deal with missing/erroneous data there are imputation methods available for missing landmarks and interactive outlier detection. For visualization there are functions to create interactive 3D plots of distance maps as well as visualizing differences between point clouds by deforming rectangular grids, both in 2D and 3D. Additionally, it includes an algorithm to retrodeform surface meshes representing structures that have suffered a series of locally affine deformations (e.g. fossils).
- Rvcg interfaces VCGLIB to provide functions for manipulating triangular surface meshes; e.g., surfaces generated from medical image segmentations. Among those manipulations are quadric-edge collapse decimation, smoothing, subsampling, closest point search or uniform remeshing. Additionally it allows the generation of isosurfaces from 3D arrays. It has capabilities for import/export of STL, PLY and OBJ files, both in binary and ASCII format.
- The package neuRosim allows users to generate fMRI
time series or 4D data. Some high-level functions are created for
fast data generation with only a few arguments and a diversity of
functions to define activation and noise. For more advanced users
it is possible to use the low-level functions and manipulate the
General Image Processing
- adimpro is a package for 2D digital (color and
B/W) images, actually not specific to medical imaging, but for
general image processing.
- The package bayesImageS implements several algorithms for segmentation of 2D and 3D images (such as CT and MRI). It provides full Bayesian inference for hidden Markov normal mixture models, including the posterior distribution for the smoothing parameter. The pixel labels can be sampled using checkerboard Gibbs or Swendsen-Wang. MCMC algorithms for the smoothing parameter include the approximate exchange algorithm (AEA), pseudolikelihood (PL), thermodynamic integration (TI), and approximate Bayesian computation (ABC-MCMC and ABC-SMC). An external field prior can be used when an anatomical atlas or other spatial information is available.
- EBImageis an R package which provides general
purpose functionality for the reading, writing, processing and
analysis of images. Furthermore, in the context of
microscopy-based cellular assays, this package offers tools to
transform the images, segment cells and extract quantitative
- The package mmand (Mathematical Morphology in Any
Number of Dimensions) provides morphological operations like
erode and dilate, opening and closing, as well as smoothing and
kernel-based image processing. It operates on arrays or
array-like data of arbitrary dimension.
- The RNiftyReg provides an interface to the NiftyReg
image registration tools. Rigid-body, affine and non-linear
registrations are available and may be applied in 2D-to-2D,
3D-to-2D and 4D-to-3D procedures.
- The package fslr contains wrapper functions that
interface with the FMRIB Sofware
Library (FSL), a powerful and widely-used neuroimaging
software library, using system commands. The goal with this
package is to interface with FSL completely in R, where you pass
R-based NIfTI objects and the function executes an FSL command
and returns an R-based NIfTI object.
Positron Emission Tomography (PET)
- The occ package provides a generic function for
estimating PET neuro-receptor occupancies by a drug, from the
total volumes of distribution of a set of regions of interest
(ROI). Fittings methods include the reference region, the
ordinary least squares (OLS, sometimes known as
"occupancy plot") and the restricted maximum likelihood
- edfReader reads some of the most popular file formats in EEG recordings.
- The EEG package (currently only available within the
eeg project on R-Forge) reads in single trial
EEG (currently only ascii-exported pre-processed and trial
segmented in Brain Vision Analyzer), computes averages (i.e.,
event-related potentials or ERP's) and stores ERP's from
multiple data sets in a data.frame like object, such
that statistical analysis (linear model, (M)ANOVA) can be done
using the familiar R modeling frame work.
- eegkit includes many useful functions for analysing EEG signals (among others, visualizing positions of electrodes).
- PTAk is an R package that uses a multiway method
to decompose a tensor (array) of any order, as a generalisation
of a singular value decomposition (SVD) also supporting
non-identity metrics and penalisations. A 2-way SVD with these
extensions is also available. The package also includes
additional multiway methods: PCAn (Tucker-n) and
PARAFAC/CANDECOMP with these extensions. Applications include
the analysis of EEG and functional MRI data.
- Task view: ChemPhys
- Bioconductor package: EBImage
- R-Forget project: eeg
- Journal of Statistical Software: Special Volume on Magnetic Resonance Imaging in R
- ANTsR is a framework that incorporates ITK and ANTs-based image processing methods into the R programming language.
- SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education, interpreted languages. SimpleITK provides support for 2D and 3D images, and a selected set of pixel types for them. Different image filters may support a different collection of pixel types, in many cases due to computational requirements. The library is wrapped for interpreted languages by using SWIG. In particular, the following wrappings are available: Python, Java, Tcl, Lua, R and Ruby.