Magnetic Resonance Imaging in R

Volume 44 of the Journal of Statistical Software was published in October 2011.  The special volume on “Magnetic Resonance Imaging in R” features articles and packages related to a variety of imaging modalities:

• functional MRI
• diffusion-weighted MRI
• dynamic contrast-enhanced MRI
• dynamic susceptibility-contrast MRI
• structural MRI

The papers describe the methodology, software implementation and provide comprehensive examples and data.  A complete list of the issues is:

• Special Volume on Magnetic Resonance Imaging in R
  Karsten Tabelow, Brandon Whitcher
  Vol. 44, Issue 1, Oct 2011
  Submitted 2011-09-29, Accepted 2011-09-29
• Markov Chain Monte Carlo Random Effects Modeling in Magnetic Resonance Image Processing Using the BRugs Interface to WinBUGS
  Martin D. King, Fernando Calamente, Chris A. Clark, David G. Gadian
  Vol. 44, Issue 2, Oct 2011
  Submitted 2010-10-01, Accepted 2011-06-10
• DATforDCEMRI: An R Package for Deconvolution Analysis and Visualization of DCE-MRI Data
  Gregory Z. Ferl
  Vol. 44, Issue 3, Oct 2011
  Submitted 2010-10-11, Accepted 2011-06-22
• cudaBayesreg: Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis
  Adelino R. Ferreira da Silva
  Vol. 44, Issue 4, Oct 2011
  Submitted 2010-10-20, Accepted 2011-06-16
• Quantitative Analysis of Dynamic Contrast-Enhanced and Diffusion-Weighted Magnetic Resonance Imaging for Oncology in R
  Brandon Whitcher, Volker J. Schmid
  Vol. 44, Issue 5, Oct 2011
  Submitted 2010-10-20, Accepted 2011-06-17
• Working with the DICOM and NIfTI Data Standards in R
  Brandon Whitcher, Volker J. Schmid, Andrew Thorton
  Vol. 44, Issue 6, Oct 2011
  Submitted 2010-10-25, Accepted 2011-06-07
• mritc: A Package for MRI Tissue Classification
  Dai Feng, Luke Tierney
  Vol. 44, Issue 7, Oct 2011
  Submitted 2010-10-28, Accepted 2011-06-20
• TractoR: Magnetic Resonance Imaging and Tractography with R
  Jonathan D. Clayden, Susana Muñoz Maniega, Amos J. Storkey, Martin D. King, Mark E. Bastin, Chris A. Clark
  Vol. 44, Issue 8, Oct 2011
  Submitted 2010-10-28, Accepted 2011-06-02
• Temporal and Spatial Independent Component Analysis for fMRI Data Sets Embedded in the AnalyzeFMRI R Package
  Cécile Bordier, Michel Dojat, Pierre Lafaye de Micheaux
  Vol. 44, Issue 9, Oct 2011
  Submitted 2010-10-29, Accepted 2011-06-16
• neuRosim: An R Package for Generating fMRI Data
  Marijke Welvaert, Joke Durnez, Beatrijs Moerkerke, Geert Berdoolaege, Yves Rosseel
  Vol. 44, Issue 10, Oct 2011
  Submitted 2010-10-31, Accepted 2011-06-21
• Statistical Parametric Maps for Functional MRI Experiments in R: The Package fmri
  Karsten Tabelow, Jörg Polzehl
  Vol. 44, Issue 11, Oct 2011
  Submitted 2010-11-10, Accepted 2011-06-15
• Beyond the Gaussian Model in Diffusion-Weighted Imaging: The Package dti
  Jörg Polzehl, Karsten Tabelow
  Vol. 44, Issue 12, Oct 2011
  Submitted 2010-11-10, Accepted 2011-06-15
• FIAR: An R Package for Analyzing Functional Integration in the Brain
  Bjorn Roelstraete, Yves Rosseel
  Vol. 44, Issue 13, Oct 2011
  Submitted 2010-11-13, Accepted 2011-06-21
• arf3DS4: An Integrated Framework for Localization and Connectivity Analysis of fMRI Data
  Wouter D. Weeda, Frank de Vos, Lourens J. Waldorp, Raoul Grasman, Hilde M. Huizenga
  Vol. 44, Issue 14, Oct 2011
  Submitted 2010-11-14, Accepted 2011-10-28
   

oro.nifti 0.3.1

The  package oro.nifti contains functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats.  This package is part of the Rigorous Analytics bundle.

Lightbox display of functional MRI "resting-state" acquisition using image().  The axial plane is used by default.

Lightbox display of functional MRI "resting-state" acquisition using image(, plane="coronal").

Llightbox display of functional MRI "resting-state" acquisition using image(, plane="sagittal").

Orthographic display of functional MRI "resting-state" acquisition using orthographic().

The latest version of oro.nifti (0.3.1) contains a substantial number of updates:

• Visualization of NIfTI and ANALYZE S4 objects
• Aspect ratio is now respected in the overloaded image() function for "nifti" and "anlz" class objects.
• The plane of acquisition (axial, coronal, sagittal) may now be specified by the user.
• Min/max values of the data are properly interrogated if cal.min/cal.max or glmin/glmax are not specified.
• Added accessor/replacement functions for cal.min and cal.max NIfTI metadata fields.
• Fixed bug in pixdim<- replacement function, should work now.
• Fixed bug in writeNIfTI so that FSLView can correctly identify the min/max values.
• Better treatment of Qform and Sform information.

Please use the mailing list at R-Forge or contact rigorousanalytics@googlemail.com with any suggestions.

oro.dicom 0.3.3

The R package oro.dicom contains data input/output functions for medical imaging data that conform to the Digital Imaging and Communications in Medicine (DICOM) standard, part of the Rigorous Analytics bundle.

The latest version of oro.dicom (0.3.3) contains a substantial number of updates:

• dicomInfo = readDICOMFile and dicomSeparate = readDICOM, but the old function calls still exist for now to smooth the transition.
• readDICOM now accepts a single file as input, creating the list-of-lists structure with one element in $hdr and $img.
• Modest speed improvements in readDICOMFile from a thorough use of Rprof().
• Added txtProgressBar() to readDICOM and dicomTable.
• Sub-routines used in readDICOM have been made private.
• Added default sform information to dicom2nifti.
• Miscellaneous bug fixes.
• Added "instance" input parameter to create4D so the user can decide whether or not to access the "InstanceNumber" DICOM header field for slice ordering.

Please use the mailing list at R-Forge or contact rigorousanalytics@googlemail.com with any suggestions.