Thursday, December 29, 2011

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




Tuesday, December 27, 2011

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.