Sunday, December 29, 2013

oro.dicom 0.4.0

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 (0.4.0) contains a substantial update:

  • The function subroutines of readDICOMFile() have been re-written from scratch.  
    • The entire DICOM file is read into R using readBin(what = "raw") and parsed in a recursive fashion.  That is, the DICOM header information is processed in the (group, element) doublets until a sequence header is found.  Once a sequence header is found, then the subroutine is called again... and so on and so forth... until the entire DICOM header is parsed.  This has reduced the total number of lines of code and, I believe, made the process more easily digestible.  
    • Assuming a PixelData or SpectroscopyData field is present, the subsequent bytes will be read into a separate R data structure.  
Other modifications have taken place, one in particular is the ability of oro.dicom to process spectroscopy data in the DICOM format.  I have had requests for this package to write DICOM files as output, but unfortunately I have not found the time myself to add this capability.

The revised code has been tested against a collection of DICOM files and works well.  However, only time will tell if the modifications work against the wide variety of DICOM headers one can find.  If you have DICOM data that you would like to contribute to the test suite for oro.dicom, please contact me at rigorousanalytics@gmail.com or post messages on this blog.

oro.nifti 0.4.0

Okay, so it's been quite a while since I provided an entry associated with oro.nifti.  That doesn't mean things haven't moved on... they have.  Let's just say I've been occupied.  One of the biggest changes to oro.nifti recently has been the "audit trail" is not turned off by default.  If you want to take advantage of this feature you must explicitly turn it on using the commands

R> options("niftiAuditTrail" = TRUE)
R> enableAuditTrail()

This modification was a consequence of severing the dependence on the XML package, since it was only required if one wanted to keep track of the operations performed during the data analysis (it is now only suggested).  Please see the vignette for more information about the audit trail feature.  Otherwise, minor improvements have been made and updates so that the package works with the most current version of R (3.0.2 at the time of this blog entry).  

Please use the mailing list at r-forge.r-project.org or contact rigorousanalytics@gmail.com with any suggestions.


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.

Tuesday, December 21, 2010

oro.nifti 0.2.4

The R 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.

Orthographic display of structural MRI acquisition from the AFNI data collection (afni_anat1+orig.BRIK).

 
The latest version of oro.nifti (0.2.4) has been submitted to CRAN and is available on R-Forge now.  New features include:
  • Read/write/visualize AFNI data (thanks to contributions by K. Tabelow)
  • writeANALZE and writeNIfTI are now S4 generic functions (suggested by K. Tabelow)
  • Conversion in both directions between fmridata-S3 (from the fmri package) and nifti-S4 classes.
  • Fixed bugs in translateCoordinate (thanks to R. Heckemann)
Please use the mailing list for any suggestions or contact rigorousanalytics@gmail.com.

Tuesday, October 26, 2010

DEADLINE EXTENDED -- CFP: Special Issue in JSS for "Magnetic Resonance Imaging in R"

Magnetic Resonance Imaging in R 

The deadline for submission to the Special Issue of the Journal of Statistical Software(JSS - http://www.jstatsoft.org) has been extended to November 14, 2010.


All MRI modalities are welcome, for example, structural MRI, functional MRI, diffusion tensor or diffusion-weighted imaging, perfusion MRI, pharmacological MRI, and others. Topics of interested include, but are not limited to,
  •  New analysis techniques for MRI data and their implementation.
  •  The implementation of established MRI analysis techniques.
  •  The incorporation of third-party open-source medical imaging software with R.
  •  Data management.
  •  (Semi-)Automated techniques for quality control.
  •  Visualization of medical imaging data and/or modelling results.
All papers will be subjected to the peer-review process, and must comply with the Guide for Authors; see http://www.jstatsoft.org for more details.

Please address any comments or inquiries as well as submission of papers to one of the guest editors below.

Sincerely,

Brandon Whitcher and Karsten Tabelow