Research Facility Software

The MR Research Facility is outfitted with a number of image analysis tools, including FSL, AFNI, Slicer3, ImageJ and BRAINS.  In addition, one workstation is outfitted with the Siemens IDEA/ICE pulse programming and image reconstruction environments.  The MRRF also possesses advanced software for fMR Imaging, complete with E-Prime, Presentation, and Neurognostics fMRI Workflow software. Below you will find a more detailed description of the software used at the MRRF.

DICOM Browser

NRG Free DICOM Browser http://nrg.wustl.edu/software/dicom-browser/

BRAINS

The BRAINS (Brain Research: Analysis of Images, Networks, and Systems) image analysis software has been in continuous, evolutionary development at The University of Iowa for over fifteen years. The BRAINS software comprises a set of reliable and validated tools for analyzing large neuroimaging studies. The methods and underlying tools are often referenced as state of the art. Large neuroimaging studies at the University of Iowa have both driven the development of BRAINS and provided a means to validate its results and user processes. Currently, the software supports 37 active projects at the University of Iowa, 46 projects from outside institutions, and has been downloaded by over 350 groups. Recently an automated image processing pipeline has been developed that is able to take images from the MRI scanner and perform the following steps automatically: anatomical AC-PC alignment, bias field correction,  signal intensity normalization, tissue classification, brain extraction, regional labeling, and measurements. We are currently fully integrating this tool with ITK. This new version of the software is still beta and can be obtained from the NITRC website. A previous version of the software, BRAINS2, is available for Linux and Mac OS X operating systems.  Two sample images from the BRAINS software are depicted below:

BRAINSFit

This is a mutual information based registration program. The program supports rigid, affine, and rigid+scale transforms. This is a flexible program for the registration of two datasets. It is available via the NITRC website.

BRAINSTracer

This is a new graphical user interface to BRAINS that builds upon NA-MIC tools. The interface supports all major platforms including Windows, Mac, Linux, and other Unix flavors. The tools is a prototype for future efforts. It currently operates as a tracing (editing) tool. The tracing tool uses the vtkContourWidget and is built on KWWidgets. The Slicer3 look and feel has been integrated. This tracing tool is nearing a beta release and will include the following features:

  1. Support for editing in multiple planes simultaneously
  2. Ability to telegraph traces into other planes
  3. Ability to export traces as binary images for integration into Slicer3
  4. Ability to export traces as BRAINS2 mask objects
  5. Traces will be saved in VTK XML format

GTRACT

The GTRACT program is a full DTI data processing pipeline. In the latest version of the tools, all of the functions exists as command line programs that integrate with Slicer3 using the Execution model framework. The standard format for the DTI data in this version is the NRRD format. Anatomical images and label maps can be in any format supported by ITK. The program support several version of fiber tracking including:

  1. Free tracking - Basic streamlines with only a starting region
  2. Streamlines - Streamlines tracking between two regions of interest
  3. Graph Search - Modified streamlines that try multiple solutions in low anisotropy regions
  4. Guided Tracking - Uses an initial guess to the fiber track to guide the tracking
  5. Fast Marching - Method based on the method proposed by Geoffrey Parker

Full details on the programs included in the software are available on our Wiki and the software is available via the NITRC website.  Two sample images from the software can be seen below:

IA-FEMesh

(http://www.ccad.uiowa.edu/mimx/IA-FEMesh/)


Outside Software

SPM (http://www.fil.ion.ucl.ac.uk/spm/)

FSL (http://www.fmrib.ox.ac.uk/fsl/)

Slicer3 (http://www.slicer.org/)

AFNI (http://afni.nimh.nih.gov/afni)