Software

These packages are available on the F. M. Kirby Center computer systems for the analysis of functional MRI data:

• Functional Image Analysis Software Computational Olio (FIASCO) 
  Department of Statistics, Carnegie-Mellon University, Pittsburgh, PA
• Analysis of Functional NeuroImages (AFNI) 
  National Institute of Mental Health (NIMH), National Institutes of Health (NIH), Bethesda, MD
• Functional Imaging Data Analysis Platform (FIDAP) 
  National Institute of Mental Health (NIMH), National Institutes of Health (NIH), Bethesda, MD
• EvIdent 3D Functional Imaging Analysis Software 
  Institute for Biodiagnostics, NRC, Winnipeg, Canada
• E-Prime Paradigm Development Software 
  Psychology Software Tools, Inc., Pittsburgh, PA
• Central Test Node  (CTN) DICOM Demonstration Software 
  RSNA and Mallinckrodt ERL, Washington University, St Louis, MO
• MEDx Image Processing Software Package 
  Sensor Systems, Inc., Sterling, VA
• Statistical Parametric Mapping (SPM99) 
  Wellcome Department of Cognitive Neurology, University College London, London, UK
• FMRIB Software Library (FSL) 
  Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, Oxford, UK
• Group ICA of fMRI Toolbox (GIFT) 
  The Mind Research Network, Medical Image Analysis Lab (MIALab), University of New Mexico, Albuquerque, NM

These software packages were written by Peter Barker, DPhil. They are available for use on systems associated with the F. M. Kirby Center and the JHU Magnetic Resonance Division. Registered users may download them for free.

• CSX 
  The CSX program was developed for the display and analysis of in vivo spectroscopy and spectroscopic imaging datasets. 
  • CSX: First Generation CSX
    • Initially developed in the OpenWindows environment of Sun Microsystems SunOS 4.x on Sparc computers.
    • Code compiled for Silicon Graphics IRIX6 system.
  • CSX2: Second Generation CSX
    • Built for Sun UltraSparc Solaris 2.x and Linux systems
  • CSX3: Third Generation CSX
    • Built for Sun UltraSparc Solaris 2.x and MacOSX systems
• IMAX 
  The IMAX program displays images, and is to be used in conjunction with CSX. This program allows users to overlay images with MRSI "grids," with a "point-and-click" selection of spectra from regions of interest. Regions of interest can also be measured, added, subtracted, or combined. IMAX supports the following file formats: General Electric SIGNA (3.X, 4.X, or 5.X image files), DICOM, and SMIS (.sur). A general import tool allows the importing of data in other formats, such as ASCII, short integer, integer, floating point, double, and any header offset or matrix size.
• DSX 
  The DSX program combines the functionality of CSX and IMAX. It was based on the CSX processing and analysis code, but has a new graphical user interface (GUI). It was developed for x86 Windows and Linux systems.

Developed at F. M. Kirby Center, these utilities can convert files from different formats, display images, etc:

• DICOM and REC File Utilities: A list of our files, as well as examples and descriptions on how to use them.

Developed by the Laboratory of Brain Anatomical MRI, these tools can process DTI data and reconstruct three-dimensional fiber trajectories. Please use this website's sidebar menu to find the following:

• DTI Studio: This software package can be used to load images, rotate volumes, create color maps, find tracts through a region of interest, etc.
• DTI Database: This in vivo human database, acquired under the Human Brain Project and the National Research Resource Center grant, contains raw and processed DTI data of the normal population. It is a public database, open to registered users. Its purpose is to facilitate research in DTI data processing and analysis, to study specific biological interests, or to be used as control data. Basic imaging parameters can also be downloaded. Detailed parameters are available upon request.

Drs. Bennett Landman and Jonathan Farrell have also developed software for analyzing DTI data: 

• CATNAP: Coregistration, Adjustment, and Tensor-solving, a Nicely Automated Program
• The BIRN site displays details about this particular tool, as well.

These software packages were developed by the Center for Imaging Science at Johns Hopkins University.

• Large Deformation Diffeomorphic Metric Mapping (LDDMM) Suite: These algorithms incorporate the volume, surface, similitude, landmarks, and DTI information in a dataset.
• CIS Software: Other packages from the CIS include a Rigid Landmark Matching (RLM) tool, CAWorks, BrainWorks, and MindView.