In particular, we focus on the following modalities:

fMRI Software Packages

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

MRS Analysis

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.

DICOM and REC Software Packages

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

DTI Processing and Utilities

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.

Functional Anatomy

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