Software: Neuroinformatics Tools and Analysis: EMMA

EMMA

EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data.

Online EMMA Documentation

  • General EMMA documentation: Explains the use of the EMMA analysis package, with examples.

  • Regional Cerebral Blood Flow (rCBF) Analysis: Explains the theory, implementation, and use of the EMMA RCBF toolkit, with examples. This is meant both as a usable application for determining kinetic constants K1 and k2, and as an example of how to write such applications with MATLAB and EMMA.

MATLAB Documentation and Information

A copy of the Mathworks' hypertext MATLAB documentation is available for local users only.

MATLAB/EMMA Demos

  • Basic EMMA image manipulation.
    • Gives a demonstration of using MATLAB and the EMMA toolkit to perform basic image manipulation (reading, viewing, and writing of images).
  • Advanced EMMA image manipulation.
    • Gives a demonstration of using MATLAB and the EMMA toolkit to perform advanced image manipulation (masking, averaging, producing time activity curves).
  • Controlling MATLAB Memory Use
    • Gives some pointers on reducing memory use within MATLAB.
  • RCBF analysis
    • Gives a demonstration of using MATLAB and the EMMA toolkit to perform two-compartment RCBF (Regional Cerebral Blood Flow) analysis.
  • Rat data analysis
    • Gives a demonstration of using MATLAB to perform two-compartment analysis on data gathered from rats. This method is also extendable to finding local values of K1 and k2 in PET studies.
  • Curve fitting
    • Gives a demonstration of using MATLAB to perform least squares curve fitting.
  • Speeding up MATLAB
    • Gives some examples of how to get the most out of your MATLAB scripts.

Pages Under Development

  • Region of Interest Analysis with MATLAB

    • Explains the use of the MATLAB/EMMA ROI package, with examples of use.

  • Tagged Region Analysis with MATLAB

    • Gives some examples of using MATLAB to analyze tagged volumes produced by Display.

 

 

 

                           

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