2D Cine DENSE Post-Processing Software
Matlab C++ C
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README.md

DENSEanalysis: Cine DENSE Processing Software

This software was developed in MATLAB to provide a user-friendly way of processing displacement encoding with stimulated echoes (DENSE) image data. Currently, the software supports analysis of 2D cine DENSE images; however, a beta version will be released in the coming months that supports full biventricular 3D analysis.

Getting Started

System Requirements

The current stable version (0.4.0) of DENSEanalysis requires:

  • MATLAB (R2009b through R2014a)
  • MATLAB Image Processing Toolbox
  • MATLAB Curve Fitting Toolbox (Spline Toolbox in later versions)
  • MATLAB C-Compiler

If you are running a newer version of MATLAB (R2014b or newer), you will want to use the master branch of the project which is the development version which includes support for all recent versions of MATLAB.

Configuration of Mex Compiler

If you have never compiled a MATLAB mex file on your current machine, you will want to configure the MATLAB environment to be able to perform the compilation. To do this you'll want to run

mex -setup

This will lead you through a series of steps where MATLAB will detect all compilers installed on your machine and ask you to select the appropriate installer.

Removal of Previous Installations

If you have previously installed DENSEanalysis, make sure to remove any existing entries in your path that point to that installation of DENSEanalysis and restart MATLAB

To do this you can either type the following command into MATLAB

pathtool

Or if you wish, you can select Set Path from the File menu.

Either of these will bring up the path dialog in which you can select the folders to remove.

Download Software

The latest stable release of DENSEanalysis can be downloaded here either as a .zip or .tar.gz archive.

If you wish to use a bleeding-edge version of DENSEanalysis or you wish to contribute to DENSEanalysis, you can go to the DENSEanalysis Github page and download the source as needed.

Once downloaded, you'll want to extract the contents of the archive to a directory of your choice on your machine.

Launch MATLAB and change folders to where you extracted the DENSEanalysis software and run the DENSEsetup script to finish the installation of the software.

cd('path/to/DENSEanalysis')
DENSEsetup

Running DENSEanalysis Programs

DENSEanalysis is launched by simply typing the following command within the MATLAB command window

DENSEanalysis

Similarly, DENSEms (Multi-Slice DENSE analysis) can be launched by using the following command

DENSEms

Additional Documentation

Additional information, including screenshots and examples, can be found at the following locations

A Note on "Motion-Guided Segmentation"

If you are used to running DENSEanalysis, you will notice that the context menu for performing motion-guided segmentation is no longer in the application. This was necessary to release this software as an open-source application. We have created a custom plugin that restores this functionality. If you are interested in obtaining this plugin, please contact Jonathan Suever.

Attribution

If you have used the DENSEanalysis software for your research or it has influenced your work, we ask that you include the following relevant citations in your work.

Spottiswoode, B. S., Zhong, X., Hess, a T., Kramer, C. M., Meintjes, E. M., Mayosi, B. M., & Epstein, F. H. (2007). Tracking myocardial motion from cine DENSE images using spatiotemporal phase unwrapping and temporal fitting. IEEE Transactions on Medical Imaging, 26(1), 15–30. http://doi.org/10.1109/TMI.2006.884215

Gilliam, A.D., Suever, J.D., and contributors (2016). DENSEanalysis. Retrieved from https://github.com/denseanalysis/denseanalysis

Contributing

We welcome contributions from any members of the DENSE user community. Feel free to submit a pull request with your contributions. Please see the CONTRIBUTING file for guidelines for contributing to DENSEanalysis.

Our contributors include: