Welcome to Madym
Madym is a C++ toolkit for quantitative DCE-MRI analysis developed in the QBI Lab at the University of Manchester. It comprises a set of command line tools and a graphical user-interface based on an extendable C++ library. It is cross-platform, and requires few external libraries to build from source. Alternatively, Madym can be downloaded and installed using pre-built binaries for Windows, MacOS or Ubuntu . We have also developed complementary interfaces in Python and Matlab, that allow the flexibility of developing in those scripting languages, while allowing C++ to do the heavy-duty computational work of tracer-kinetic model fitting. We strongly support the aims of reproducible research. Madym has been made open-source in line with these goals, and many of the features within the toolbox are designed to aid reproducible research.
Madym version 4.15.2 was reviewed and accepted for the Journal of Open Source Software. The accompanying paper is available here:
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Key features
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T1 mapping including variable flip-angle (VFA) and inversion recovery (IR) methods
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DCE-MRI tracer-kinetic model fitting, including the extended-Tofts, Patlak, two-compartment exchange and active uptake models, with support for single and dual-supply vascular input functions
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Auto-detection of arterial input functions (AIF), generation of AIFs from input ROIs and dose scaled generation of the Parker population AIF
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Estimation of portal vein input functions (PIF) from an AIF - ideal for fitting models to liver tissue
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Flexible fitting routines, including:
- Choice of optimisation, include linear least-squares fitting for the extended Tofts model (>100 times faster than non-linear fitting)
- selecting initial model parameters either for all voxels or individually per-voxel
- fixing any subset of parameters to enable refits and/or nested model fitting
- limiting parameters to within a range of their initial value to enable grid search fitting
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Strong focus on reproducible research, with:
- easy to use interface for setting analysis options, either at the command-line, from config files or in the GUI tool
- default values for options consistently applied across the different tools
- extensive audit and program logs generated for each analysis
- output config files generated with analysis recording the complete set of options used
- semantic versioning to map analyses to specific open-source Madym versions
For details on building and using Madym, please follow the links below. If you have any queries please contact Michael Berks or use the issue tracker.