Multiparametric Image Analysis
MIA is shorthand for “Multiparametric Image Analysis”. It is intended to be a complete image processing environment mainly targeted at the analysis and visualization of large amounts of MRI data.
MRI data analysis often requires a complex succession of data processing pipelines applied to a set of data acquired in an MRI exam or over several MRI exams. This analysis may need to be repeated a large number of times in studies involving a large number of acquisition sessions. Such that manual execution of the processing modules or simple ad-hoc scripting of the process may become error-prone, cumbersome and difficult to reproduce. Data processing pipelines exist in separate heterogeneous toolboxes, developed in-house or by other researchers in the field. This heterogeneity adds to the complexity of the modules are to be invoked manually.
Populse_MIA aims to provide easy tools to perform complex data processing based on a definition of the inputs and outputs of the individual pipelines on a conceptual level, and implies identifying data with respect to their role in an analysis project: “the scan type”, “the subject being scanned”, “the group of this subject is part of”, etc.
- From PyPI, for users
- By cloning the package, for developers
- From source, to use the latest version of populse_mia
- Third-party software
After an installation in user mode:
python3 -m populse_mia
After an installation in developer mode, interprets the main.py file from the source code directory:
cd [populse_install_dir]/populse_mia/python/populse_mia python3 main.py
Depending on the operating system used, it was observed some compatibility issues with PyQt5/SIP. In this case, we recommend, as a first attempt, to do:
python3 -m pip install --force-reinstall pyqt5==5.14.0 python3 -m pip install --force-reinstall PyQt5-sip==5.0.1
Contributing to the project
Unit tests written thanks to the python module unittest
Continuous integration made with Travis (Linux, OSX), and AppVeyor (Windows)
Code coverage calculated by the python module codecov
The module is ensured to work with Python >= 3.6
The module is ensured to work on the platforms Linux, OSX and Windows
The script of tests is python/populse_mia/test.py, so the following command launches the tests:
python3 python/populse_mia/test.py (from populse_mia root folder, for example [populse_install_dir]/populse_mia)
Other packages used