matteomancini / microsuite

A collection of Dockerfiles to run several microstructural MRI tools.

microsuite - a collection of containers for MRI microstructural models

This repository has been created during Brainhack Micro2Macro, and includes several implementations of microstructural models that are ready-to-use. We use the QMENTA SDK to:

• realize a shared template and API across different workflows;
• make containers that are ready-to-run on the QMENTA platform;
• make easy to define input and output.

The test_sdk_tool.py script from QMENTA included in this repository can be used to run locally the containers. Here is an example with the amico implementation of NODDI. First we build the image:

docker build -t amico-noddi AMICO-NODDI/

And then the workflow can be launched:

python test_sdk_tool.py amico-noddi ~/test_data ~/test_output/ --settings settings.json --values settings_values.json

To make the first tests, we used the MICRA dataset.

To-do list

• making all the containers following the same specifications;
• cover more workflows;
• prepare multiple versions of settings_values.json for testing on multiple shared datasets;

Contributors

• Matteo Mancini
• Ricardo Rios - RicardoRios46

References

Koller et al. (2021) "MICRA: Microstructural image compilation with repeated acquisitions", NeuroImage- 10.1016/j.neuroimage.2020.117406