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.
- making all the containers following the same specifications;
- cover more workflows;
- prepare multiple versions of
settings_values.json
for testing on multiple shared datasets;
- Matteo Mancini
- Ricardo Rios - RicardoRios46
Koller et al. (2021) "MICRA: Microstructural image compilation with repeated acquisitions", NeuroImage- 10.1016/j.neuroimage.2020.117406