bids-statsmodels-design-synthesizer

Project migrated !!!!!

Efforts migrated to: bids-standard/pybids#724

For now this is a prototype to explore the possibility of creating self-contained tool to perform the data aggregation necessary to jump from BIDS events.tsv files/model.json/other time series metadata to a design matrix for downstream implementers (or an appropriate sparse precursor of the design matrix).

Design notes: https://hackmd.io/QdwXR8XwRcmZaXp1zw6Ukg

• Free software: MIT license
• Documentation: https://bids-statsmodels-design-synthesizer.readthedocs.io.

Developer setup

While this tool attempts to have no dependencies, the development dependencies for now can be installed with (very hacky for now):

# you may need to brew install git-annex
# first step is to install git-annex with something like:
brew install git-annex
conda create -c conda-forge -n bids-stats-synth python=3
conda activate bids-stats-synth

pip install datalad
pip install -r requirements_dev.txt
pip install -e .

mkdir tests/data
cd tests/data
datalad install ///openneuro/ds000003
mkdir ds000003/models
curl -fsSL https://raw.githubusercontent.com/poldracklab/fitlins/master/examples/models/ds000003/models/model-001_smdl.json > ds000003/models/model-001_smdl.json

cd ..
pytest

Features

Works for at least one test case!

TODO

• Try to get some transformations working without dependencies.
• Deal with the absence of dependicies gracefully.
• Get a single file implementation built with https://github.com/Akrog/pinliner.
• Drop boutiques.
• Write up a description of the transformation spec.
• Translation to formats easy for other implmenters to injest.
• Maybe a way to stop prior to densifying transformation.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.