Supported Formats

sovabids reads EEG files via MNE-Python’s read_raw, which supports a wide range of formats including BrainVision, EDF/BDF, EEGLAB, FIF, CNT, KIT/SQD, CTF, and more. See the full list in the MNE documentation.

Output is always written as a valid BIDS dataset. The table below lists formats that can also be exported natively (i.e., the BIDS data files stay in that format rather than being converted to BrainVision):

Install export support for EDF and EEGLAB:

pip install "sovabids[formats]"

For all other readable formats, sovabids converts the data to BrainVision on output (the default mne-bids behaviour).

Architecture

The main elements of sovabids are:

• A source path with the original dataset.

• A bids path that will be the output path of the conversion.

• A rules file that configures how the conversion is done from the general perspective.

• A mapping file that encodes how the conversion is performed to each individual file of the dataset.

Internally sovabids uses MNE-Python and MNE-BIDS to perform the conversion. In a sense is a wrapper that allows to do conversions from the command line.

Basic Usage

Installation for TUI usage

This will install sovabids with the terminal user interface dependencies.

pip install "sovabids[tui]"

Running the TUI

sovatui

See the TUI tutorial video for a walkthrough and its example.

pip install sovabids

sovapply source_path bids_path rules_path

bids_path/code/sovabids/mappings.yml

sovaconvert mapping_file

Installation for WEB GUI usage

This will install sovabids for usage with an experimental web gui.

pip install "sovabids[gui]"

See the WEB GUI tutorial video for a walkthrough and its example.

pip install "git+https://github.com/yjmantilla/bidscoin.git@sovabids"

Installation for developers

Fork this repo and run:

git clone https://github.com/<gh-username>/sovabids.git
cd sovabids
pip install -e ".[dev]"

Contributing

Contributions are welcome. See the Contributing guide for how to set up a development environment, run the tests, and open a pull request. The guide also lives at .github/CONTRIBUTING.md.

To report a bug, open an issue on the issue tracker. For usage questions and general help, use GitHub Discussions. The project follows a Code of Conduct.

Funding

Acknowledgments

sovabids is developed with the help of the following entities:

Academic Works

• Poster for the Big Data Neuroscience Workshop 2022 (Austin, Texas)

• Poster for OHBM 2022 Anual Meeting

• Video for OHBM 2022 Anual Meeting

• Poster for the eResearch Australasia Conference 2021

What does sova means?

sova is a contraction of ‘eso va’ which mean ‘that goes’ in spanish.

Nevertheless the real usage by the original developers is just to convey the idea of :

we will make it happen, we dont know how, but we will