sovabids 0.4.2

Automated eeg2bids conversion

sovabids

Visit the documentation

• sovabids is a python package for automating eeg2bids conversion.

• New to sovabids? Start with the Quickstart guide.

• sovabids can be used through (click to see the examples):

  1. its python API

  2. its CLI entry points

  3. its terminal user interface (TUI)

  4. its JSON-RPC entry points (needs a server running the backend)

  5. its minimal web-app GUI

Note

The advantage of the JSON-RPC way is that it can be used from other programming languages.

Limitation:

Do notice that at the moment the files have to be on the same computer that runs the server.

Warning

Currently meg2bids conversion is not supported, but this is a targeted feature.

Tip

By default sovabids will skip files already converted. If you want to overwrite previous conversions currently you need to delete the output folder (by yourself) and start sovabids over again.

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

Terminal User Interface (sovatui)

The easiest way to use sovabids is through its terminal user interface (TUI) called sovatui. This will allow you to do the conversion without having to write any command line code, and also to have a more visual experience of the conversion process. The TUI guides you through the full conversion workflow in four tabs: Setup, Rules, Mappings, and Convert.

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.

Command Line Interface (CLI) entry-points

Use sovabids through its CLI entry-points as follows:

Installation

pip install sovabids

sovapply

Use the sovapply entry-point to produce a mapping file from a source path, an output bids root path and a rules filepath.

sovapply source_path bids_path rules_path

By default the mapping file made will have the following filepath:

bids_path/code/sovabids/mappings.yml

sovaconvert

Use the sovaconvert entry-point to convert the dataset given its mapping file.

sovaconvert mapping_file

Using the experimental web GUI

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.

Using the experimental bidscoin plugin

For the experimental bidscoin plugin, install the sovabids fork of bidscoin manually:

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

Follow the example at https://sovabids.readthedocs.io/en/latest/auto_examples/bidscoin_example.html to see how to use the plugin.

Installation for developers

Fork this repo and run:

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

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