LSLAutoBIDS

Tools to convert LSL + friends automatically to BIDS, and upload it to a Dataverse

🚀 Getting Started

Get started with LSLAutoBIDS by installing the package and its dependencies.

🔰 About the package

This package automates the conversion of EEG recordings (xdf files) to BIDS (Brain Imaging Data Structure) format, integrates Datalad and uploads the data to Dataverse. lslautobids is an open-source package written in python and available as a pip package.

How to run the software?

Step 1: Clone the repository

git clone https://github.com/s-ccs/LSLAutoBIDS.git

Step 2: Install the package

pip3 install lslautobids

It is advised to install the package in a seperate environment (e.g. using conda or virtualenv).

Note

If you are using conda, you can create a new conda environment using the following command and activate it.

conda create -n <ENV_NAME> python=3.11
conda activate <ENV_NAME>

Step 3: Data Organization

The package requires the recorded XDF data to be organized in a specific directory structure which is semi-compliant with the BIDS (Brain Imaging Data Structure) format. The BIDS format is a standard for organizing and describing neuroimaging data, making it easier to share and analyze.

• The projects root location is the root directory where all the eeg raw recordings (say .xdf files) are stored e.g. projects/sub-A/ses-001/eeg/sub-A_ses-001_task-foo.xdf.
• The (optional) project_stimulus root location is the directory where the experiments (e.g .py, .oxexp) and behavioral files (e.g. eye-tracking recordings, labnotebook, participant forms, etc ) are stored.
• The bids root location is the directory where the converted BIDS data is stored, along with source data and code files which we want to version control using Datalad.

Important

Please follow the BIDS data organization guidelines for storing the neuroimaging data for running this package. The BIDS conversion guidelines are based on the recommended directory/files structure. You only can change the location of the root directories according to your preference. You must also strictly follow the naming convention for the project and subject subdirectories.

Here you will find the recommended directory structure for storing the project data (recorded, stimulus and converted data) in the data_organization file.

Step 4: Generate the configuration files

This configuration is required to run for running the automation pipeline of lslautobids.

1. AutoBIDS and Dataverse Configuration :

• Run the command below to create a configuration file template in folder ~/.config/lslautobids/ folder. This will create a config file with the dataverse details and the root directories for the projects.

lslautobids gen-dv-config

• Edit the file e.g. via nano ~/.config/lslautobids/autobids_config.yaml to add the dataverse and project root details.

This will be mostly same for all the projects, thus running this command is only recommended once per system.

2. Project Configuration : This is to be done once for each new project. This store the project details like project name, project id, project description etc. and is saved in a projects/<PROJECT_NAME>/project_<PROJECT_NAME>.toml file

• Run the command below to create a configuration file template in projects/<PROJECT_NAME>/ folder (according to the selected root directories).

lslautobids gen-proj-config -p <projectname> 

Step 6: Run the conversion scripts

Run the conversion scripts to convert the xdf files to BIDS format and upload the data to the dataverse.

lslautobids run -p TestData2025

Note

You can run the --help for all the commands to get more information about the available options and directly lsl-autobids help to get the list of available commands.

Disclaimer

The package is still in development and currently is only supported in MacOS and Linux.