BIDS (Brain Imaging Data Structure; BIDS | INCF - International Neuroinformatics Coordinating Facility) is a standard for organising neuroimaging and behavioural raw data. It enables interoperability by allowing multiple tools to analyse a given dataset without extra modifications, and reproducibility, by facilitating reanalysis of the same dataset by multiple research groups. Although originally developed for MRI data analysis, BIDS has also gained popularity for EEG/MEG data analysis, and with more analysis tools supporting BIDS, converting raw data to the BIDS standard has become an important first-step for EEG/MEG data analysis. Unfortunately, however, available tools are often too complicated to use for scientists with limited technical or scripting experience, a situation that is especially prevalent in EEG labs which are less likely to employ informatics support personnel.
One major barrier to user-friendly conversion of data to the BIDS standard is that most tools do not include a graphical interface. Moreover, the few general-purpose BIDS conversion tools that do have a GUI in addition to a command line interface, do not support conversion of EEG/MEG data. The proposed project aims to extend one of these existing BIDS conversion tools to add EEG/MEG support, resulting in a tool that is both easy to use, and as general as possible.
The converter will be cross-platform (Windows, Mac, Linux) for maximum applicability allowing a wide reach of EEG/MEG labs and users. Moreover, it will be integrated into AEDAPT/NeuroDesk (GitHub - NeuroDesk/neurodesk: A flexible, scalable, and easy to use data analysis environment for reproducible neuroimaging), a Docker virtual machine incorporating a complete EEG/MEG (as well as MRI) analysis desktop environment. AEDAPT/NeuroDesk is an open-source project supported by the Australian Research Data Commons and actively developed by several universities in Australia.
- Extending an existing GUI-based BIDS conversion tool to support EEG/MEG (see list at Brain Imaging Data Structure (BIDS) | INCF - International Neuroinformatics Coordinating Facility)
- Incorporating continuous integration to ensure backward compatibility
- Enhancing the tool so users can enter additional information, not recorded in the original EEG/MEG raw data files
- Redesigning the tool to allow either bulk or incremental conversion
- Improving support for multiple-session acquisitions of the same individual
- Adding automatic suggestions based on mappings provided by the community
Skill level needed:
- Python GUI programming - intermediate
- Text manipulation (regular expressions) in Python - intermediate
- Familiarity with EEG - advantage
- Familiarity with BIDS - advantage
- PyQt5, Tkinter, or wxPython
- Circleci or Github actions
Mentors: Oren Civier @oren_civier (Swinburne University of Technology), Steffen Bollmann (University of Queensland), Aswin Narayanan (University of Queensland), Tom Johnstone @TomJ (Swinburne University of Technology)
Tags: BIDS, neuroimaging, GUI, EEG/MEG, NeuroDesk