Standardization of neuroimaging data in Synapsy

Synapsy DMP Online Meeting

by Sebastien Tourbier

April 21, 2021

Why is it useful?

Execution of DMP satisfying open science requirements

Advantages of adopting a standard

How?

Keys towards FAIR neuroimaging data in Synapsy

The Road Map

Step 1: Understanding how datasets are organized in each lab

Step 2: Creation of BIDS datasets for raw data

Step 3: Adoption of Datalad

Step 4: Creation of dataset catalog

Step 5: Dataset publication

What is BIDS?

Specifications to organize and describe neuroimaging data that complies with the FAIR concept


https://doi.org/10.1038/sdata.2016.44

Comprehensible organization and naming with well-accepted formats

from https://bids-specification.readthedocs.io

Consistent image acquisition metadata

Consistent dataset documentation and experiment metadata

Why BIDS?

Neuroimaging data standard originating from MRI

Allow use to make Synapsy neuroimaging data FAIR and ready to be compliant with the SNSF requirements

Make data fully understandable by itself thanks to its consistent metadata and documentation

Facilitate data sharing between lab members and collaborators part of Synapsy

Make code interoperable between projects, lab members, and collaborators part of Synapsy

Very little effort to deposit neuroimaging Synapsy neuroimaging data to open databases

Databases such as OpenNeuro, LORIS, COINs, XNAT, SciTran and others accept and export datasets organized following BIDS

Benefit of dedicated and well documented tools

For validation and data curation support

https://bids-standard.github.io/bids-validator

For dataset query

For analysis

A number of processing pipelines handling BIDS datasets (BIDS Apps) are available, ranging from quality control to preprocessing, connectome mapping, and statistical analysis

https://bids-apps.neuroimaging.io/apps/

How does BIDS apply for EEG?

BIDS extension for EEG


https://doi.org/10.1038/s41597-019-0104-8

An overview

Follow the general BIDS data structure originating from MRI with some modifications to accommodate EEG data types

Figure adapted from https://doi.org/10.1038/s41597-019-0104-8

EEG tools supporting BIDS


  • MNE-BIDS: Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.

  • FieldTrip: Can read data from all EEG and MRI file formats that are supported in BIDS and includes the data2bids function to convert data to the BIDS structure.

  • bids-matlab-tools: Collection of functions to import and export BIDS-formated experiments, tailored for use as an EEGLAB plugin

Progress

Thank you for your attention!