scholarly journals EEG-BIDS, an extension to the brain imaging data structure for electroencephalography

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Cyril R. Pernet ◽  
Stefan Appelhoff ◽  
Krzysztof J. Gorgolewski ◽  
Guillaume Flandin ◽  
Christophe Phillips ◽  
...  
GigaScience ◽  
2016 ◽  
Vol 5 (suppl_1) ◽  
Author(s):  
Daniel Clark ◽  
Krzysztof J. Gorgolewski ◽  
R. Cameron Craddock

2021 ◽  
Author(s):  
Agah Karakuzu ◽  
Stefan Appelhoff ◽  
Tibor Auer ◽  
Mathieu Boudreau ◽  
Franklin Feingold ◽  
...  

The Brain Imaging Data Structure (BIDS) established community consensus on the organization of data and metadata for several neuroimaging modalities. Traditionally, BIDS had a strong focus on functional magnetic resonance imaging (MRI) datasets and lacked guidance on how to store multimodal structural MRI datasets. Here, we present and describe the BIDS Extension Proposal 001 (BEP001), which adds a range of quantitative MRI (qMRI) applications to the BIDS. In general, the aim of qMRI is to characterize brain microstructure by quantifying the physical MR parameters of the tissue via computational, biophysical models. By proposing this new standard, we envision standardization of qMRI which makes multicenter dissemination of interoperable data possible. As a result, BIDS can act as a catalyst of convergence between qMRI methods development and application-driven neuroimaging studies that can help develop quantitative biomarkers for neural tissue characterization. Finally, our BIDS extension offers a common ground for developers to exchange novel imaging data and tools, reducing the practical barriers to standardization that is currently lacking in the field of neuroimaging.


2018 ◽  
Author(s):  
Christopher Holdgraf ◽  
Stefan Appelhoff ◽  
Stephan Bickel ◽  
Kristofer Bouchard ◽  
Sasha D'Ambrosio ◽  
...  

Intracranial electroencephalography (iEEG) data offer a unique combination of high spatial and temporal resolution measures of the living human brain. However, data collection is limited to highly specialized clinical environments. To improve internal (re)use and external sharing of these unique data, we present a structure for storing and sharing iEEG data: BIDS-iEEG, an extension of the Brain Imaging Data Structure (BIDS) specification, along with freely available examples and a bids-starter-kit. BIDS is a framework for organizing and documenting data and metadata with the aim to make datasets more transparent and reusable and to improve reproducibility of research. It is a community-driven specification with an inclusive decision-making process. As an extension of the BIDS specification, BIDS-iEEG facilitates integration with other modalities such as fMRI, MEG, and EEG. As the BIDS-iEEG extension has received input from many iEEG researchers, it provides a common ground for data transfer within labs, between labs, and in open-data repositories. It will facilitate reproducible analyses across datasets, experiments, and recording sites, allowing scientists to answer more complex questions about the human brain. Finally, the cross-modal nature of BIDS will enable efficient consolidation of data from multiple sites for addressing questions about generalized brain function.


2015 ◽  
Author(s):  
Krzysztof J. Gorgolewski ◽  
Tibor Auer ◽  
Vince D. Calhoun ◽  
R. Cameron Craddock ◽  
Samir Das ◽  
...  

AbstractThe development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain. Despite the fact that MRI is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. This renders sharing and reusing data (within or between labs) difficult if not impossible and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. To solve this problem, we have developed the Brain Imaging Data Structure (BIDS), a standard for organizing and describing MRI datasets. The BIDS standard uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations.


2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Guiomar Niso ◽  
Krzysztof J. Gorgolewski ◽  
Elizabeth Bock ◽  
Teon L. Brooks ◽  
Guillaume Flandin ◽  
...  

2021 ◽  
Author(s):  
Martin Norgaard ◽  
Granville James Matheson ◽  
Hanne D Hansen ◽  
Adam G Thomas ◽  
Graham Searle ◽  
...  

The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging datasets. It serves not only to facilitate the process of data sharing and aggregation, but also to simplify the application and development of new methods and software for working with neuroimaging data. Here, we present an extension of BIDS to include positron emission tomography (PET) data (PET-BIDS). We describe the PET-BIDS standard in detail and share several open-access datasets curated following PET-BIDS. Additionally, we highlight several tools which are already available for converting, validating and analyzing PET-BIDS datasets.


2017 ◽  
Author(s):  
Guiomar Niso ◽  
Krzysztof J. Gorgolewski ◽  
Elizabeth Bock ◽  
Teon L. Brooks ◽  
Guillaume Flandin ◽  
...  

AbstractWe present a significant extension of the Brain Imaging Data Structure (BIDS) to support the specific aspects of magnetoencephalography (MEG) data. MEG provides direct measurement of brain activity with millisecond temporal resolution and unique source imaging capabilities. So far, BIDS has provided a solution to structure the organization of magnetic resonance imaging (MRI) data, which nature and acquisition parameters are different. Despite the lack of standard data format for MEG, MEG-BIDS is a principled solution to store, organize and share the typically-large data volumes produced. It builds on BIDS for MRI, and therefore readily yields a multimodal data organization by construction. This is particularly valuable for the anatomical and functional registration of MEG source imaging with MRI. With MEG-BIDS and a growing range of software adopting the standard, the MEG community has a solution to minimize curation overheads, reduce data handling errors and optimize usage of computational resources for analytics. The standard also includes well-defined metadata, to facilitate future data harmonization and sharing efforts.


2016 ◽  
Vol 3 (1) ◽  
Author(s):  
Krzysztof J. Gorgolewski ◽  
Tibor Auer ◽  
Vince D. Calhoun ◽  
R. Cameron Craddock ◽  
Samir Das ◽  
...  

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Christopher Holdgraf ◽  
Stefan Appelhoff ◽  
Stephan Bickel ◽  
Kristofer Bouchard ◽  
Sasha D’Ambrosio ◽  
...  

2018 ◽  
Author(s):  
Cyril R Pernet ◽  
Stefan Appelhoff ◽  
Guillaume Flandin ◽  
Christophe Phillips ◽  
Arnaud Delorme ◽  
...  

The Brain Imaging Data Structure (BIDS) project is a quickly evolving effort among the human brain imaging research community to create standards allowing researchers to readily organize and share study data within and between laboratories. The first BIDS standard was proposed for the MRI/fMRI research community and has now been widely adopted. More recently a magnetoencephalography (MEG) data extension, BIDS-MEG, has been published. Here we present an extension to BIDS for electroencephalography (EEG) data, BIDS-EEG, along with tools and references to a series of public EEG datasets organized using this new standard. A shortened version is now published in Nature Scientific Data: https://www.nature.com/articles/s41597-019-0104-8.


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