BIDS - podcast bids maintainers

Kay Robbins and Dung Truong come to tell us about Hierarchical event descriptors and how they integrate with BIDS.

Slides: https://osf.io/vxe4y/

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Hierarchical event descriptors



Who are we?

We are members of the HED working group…. our group wants to make large-scale neuroimaging analyses easy and reliable. We see HED as THE enabling technology for doing this. We’re not there yet, but we’re making really good progress. 



What is HED?

HED stands for Hierarchical Event Descriptors. HED is a system for describing events in a way that is understandable to people but also directly usable by computer programs. Think of it as structured keywords on steroids. 



Why do we need HED if we have BIDS?

BIDS is great, but it focuses mainly on data format and file structure. This information is usually not enough to do serious (and correct analysis) without delving into the methods sections of the underlying publications and then writing code to extract parts of the data based on the experimental design. The goal of HED is to eliminate a lot of this with machine-actionable annotation.

Sounds complicated? Well, the ideas behind it really aren’t……

There are three important points here:


Most imaging files have (or should have) an accompanying events file that contains a list of times at which various things happen in the experiment --- like recording turns on, an experimental condition changes, the subject is shown a stimulus, etc.
The meanings of the things in the event file should be given in an accompanying metadata file that BIDS calls a JSON sidecar. HED annotation gives these meanings in a machine-actionable form.
The HED meanings are usually the same for all of the events files in the entire BIDS dataset so you only need one JSON sidecar file placed at the top level in your BIDS dataset.

Once a BIDS data set has this metadata file, tools can allow very powerful searching and analysis based on entering a string of HED tags rather than writing code for each case.

We have some nice interactive tools such as CTAGGER that guide users through the tagging process.

We also have online validation tools that allow users to check an events file and the applicable JSON sidecar. We recommend that users use the HED online tools to make sure that their JSON sidecar validates before validating the BIDS dataset as a whole with the bids-validator.



Useful links:

HED schema browser: https://www.hedtags.org/display_hed.html 

HED homepage: https://www.hedtags.org/ 

HED online tools: https://hedtools.ucsd.edu/hed/ 

HED organization Github site: https://github.com/hed-standard

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

BIDS starter kit: https://github.com/bids-standard/bids-starter-kit BIDS

examples: https://github.com/bids-standard/bids-examples

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License: CC-BY

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Intro music: https://www.bensound.com

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Kirstie Whitaker and Franklin Feingold come to tell us more about the BIDS steering group and the incoming election of a new member.

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If you want to know more about the election, check the BIDS website.

https://bids.neuroimaging.io/benefits.html#bids-steering-group-election

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

BIDS starter kit: https://github.com/bids-standard/bids-starter-kit BIDS

examples: https://github.com/bids-standard/bids-examples

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License: CC-BY

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Intro music: Memories from https://www.bensound.com

Julia Sprenger and Sylvain Takerkart join us to talk about the work on the extension to BIDS to support animal electrophysiology data.

The animal electrophysiology BIDS extension proposal: https://bids.neuroimaging.io/bep032

The INCF working group on standardized data: https://incf.org/sig/incf-working-group-standardized-data

Associated Github repository for discussions: https://github.com/INCF/neuroscience-data-structure/issues

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

BIDS starter kit: https://github.com/bids-standard/bids-starter-kit BIDS

examples: https://github.com/bids-standard/bids-examples

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License: CC-BY

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Intro music: https://www.bensound.com

Patricia Clement and Henk Mutsaerts tell us about their work to extend BIDS to support arterial spin labeling data.

BIDS ASL specification: https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#arterial-spin-labeling-perfusion-data

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

BIDS starter kit: https://github.com/bids-standard/bids-starter-kit BIDS

examples: https://github.com/bids-standard/bids-examples

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License: CC-BY

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Intro music: https://www.bensound.com

Agah Karakuzu and Gilles de Holander tell us about the journey to extend BIDS to support quantitative MRI data.

BIDS qMRI specification:

https://bids-specification.readthedocs.io/en/stable/99-appendices/11-qmri.html

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

BIDS starter kit: https://github.com/bids-standard/bids-starter-kit BIDS

examples: https://github.com/bids-standard/bids-examples

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License: CC-BY

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Intro music: https://www.bensound.com

Melanie Ganz and Martin Nørgaard tell us about the development and the future of the BIDS extension proposal for Positron Emission Tomography.

BIDS PET specification:

https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/09-positron-emission-tomography.html

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

BIDS starter kit:  https://github.com/bids-standard/bids-starter-kit

BIDS examples:  https://github.com/bids-standard/bids-examples

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License: CC-BY

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Intro music: https://www.bensound.com