PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

Martin Norgaard^{1

2}, Granville J Matheson^{3

4}, Hanne D Hansen^{1

5}, Adam Thomas⁶, Graham Searle⁷, Gaia Rizzo⁷, Mattia Veronese^{8

9}, Alessio Giacomel⁸, Maqsood Yaqub¹⁰, Matteo Tonietto¹¹, Thomas Funck¹², Ashley Gillman¹³, Hugo Boniface¹⁴, Alexandre Routier¹⁵, Jelle R Dalenberg¹⁶, Tobey Betthauser¹⁷, Franklin Feingold², Christopher J Markiewicz², Krzysztof J Gorgolewski², Ross W Blair², Stefan Appelhoff¹⁸, Remi Gau¹⁹, Taylor Salo²⁰, Guiomar Niso²¹, Cyril Pernet¹, Christophe Phillips²², Robert Oostenveld^{23

24}, Jean-Dominique Gallezot²⁵, Richard E Carson²⁵, Gitte M Knudsen¹, Robert B Innis²⁶, Melanie Ganz^{27

28}

Affiliations

¹ Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark.
² Department of Psychology, Stanford University, California, USA.
³ Department of Psychiatry, Columbia University, New York, NY, 10032, USA.
⁴ Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm Health Care Services, Stockholm, Sweden.
⁵ Athinoula A. Martinos Center for Biomedical Imaging, MGH/HST, Charlestown, MA, USA.
⁶ Intramural Research Program, NIMH, Bethesda, USA.
⁷ Invicro and Division of Brain Sciences, Imperial College London, London, UK.
⁸ Centre for Neuroimaging Sciences, King's College London, London, UK.
⁹ Department of Information Engineering, University of Padua, Padua, Italy.
¹⁰ Amsterdam UMC, location VUmc, department of radiology and nuclear medicine, Amsterdam, Netherlands.
¹¹ Université Paris-Saclay, CEA, CNRS, Inserm, BioMaps, Service Hospitalier Frédéric Joliot, Orsay, France.
¹² INM-1, Jülich Forschungszentrum, Jülich, Germany.
¹³ Aust. e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Townsville, Australia.
¹⁴ Centre d'Acquisition et de Traitement des Images, CEA, Paris, France.
¹⁵ Inria, Aramis project-team, Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtriére, Paris, France.
¹⁶ Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
¹⁷ Wisconsin Alzheimer's Disease Research Center, Division of Geriatrics, Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
¹⁸ Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany.
¹⁹ Institute of psychology, Université catholique de Louvain, Louvain la Neuve, Belgium.
²⁰ Department of Psychology, Florida International University, Miami, FL, USA.
²¹ Psychological Brain Sciences, Indiana University, Bloomington, IN, USA.
²² GIGA Cyclotron Research Centre in vivo imaging, University of Liege, Liege, Belgium.
²³ Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.
²⁴ NatMEG, Karolinska Institutet, Stockholm, Sweden.
²⁵ Department of Radiology and Biomedical Imaging, Yale University, New Haven, USA.
²⁶ Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, USA.
²⁷ Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark. mganz@nru.dk.
²⁸ Department of Computer Science, University of Copenhagen, Copenhagen, Denmark. mganz@nru.dk.

PMID: 35236846
PMCID: PMC8891322
DOI: 10.1038/s41597-022-01164-1

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

Martin Norgaard et al. Sci Data. 2022.

. 2022 Mar 2;9(1):65.

doi: 10.1038/s41597-022-01164-1.

Authors

Affiliations

¹ Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark.
² Department of Psychology, Stanford University, California, USA.
³ Department of Psychiatry, Columbia University, New York, NY, 10032, USA.
⁴ Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm Health Care Services, Stockholm, Sweden.
⁵ Athinoula A. Martinos Center for Biomedical Imaging, MGH/HST, Charlestown, MA, USA.
⁶ Intramural Research Program, NIMH, Bethesda, USA.
⁷ Invicro and Division of Brain Sciences, Imperial College London, London, UK.
⁸ Centre for Neuroimaging Sciences, King's College London, London, UK.
⁹ Department of Information Engineering, University of Padua, Padua, Italy.
¹⁰ Amsterdam UMC, location VUmc, department of radiology and nuclear medicine, Amsterdam, Netherlands.
¹¹ Université Paris-Saclay, CEA, CNRS, Inserm, BioMaps, Service Hospitalier Frédéric Joliot, Orsay, France.
¹² INM-1, Jülich Forschungszentrum, Jülich, Germany.
¹³ Aust. e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Townsville, Australia.
¹⁴ Centre d'Acquisition et de Traitement des Images, CEA, Paris, France.
¹⁵ Inria, Aramis project-team, Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtriére, Paris, France.
¹⁶ Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
¹⁷ Wisconsin Alzheimer's Disease Research Center, Division of Geriatrics, Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
¹⁸ Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany.
¹⁹ Institute of psychology, Université catholique de Louvain, Louvain la Neuve, Belgium.
²⁰ Department of Psychology, Florida International University, Miami, FL, USA.
²¹ Psychological Brain Sciences, Indiana University, Bloomington, IN, USA.
²² GIGA Cyclotron Research Centre in vivo imaging, University of Liege, Liege, Belgium.
²³ Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.
²⁴ NatMEG, Karolinska Institutet, Stockholm, Sweden.
²⁵ Department of Radiology and Biomedical Imaging, Yale University, New Haven, USA.
²⁶ Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, USA.
²⁷ Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark. mganz@nru.dk.
²⁸ Department of Computer Science, University of Copenhagen, Copenhagen, Denmark. mganz@nru.dk.

PMID: 35236846
PMCID: PMC8891322
DOI: 10.1038/s41597-022-01164-1

Abstract

The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging datasets, serving 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, also known as PET-BIDS, and share several open-access datasets curated following PET-BIDS along with tools for conversion, validation and analysis of PET-BIDS datasets.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1**
Overview of a common PET experiment. This example includes blood measurements and is defined on a common time scale. Note, “time zero” can either be defined as time of injection or scan start, and all the PET and blood data should be decay-corrected to this time point.

**Fig. 2**
Exemplary PET-BIDS dataset with a dataset description. This includes the adequate acknowledgements (1), previews of PET files (2,3), including blood (4,5) and MRI data (6). The left side shows a directory tree of a common PET-BIDS dataset, with files in the root directory describing the dataset (README and data description.json), a file with participant-specific information (participants.tsv), and a JSON sidecar file describing the metadata needed to understand the corresponding TSV file. Next to the files in the root directory, there are subject directories named sub- for each study participant. In the subject directory lies all acquired data divided into modalities (anat and pet, for the structural MRI and PET, respectively). The content of the pet directory are displayed in the right side of the figure, including the metadata of the raw PET data (2), and the associated imaging data (3). The metadata for the blood data acquired using manual sampling is stored in a JSON sidecar file (4), with the corresponding blood specified in the TSV file (5). The columns in the TSV file contain (1) time, (2) plasma radioactivity, (3) whole blood radioactivity, (4) metabolite parent fraction, and (5) metabolite polar fraction. Blood data acquired using an autosampler is also available following a similar structure as (4) and (5). The PET data may be accompanied with MRI data for co-registration and region definition (6). In this case, it is required to specify if the MRI data has been corrected for gradient non-linearities (*NonLinearGradientCorrection*) to allow for correct co-registration with the PET data.

See this image and copyright information in PMC

References

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PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

Affiliations

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding