PET2BIDS: a library for converting Positron EmissionTomography data to BIDS
successful and popular in the community with adoption by brain imaging repositories (e.g., OpenNeuro (Markiewicz et al., 2021), PublicnEUro (Public nEUro, 2023)), data management tools (e.g., COINS (Landis et al., 2016), XNAT (Marcus et al., 2007)) and computational platforms (e.g.BrainLife (Hayashi S, 2023)).BIDS allows data to be shared much more efficiently, enables the development of automated data analysis pipelines, and improves reproducibility.The BIDS extension for Positron Emission Tomography (PET-BIDS) (Norgaard et al., 2022) provides nomenclature for structured data and metadata, including all the necessary information to share and report on PET blood and metabolite (Knudsen et al., 2020).Here we present a code library, developed in both Matlab and Python, allowing the conversion of DICOM (DICOM PS3.3 2020b -Information Object Definitions, 2020) and ECAT (CTI/Siemens proprietary data format) PET imaging data and metadata (e.g., timing information such as 'time zero' or blood measurements) into files that follow the BIDS specification (nifti, json, tsv).
Authors
- Adam G. Thomas
- Gabriel González‐Escamilla (ORCID: https://orcid.org/0000-0002-7209-1736)
- Granville J. Matheson (ORCID: https://orcid.org/0000-0002-5646-4547)
- Gitte M. Knudsen (ORCID: https://orcid.org/0000-0003-1508-6866)
- Claus Svarer (ORCID: https://orcid.org/0000-0001-7811-1825)
- Melanie Ganz (ORCID: https://orcid.org/0000-0002-9120-8098)
- Anthony Galassi (ORCID: https://orcid.org/0000-0001-6550-4574)
- Cyrus Eierud (ORCID: https://orcid.org/0000-0002-9942-676X)
- Robert B. Innis (ORCID: https://orcid.org/0000-0003-1238-7209)
- Cyril Pernet (ORCID: https://orcid.org/0000-0003-4010-4632)
- Chris Rorden (ORCID: https://orcid.org/0000-0002-7554-6142)
- Martin Nørgaard (ORCID: https://orcid.org/0000-0003-2131-5688)
- Murat Bilgel (ORCID: https://orcid.org/0000-0001-5042-7422)
Institutions
- University of Copenhagen (DK)
- National Institutes of Health (US)
- University of South Carolina (US)
- Georgia State University (US)
- Johannes Gutenberg University Mainz (DE)
- Stockholm County Council (SE)
- Rigshospitalet (DK)
- Karolinska Institutet (SE)
- University Medical Center of the Johannes Gutenberg University Mainz (DE)
- Center for Translational Research in Neuroimaging and Data Science (US)
- National Institute on Aging (US)
- Columbia University (US)
- Stanford University (US)
Publication Details
- Journal
- The Journal of Open Source Software
- Published
- 2024-08-23
- DOI
- https://doi.org/10.21105/joss.06067
- Citations
- 4
- Primary Topic
- Medical Imaging Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 1.62
Funders
- Novo Nordisk
- Novo Nordisk Fonden