BRAIN project: OpenNeuroPET: An Archive for PET data

National Institute Of Mental Health

Investigators

Linked publications & trials

Abstract

In recent years, the importance of data sharing has increasingly been recognized by the neuroimaging community because of the poor replicability of findings, the need for appropriate quality control, the greater statistical power provided by larger samples, and the higher scientific impact of multilateral collaborations. Our funding bodies and scientific journals also increasingly encourage or require that the data be shared. However, data sharing can be clumsy and cumbersome in the absence of well articulated guidelines, clear data formatting standards, and well managed repositories. Building on the recommendations of leaders in the PET field, and in collaboration with other highly successful repositories of human neuroimaging data, an application was submitted to the NIH BRAIN initiative for funding to establish a useful and freely-shared repository for human brain PET data. That application was favorably reviewed and awarded funding in 2021 and our work commenced. Standards & Nomenclature From the beginning, we have understood that open standards for both nomenclatures and data formats were critical to this project's success. Following a highly collaborative process including a wide array of leading PET researchers in the field, our paper on consensus nomenclature was published last year in Journal of Cerebral Blood Flow & Metabolism. The next step was to standardize PET data formats for sharing. Our colleagues in Copenhagen led the effort to establish this new standard as an extension to the Brain Imaging Data Structure (BIDS). This standard was finalized into the BIDS Standard on April 7th 2021 and the associated paper is available on the bioRxiv preprint server and Natures Scientific Data server. Members of our group along with the BIDS maintainers are now engaged in further developing the BIDS standard into a machine-readable document. A machine-readable standard will help to ensure a uniform application of the standard across institutions and tools that handle BIDS and BIDS PET formatted data. Tools Since 2021 the development of software and tooling to convert and manipulate PET data into BIDS has been ongoing. We have been working with our collaborators in Copenhagen to develop conversion tools (PET2BIDS Library) that can be comfortably used in the typical environments that PET researchers work and do analysis. These tools have been built to take data as it comes off the PET scanner, add additional information such as radiotracer concentration blood measurements), and then convert them into BIDS formatted data. These tools are presently being used to convert and deliver PET data from Stanford, the NRU, and the NIMH into the repository mentioned below. We are also collaborating with the authors of leading PET analysis and popular neuroimaging software packages (e.g. Doug Greve author of PET Surfer) to make BIDS-formatted PET dataset easily loaded and analyzed. Our work with Doug and MGH is on going. Additionally, we continue to reach out and collaborate with other popular neuroimaging tool developers (e.g. Chris Rorden author of Dcm2niix) to better support PET. We hope to amplify the impact of our efforts by supporting well established tools and software by providing direct contributions, domain knowledge, and supplying open PET datasets for tool development. Repository Finally this project requires a data repository that is well-designed, easy-to-use, and built upon community standards. The contracted team at Squishy media has built out the site to include PET in concert with its addition to the BIDS Standard. The new site will not only advance PET data sharing, but will also allow OpenNeuro to better integrate many other neuroimage modalities for which new BIDS specification have recently been published (e.g. EEG, iEEG, MEG, Microscopy). After significant testing, solicitation of user feedback, and the implementation of additional suggestions and improvements the new site is now live. Our collaborators at Stanford continue to maintain and improve the site retaining some of the critical maintainers to the project.