Nomination Statement: NiPreps for the 2026 OHBM Open Science Prize

--- tags: Collecting-feedback --- # Nomination Statement: NiPreps for the 2026 OHBM Open Science Prize NiPreps (NeuroImaging Preprocessing toolS) is a framework deriving from the *fMRIPrep* philosophy, to offer neuroimaging preprocessing tools and software infrastructure for transparent and reproducible data preprocessing. Furthermore, it also offers quality assurance and control, across modalities (e.g., fMRI, dMRI, ASL, PET) and populations/species (e.g., infants, rodents, etc.). ## Introduction Beyond setting a baseline on making software available, Open Science endeavors to ensure tools are transparent, usable, reliable, continuously improving, and scalable. NiPreps exemplifies these principles through sustained innovation, rigorous validation, glass-box principles, and a thriving global community. Over the past several years, NiPreps has evolved from a successful fMRI pipeline - innovative in adopting best engineering practices from industrial Data Science - into a comprehensive, multimodal preprocessing ecosystem, culminating most recently in the maturation and widespread adoption of PETPrep. By providing standardized, rigorously validated preprocessing pipelines across imaging modalities, NiPreps continues to define best practices in neuroimaging. For these reasons, NiPreps is an exceptional candidate for the 2026 OHBM Open Science Prize. ## Advancing Open Science Through Multimodal Standardization Standardization remains one of the most pressing challenges in neuroimaging, particularly as the field moves toward multimodal integration. Building on the foundational success of fMRIPrep, NiPreps has expanded and consolidated a family of rigorously validated workflows, including structural (sMRIPrep), diffusion (dMRIPrep), arterial spin labeling (ASLPrep), Nibabies, NiRodents and most recently Positron Emission Tomography (PETPrep). PETPrep represents a major recent milestone for the project. PET data have historically lacked consensus preprocessing standards, limiting reproducibility and cross-study comparison. PETPrep addresses this gap by providing a BIDS-aware, end-to-end PET preprocessing workflow, within a transparent, reproducible framework. Its release marks a significant extension of NiPreps’ philosophy into one of the most technically and methodologically challenging domains in neuroimaging, enabling robust multimodal MRI–PET analyses for the first time at scale. ## Sustained Growth and Impact on the Neuroimaging Community NiPreps’ impact continues to grow, both in scale and scope with +100 contributors. fMRIPrep alone has accrued over 4,200 citations and is executed tens of thousands of times per week worldwide, forming the backbone of contemporary functional MRI research. The broader NiPreps ecosystem is now routinely used in large-scale studies of psychiatric illness, neurodegeneration, development, aging, and translational neuroscience. Recent years have seen a marked increase in clinical and translational use cases. This expansion underscores NiPreps’ ability not only to support cutting-edge methodology, but also to translate open science principles into domains with direct clinical relevance. In parallel, NiPreps continues to drive upstream innovation across the neuroimaging software stack, shaping tools such as Nipype, NiBabel, and PyBIDS. NiPreps also drives downstream projects such as tedana and nilearn adopting fMRIPrep outputs as inputs. Improvements motivated by multimodal workflows have benefited the entire ecosystem, reinforcing NiPreps’ role as a catalyst for community-wide progress. ## Leadership in Reproducible and Transparent Development NiPreps remains a model for open and reproducible scientific software development. All workflows are open-source, extensively tested, and accompanied by machine-readable provenance and detailed visual reports. Importantly, the project has continued to refine its governance and sustainability model, with the NiPreps Community operating under a formal, elected Steering Committee that ensures continuity, accountability, and openness (https://github.com/nipreps). NiPreps has also been a leader in pushing the boundaries of open and reproducible methodologies. For example, MRIQC, a companion tool within the NiPreps ecosystem, was one of the first neuroimaging software projects to be registered as a pre-registered report, reinforcing its commitment to transparency and rigorous evaluation. Furthermore, recent development cycles—including PETPrep—have demonstrated NiPreps’ commitment to methodological transparency, with design decisions, limitations, and validation openly documented and discussed. ## Lowering Barriers to Complex Methods As neuroimaging becomes increasingly multimodal and computationally demanding, NiPreps has played a crucial role in lowering barriers to entry into neuroimaging analyses. NiPreps encapsulates best practices that previously required deep modality-specific expertise, enabling researchers to apply appropriate state-of-the-art methods with minimal manual intervention. NiPreps’ strict adherence to the Brain Imaging Data Structure (BIDS), combined with containerized execution and cloud compatibility, ensures that even resource-limited labs can perform high-quality preprocessing. This democratization is especially impactful within some imaging modalities (such as PET), where methodological complexity has historically restricted access to well-resourced institutions. ## Commitment to Equity, Diversity, and Community Growth NiPreps’ recent expansion has gone hand-in-hand with sustained investment in equity, diversity, and inclusion. The project continues to support researchers from underrepresented backgrounds through mentorship, leadership opportunities, and paid open-source contributions. Women and BIPOC scientists remain central to NiPreps’ technical leadership, governance, and training efforts. NiPreps has also spearheaded training initiatives, including workshops at major conferences (e.g., OHBM BrainHacks) and standalone hackathons, which bring together diverse communities of scientists to collaborate and build expertise. These efforts help ensure that advances in open science benefit the entire field, not just a privileged subset. ## Shaping the Next Era of Neuroimaging NiPreps’ most recent advances demonstrate that it is not a static success story, but a living infrastructure project that continues to evolve alongside the field. By extending robust, standardized preprocessing into multimodal workflows, NiPreps is laying the groundwork for the next generation of reproducible, clinically relevant neuroscience. The OHBM Open Science Prize honors projects that transform both scientific practice and scientific culture. Through sustained impact, continued innovation, and recent breakthroughs such as PETPrep, NiPreps exemplifies this mission. It has not only changed how neuroimaging is done—it has ensured that the future of the field is open, reproducible, and inclusive. Finally, OHBM has been fundamental for NiPreps to thrive, and likewise NiPreps has contributed a lot back to the OHBM community.