The AxonLab © 2020-2026
Site based on the Allan Lab
Site based on the Allan Lab
Oct 15, 2026
After a long collaborative effort led by Dr. Marta Topor and Oscar with 88 authors, the preprint is now available on PsyArXiv. It argues that traditional publishing rewards speed, volume and tidy positive narratives, which blurs the line between exploration and confirmation, and that Registered Reports should become the default pathway for publishing confirmatory research.
Oct 2026
As of October 2026 (citation counts from Google Scholar):
Thank you to everyone who uses, tests and contributes to these tools!
Oct 9, 2026
Oscar served as examiner (Examinateur) on the jury of Gabriela Gómez Jiménez’s doctoral thesis, Predictive Modelling in Diffusion MRI: Benchmarking, Interpretability, and a Cortical Microstructure Application, prepared at Inria Saclay-Île-de-France under the direction of Demian Wassermann, with Reuben Dorent as co-supervisor, and defended at Université Paris-Saclay on 9 October 2026. Congratulations, Dr. Gómez Jiménez!
Oct 2, 2026
Oscar co-organized with Guiomar Niso the Training School of Working Group 3 of the COST Action INDoS, a three-day hybrid event hosted at CSIC (c/ Serrano 113, Madrid). In total, 98 people attended: 30 in person in Madrid and 68 online. Oscar and Mélanie Garcia were among the trainers, with Yasser Alemán-Gómez, Lea Waller, Steffen Bollmann and Martin Nørgaard, and the programme covered standardized preprocessing, BIDS across modalities, PET, EEG/MEG, and fMRI preprocessing with fMRIPrep. The training materials are openly available under CC BY 4.0.
Sep 2026
The Chan Zuckerberg Initiative’s Essential Open Source Software for Science grant NiPreps: a Community Framework for Reproducible Neuroimaging (Cycle 5, with Oscar as PI) concluded in September 2026. Since November 2022, it supported the growth of the NiPreps community through documentation, the maintenance of the foundational components, and the roadmaps of fMRIPrep, dMRIPrep and MRIQC. We are deeply grateful to CZI, which earlier also funded NiBabel through the Cycle 3 grant Strengthening Community and Code Foundations for Brain Imaging (2021 to 2024).
Sep 2026
WebMRIQC: A Web-Based Implementation of MRIQC for Accessible MRI Image Quality Assessment in Resource-Constrained Settings, by Philip Nkwam with Udunna Anazodo, Maruf Adewole, Sekinat Zurakat-Aderibigbe and colleagues at the Medical Artificial Intelligence Laboratory (MAI Lab) and CAMERA MRI Africa, has been accepted at the MIRASOL Workshop of MICCAI 2026 in France. WebMRIQC is a free, zero-installation platform that runs the full, unmodified MRIQC pipeline from the browser: users upload a DICOM or BIDS folder, and it converts DICOM to BIDS, runs MRIQC on shared compute, and returns an interactive quality dashboard with normative benchmarks. Validated against native MRIQC on the BraTS-Africa and BraTS 2021 datasets, it showed near-perfect agreement across all image quality metrics. It lowers the barriers that keep many imaging centres in Africa and other low- and middle-income settings out of standardized MRI quality control. Try it at webmriqc.mailab.io and find the code on GitHub. Thank you, Philip and team, for the kind acknowledgment of Oscar and MRIQC!
Sep 2026
Aug 2026
The Federated Journal Club is a trainee-oriented activity of Working Group 3 of the COST Action INDoS, in which participants collaboratively read and critically annotate the neuroimaging-preprocessing literature across nine imaging modalities plus a cross-modality methods category. It is open to everyone, with no INDoS membership required, and especially welcomes trainees and early-career researchers. For the pilot, Oscar deployed a pipeline that coordinates the club entirely on GitHub (Issues, Actions and Pages): participants claim up to three papers by opening an issue, a bot sets the 12-day deadlines and sends reminders, the annotated reviews are graded against a five-axis rubric, and a live leaderboard shows the progress. Join the Journal Club!
Jul 15, 2026
Oscar added a prediction gallery to the documentation of NiFreeze. It shows the diffusion volumes predicted by NiFreeze’s models on four real OpenNeuro datasets spanning the acquisition-scheme spectrum: legacy DTI (ds000206), single-shell HARDI (ds000114), multi-shell (ds003138) and compressed-sensing DSI (ds004737). Every applicable model runs in two modes: leave-one-volume-out (LOVO), where each held-out orientation is predicted from all the other volumes, and single-fit, where the model is fit once on all volumes. Each page reports a coverage table of what was run and why any combination was skipped, and a GitHub Actions workflow regenerates the panels, so the gallery is a living record of what the models are validated to do on real data.
Jun 2026
Jun 2026
Oscar spoke at:
Jun 2026
Oscar has served on the editorial board of Scientific Data since 2025. In 2026 he became the Registered Reports Editor of Aperture Neuro, where he is setting up the journal’s Registered Reports track, and he led the organization of the OHBM 2026 roundtable on Registered Reports (Bordeaux, Jun 15).
May 11, 2026
Quality assessment and control of unprocessed anatomical, functional and diffusion MRI of the human brain using MRIQC (Hagen et al.) is a step-by-step protocol for screening unprocessed MRI with MRIQC (doi:10.1038/s41596-026-01352-y). The preprint is openly available on bioRxiv (doi:10.1101/2024.10.21.619532).
Apr 30, 2026
Oscar organized the fifth NiPreps hackathon, held in Copenhagen from Tuesday, April 28 to Thursday, April 30, 2026, with contributors to the NiPreps tools.
Dec 2025
Oscar spoke at:
Nov 2025
Nov 3, 2025
Oscar was a member of the jury of Tommaso Pavan’s doctoral thesis in neurosciences at the University of Lausanne (UNIL), Diffusion MRI of White Matter Microstructure and Biological Correlates in Early Psychosis and Schizophrenia, directed by Ileana Jelescu with the co-supervision of Patric Hagmann at the Department of Radiology of the Lausanne University Hospital (CHUV), and defended at CHUV on 3 November 2025. Congratulations, Dr. Pavan!
Oct 2025
Oscar was awarded two talent-attraction awards to join the Department of Bioengineering of the Universidad Carlos III de Madrid (UC3M): the UC3M Atrae Excelencia Internacional (2024 call) and a Beatriz Galindo senior distinguished researcher award (2024 call) from the Spanish Ministry of Science. He declined both to continue at HES-SO Valais/Wallis in Sion.
Sep 30, 2025
COST Action CA24161 Improving Neuroimaging Data for Sharing (INDoS) brings together European researchers working on the preparation and sharing of neuroimaging data, from 2025 to 2029. Oscar represents Switzerland on its Management Committee and co-chairs Working Group 3 (Automated Preprocessing Pipelines) with Guiomar Niso.
Sep 2025
In the Informatique et systèmes de communication (ISC) bachelor programme of HES-SO Valais-Wallis, Oscar is responsible for module 302 Data Computation (data infrastructures), which started in September 2025 with project-based labs on containerized environments (Docker, Airflow), and, since February 2026, leads the Medical Informatics major option track (module 304).
Aug 1, 2025
Oscar joined the School of Engineering (HEI) of HES-SO Valais-Wallis in Sion as Associate UAS Professor, and the lab moved with him from the Department of Radiology of the Lausanne University Hospital (CHUV). At HEI, Oscar teaches in the Informatique et systèmes de communication (ISC) bachelor programme.
Jul 2025
After four and a half years with the Axonlab, first as a PhD student and then as a post-doctoral research software engineer, Céline moves on to her next adventure. We are grateful for everything she brought to the lab and wish her the very best.
Jul 26, 2025
Structural mediation of the default mode network in children with callosal agenesis (Provins et al.) studies how brain structure shapes the default mode network in children born without a corpus callosum (doi:10.1093/cercor/bhaf190).
Jun 2025
Jun 2025
Oscar was elected to the Council of the Organization for Human Brain Mapping, as Secretary-Elect for 2025 to 2026 and Secretary for 2026 to 2027.
May 14, 2025
fMRIPrep Lifespan: Extending A Robust Pipeline for Functional MRI Preprocessing to Developmental Neuroimaging (Goncalves et al.) is available on bioRxiv (doi:10.1101/2025.05.14.654069).
May 2025
Jon Haitz Legarreta Gorroño received the ISMRM 2025 Diffusion Study Group Trainee Award for best methodological paper in Honolulu, for An open implementation of FSL’s eddy with volume-to-volume artifact estimation for neuroimaging beyond diffusion MRI (doi:10.31234/osf.io/gfny9), the work behind NiFreeze. Congratulations, Jon!
May 2025
The NiPreps team organized the fourth NiPreps hackathon, held in Boston, MA, with contributors to the NiPreps tools.
May 2025
Apr 30, 2025
Removing facial features from structural MRI images biases visual quality assessment (doi:10.1371/journal.pbio.3003149) completes the registered report that received Stage 1 in principle acceptance from PCI RR in May 2023. Defacing structural MRI for privacy biases human visual quality assessment, while MRIQC’s automated quality metrics are largely unaffected.
Mar 6, 2025
Céline defended her thesis Characterizing and Improving the Reliability of Brain Connectivity extracted with Magnetic Resonance Imaging at the University of Lausanne (thesis). She will stay with the lab as a post-doctoral research software engineer.
Jan 14, 2025
Céline has successfully completed her private thesis defense. In Switzerland, the private defense is a critical prelude to the finalization of Ph.D. programs with the public defense. Her public defense will take place in March 6, 2025. The committee praised her rigorous methodology, and the clarity and substantial contributions to the field of her thesis manuscript. This achievement is a testament to her hard work and dedication over the past 4 years. Congratulations, Céline!
Sep 6, 2024
We acquired the last session of the Human Connectome PHantom’s standard protocols.
Stage 1 acceptance in principle.
Nov 14, 2023
The registered report study Reliability characterization of MRI measurements for analyses of brain networks on a single human reached Stage 1 (accepted in principle) (doi:10.6084/m9.figshare.19579873.v1).
Nov 14, 2023
We acquired the last session of the Human Connectome PHantom’s reliability protocols, which concluded a few minutes before midnight.
Oct 20, 2023
A single subject will go in the scanner 36 times within a few weeks, following our Standard Operating Procedures.
Aug 28, 2023
Alexandre Cionca is joining the Axon Lab through December 2023. Alex graduated from EPFL with a specialization in Computational Science and Engineering later focused on data science and statistical learning in neuroimaging with the University of Geneva.
Jun 27, 2023
After securing an SNSF Mobility grant, Céline started a doctoral research visit to the Poldrack Lab at Stanford. Congratulations and enjoy! The AxonLab will be waiting for your return with expectation and excitement.
from the PCIRR.
May 31, 2023
The pre-registered study Defacing biases in manual and automated quality assessments of structural MRI with MRIQC has been recommended for Stage 1 in principle acceptance. We will now initiate data collection and work toward Stage 2.
Feb 1, 2023
Elodie will be presenting in Montreal (OHBM’23) her Q’Kay manager to assess the quality of large neuroimaging studies. At the same conference, Céline will present her work on QA of fMRI using the wavelet tranform, and the outcome of the BrainHack’22 Geneva project on the interpretation of image quality metrics.
Dec 19, 2022
Céline received the acceptance notice corresponding to her latest quality control paper.
Dec 1, 2022
Our open-access paper is now available at Nature Methods. Don’t miss the corresponding Research Briefing entitled “Harnessing the multiverse of neuroimaging standard references.”
Dec 1, 2022
Elodie Savary, Ph.D., has joined The AxonLab to take over the development and community of NiPreps.
Sep 16, 2022
Céline passed the exam with flying colors.
Sep 08, 2022
A new 1yr (extensible to 2yr) position (link) is available to push the NiPreps project forward.
Feb 1, 2022
Céline will be presenting in London (ISMRM’22) and Glasgow (OHBM’22) her work on fMRI QC and consequences of defacing, respectively.
Jul 19, 2021
As previously announced by Prof. Poldrack, we have received support from the NIMH to continue NiPreps.
Jan 4, 2021
Céline Provins, M.Sc., has joined The AxonLab to start a Ph.D. program on MRI reliability and networks.
March 1, 2020
Reusing code from the Allan Lab (thanks!), we have set up this website.