Scientific outputs

Below we list the most outstanding communications our lab has produced, next to the number of citations if applicable. Number of citing references extracted from Google Scholar on Jun 14, 2023.

2023

Provins, C., … Esteban, O. (2023). Quality Control in functional MRI studies with MRIQC and fMRIPrep. Frontiers in Neuroimaging 1:1073734. doi:10.3389/fnimg.2022.1073734 (OA). 2
Grandjean, C., … Hess, A. (2023). A consensus protocol for functional connectivity analysis in the rat brain. Nature Neuroscience 1-9. doi:10.1038/s41593-023-01286-8 (OA). 8

2022

Ciric, R., … Esteban, O. (2022). TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models. Nature Methods 1-4. doi:10.1038/s41592-022-01681-2 (OA). 22
Niso, G., … Rieger, J. W. (2022). Open and reproducible neuroimaging: from study inception to publication. NeuroImage 119623. doi:10.1016/j.neuroimage.2022.119623 (OA). 19
MacNicol, E., … Cash, D. (2022). Age-Specific Adult Rat Brain MRI Templates and Tissue Probability Maps. Frontiers in Neuroinformatics. doi:10.3389/fninf.2021.669049 (OA). 8
Adebimpe, A., … the ALLFTD Consortium. (2022). ASLPrep: a platform for processing of arterial spin labeled MRI and quantification of regional brain perfusion. Nature Methods 19 (6), 683-686. doi:10.1038/s41592-022-01458-7. OA. 7
Di Noto, T., … Richiardi, J. Towards Automated Brain Aneurysm Detection in TOF-MRA: Open Data, Weak Labels, and Anatomical Knowledge. Neuroinformatics 1-14. doi:10.1007/s12021-022-09597-0 (OA). 5

Before 2022

Esteban, O., … Gorgolewski, K. J. (2019). fMRIPrep: a robust preprocessing pipeline for functional MRI. Nature Methods doi:10.1038/s41592-018-0235-4. OA. 1656
Esteban, O., … Gorgolewski, K. J. (2017). MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites. Plos One. doi:10.1371/journal.pone.0184661 (OA). 564
Markiewicz, C. J., … Poldrack, R. (2021). The OpenNeuro resource for sharing of neuroscience data. eLife. doi:10.7554/eLife.71774 (OA). 116
Esteban, O., … Gorgolewski, K. J. (2020). Analysis of task-based functional MRI data preprocessed with fMRIPrep. Nature Protocols. doi:10.1038/s41596-020-0327-3. OA. 65
Esteban, O., … Gorgolewski, K. J. (2019). Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines. Scientific Data. doi:10.1038/s41597-019-0035-4 (OA). 42
Gau, R., … Zuo, X.-N. (2021). Brainhack: Developing a culture of open, inclusive, community-driven neuroscience. Neuron. doi:10.1016/j.neuron.2021.04.001 (OA). 23
Levitis, E., … Maumet, C. (2021). Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective, GigaScience, Volume 10, Issue 8, August 2021, giab051. doi:10.1093/gigascience/giab051 (OA). 19
Esteban, O., … Santos, A. (2016). Surface-driven registration method for the structure-informed segmentation of diffusion MR images. NeuroImage. doi:10.1016/j.neuroimage.2016.05.011. OA. 14
Rodrigue, A. L., … Glahn, D. C. (2021). Searching for Imaging Biomarkers of Psychotic Dysconnectivity. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging. doi:10.1016/j.bpsc.2020.12.002 (OA). 2
Goncalves, M., … Esteban, O. (2021). NiTransforms: A Python tool to read, represent, manipulate, and apply dimensional spatial transforms. Journal of Open Source Software. doi:10.21105/joss.03459 (OA). 1

2024

Provins, C., … Esteban, O. (2024). Effects of phase-encoding on BOLD data with a positive control task. 30th Annual Meeting of the Organization for Human Brain Mapping (OHBM), (accepted). Seoul, Korea. doi: 10.31219/osf.io/nuqs2 (preprint). n/a
Cionca A., … Esteban, O. (2024). A high-definition anatomical brain template of one individual healthy subject. 30th Annual Meeting of the Organization for Human Brain Mapping (OHBM), (accepted). Seoul, Korea. n/a
Markiewicz, C., … Esteban, O. (2024). FMRIPrep-next: Preprocessing as a fit-transform model. 30th Annual Meeting of the Organization for Human Brain Mapping (OHBM), (accepted). Seoul, Korea. n/a
Esteban, O., … Hagmann, P. (2024). The Human Connectome Phantom (HCPh) dataset. 30th Annual Meeting of the Organization for Human Brain Mapping (OHBM), (accepted). Seoul, Korea. n/a
Esteban, O., … Markiewicz, C. (2024). SDCFlows: convergent formalization of MRI field mappings for reliable distortion correction. 30th Annual Meeting of the Organization for Human Brain Mapping (OHBM), (accepted). Seoul, Korea. n/a
Tammurello, C., … Fornari, E. (2024). Hi-Fi BOLD fMRI - High-resolution, Fast-sampling Blood Oxygen Level Dependent functional MRI: a validation study in the auditory domain. 30th Annual Meeting of the Organization for Human Brain Mapping (OHBM), (accepted). Seoul, Korea. n/a

2023

Provins, C., … Esteban, O. (2023). Assessment of B1 field dynamics of rats BOLD fMRI using the wavelet transform. 29th Annual Meeting of the Organization for Human Brain Mapping (OHBM), 834. Montréal, Canada. doi: 10.31219/osf.io/hnpyt (preprint). n/a
Provins, C., … Esteban, O. (2023). Signal-to-noise ratio estimates predict head motion presence in T1-weighted MRI. 29th Annual Meeting of the Organization for Human Brain Mapping (OHBM), 787. Montréal, Canada. doi: 10.31219/osf.io/7vqzr (preprint). n/a
Savary, E., … Esteban, O. (2023). Q’kay: a manager for the quality assessment of large neuroimaging studies. 29th Annual Meeting of the Organization for Human Brain Mapping (OHBM), 2467. Montréal, Canada. doi: 10.31219/osf.io/edx6t (preprint). n/a
Alemán-Gómez, Y., … Hagmann, P. (2023). CHIMERA:An open source framework for combining multiple parcellations. 29th Annual Meeting of the Organization for Human Brain Mapping (OHBM), 2478. Montréal, Canada. n/a
Lajous, H., … Bach-Cuadra, M. (2023). Minimizing the Need for Clinical MRI Data in Supervised Fetal Brain Tissue Segmentation. 29th Annual Meeting of the Organization for Human Brain Mapping (OHBM), 857. Montréal, Canada. n/a
Goncalves, M., … Fair, D. A. (2023). They grow up so fast - Augmenting the NiBabies infant MRI workflow. 29th Annual Meeting of the Organization for Human Brain Mapping (OHBM), 2504. Montréal, Canada. n/a
Barranco, J., … Bach-Cuadra, M. (2023). A-Eye: Towards a large-scale MRI-based model of the complete eye. ARVO Imaging in the Eye Conference Abstract in Investigative Ophthalmology & Visual Science 64(9):PP0010, New Orleans, LA, USA. n/a
Barranco, J., … Bach-Cuadra, M. (2023). A-Eye: Large-scale MRI automatic biomarkers extraction. ARVO Annual Meeting Abstract in Investigative Ophthalmology & Visual Science 64(8):5039, New Orleans, LA, USA. n/a

Before 2023

Provins, C., … Esteban, O. (2022). Defacing biases manual and automated quality assessments of structural MRI with MRIQC. 28th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. WTh566. Glasgow, Scotland, UK. doi:10.31219/osf.io/t9ehk. n/a
MacNicol, E., … Esteban, O. (2022). Extending MRIQC to rodents: image quality metrics for rat MRI. 17th Annual Meeting of the European Society for Molecular Imaging (EMIM), PW23-913. Thessaloniki, Greece. n/a
Di Noto, T., … Richiardi, J. (2022). Weak labels for deep-learning-based detection of brain aneurysms from MR angiography scans. Medical Imaging with Deep Learning (MIDL). Zurich, Switzerland. OA. n/a
Provins, C., … Esteban, O. (2022). Quality control and nuisance regression of fMRI, looking out where signal should not be found. Proc. Intl. Soc. Mag. Reson. Med. 31 (ISMRM), pp. 2683. London, England, UK. doi:10.31219/osf.io/hz52v. n/a
Markiewicz, C. J., … You, X. (2022). Standardizing support for multi-echo fMRI data across the NiPreps ecosystem. 28th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. WTh563. Glasgow, Scotland, UK. n/a
Ciric, R., … Poldrack, R. A. (2022). Across the multiverse: differentiable programming for deep connectivity pipeline optimisation. 28th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. WTh556. Glasgow, Scotland, UK. n/a
Veraart, J., … Descoteaux, M. (2022). A data-driven variability assessment of brain diffusion MRI preprocessing pipelines. Proc. Intl. Soc. Mag. Reson. Med. 31 (ISMRM), pp. 4983. London, England, UK. n/a
Li, X., … Milham, M. P. (2022). Moving beyond processing and analysis-related variation in neuroscience. 28th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. WTh877. Glasgow, Scotland, UK. n/a
Esteban, O., … Provins, C. (2021). The Bermuda Triangle of d-and f-MRI sailors-software for susceptibility distortions (SDCFlows). 27th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 1653. (Virtual Meeting). doi:10.31219/osf.io/gy8nt. n/a
Markiewicz, C., … Maumet, C. (2021). BIDS Statistical Models - An implementation-independent representation of General Linear Models. 27th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 1207. (Virtual Meeting). OA. n/a
Adebimpe, A., … Covitz, S. (2021). ASLPrep: A Generalizable Workflow for Processing of Arterial Spin Labeled MRI. 27th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 1814. (Virtual Meeting). n/a
Milham, M., … Esteban, O. (2021). Putting pipeline implementation-related variation into perspective for functional connectomics. 27th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 2405. (Virtual Meeting). n/a
Goncalves, M., … Esteban, O. (2021). NiBabies: A robust preprocessing workflow tailored for neonate and infant MRI. 27th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 2452. (Virtual Meeting). n/a
Jarecka, D., … Ghosh, S. (2021). Nipype 2.0: A new ecosystem for neuroimaging workflows. 27th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 2796. (Virtual Meeting). n/a
MacNicol, E., … Esteban, O. (2021). Atlas-based brain extraction is robust across rat MRI studies. IEEE 18th International Symposium on Biomedical Imaging (ISBI), pp. 312-315. Nice, France. doi:10.1109/ISBI48211.2021.9433884. OA. n/a
Joseph, M. J., … Esteban, O. (2021). dMRIPrep: a robust preprocessing pipeline for diffusion MRI. Proc. Intl. Soc. Mag. Reson. Med. 30 (ISMRM), pp. 2473. (Virtual Meeting). URL. n/a
Di Noto, T., … Richiardi, J. (2021). Improving automated aneurysm detection on multi-site MRA data: lessons learnt from a public machine learning challenge. Proc. Intl. Soc. Mag. Reson. Med. 30 (ISMRM), pp. 2655. (Virtual Meeting). URL. n/a
Esteban, O., … Ghosh, S. (2020). NiPreps: enabling the division of labor in neuroimaging beyond fMRIPrep. 26th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 1960. (Virtual Meeting). doi:10.31219/osf.io/ujxp6. n/a
Markiewicz, C. J., … Harms, M. (2020). BIDS Derivatives – Standardization of Processing Results in Brain Imaging. 26th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 1895. (Virtual Meeting). doi:10.5281/zenodo.3941040. n/a
Goncalves, M., … Esteban, O. (2020). FMRIPrep: extending the scanner to produce ready-for-analysis fMRI data. 26th Annual Meeting of the Organization for Human Brain Mapping (OHBM), pp. 1961. (Virtual Meeting). n/a
Esteban, O., … Poldrack, R. (2020). Software tool to read, represent, manipulate, and apply n-dimensional spatial transforms. IEEE 17th International Symposium on Biomedical Imaging (ISBI), pp. 709-712. Iowa City, IA, USA. doi:10.1109/ISBI45749.2020.9098466. OA. n/a
Jarecka, D., … Ghosh, S. (2020). Pydra-a flexible and lightweight dataflow engine for scientific analyses. Proceedings of the 19th Python in Science Conference (SciPy), pp. 132-139. Austin, TX, USA. doi:10.25080/Majora-342d178e-012. n/a

2023

Registered Report Provins, C., … Esteban, O. (2023). Reliability characterization of MRI measurements for analyses of brain networks on a single human, Stage 1 AIP (acceptance in principle) by Nature Methods.
Registered Report Provins, C., … Esteban, O. (2023). Defacing biases in manual and automated quality assessments of structural MRI with MRIQC, Stage 1 IPA (in principle acceptance) of Version 3 by Peer Community in Registered Reports.
Preprint Sanchez, T., … Bach-Cuadra, M. (2023). FetMRQC: Automated Quality Control for fetal brain MRI, arXiv 2304.05879. doi:10.48550/arXiv.2304.05879.
Preprint Chatelain, Y., … Glatard, T. (2023). A numerical variability approach to results stability tests and its application to neuroimaging, arXiv 2307.01373. doi:10.48550/arXiv.2307.01373.

2022

Feature Harnessing the multiverse of neuroimaging standard references. Nat Methods 19, 1526–1527 (2022). doi:10.1038/s41592-022-01682-1.
Preprint Li, X., … Milham, M.P. (2022) Moving Beyond Processing and Analysis-Related Variation in Neuroscience, bioRxiv 2021.12.01.470790. doi:10.1101/2021.12.01.470790.

Before 2022

Preprint Bansal, S., … Esteban, O. (2021) High-sensitivity detection of facial features on MRI brain scans with a convolutional network, bioRxiv 2021.04.25.441373. doi:10.1101/2021.04.25.441373.