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bids

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nipreps

 

 

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Center for Reproducible Neuroscience platforms

Community driven initiatives in collaboration with the Center for Reproducible Neuroscience

Recent Media


Recent Publications

  • Esteban, O., Ciric, R., Finc, K. et al. Analysis of task-based functional MRI data preprocessed with fMRIPrep. Nat Protoc 15, 2186–2202 (2020). Available from: https://doi.org/10.1038/s41596-020-0327-3
  • Esteban, O., Goncalves, M., Markiewicz, C.J., Ghosh, S.S. and Poldrack, R.A., “Software Tool to Read, Represent, Manipulate, and Apply N-Dimensional Spatial Transforms,” 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), Iowa City, IA, USA, 2020, pp. 709-712, Available from: https://doi.org/10.1109/ISBI45749.2020.9098466.
  • Esteban, O., Blair, R.W., Nielson, D.M. et al. Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines. Sci Data 6, 30 (2019). Available from: https://doi.org/10.1038/s41597-019-0035-4
  • Poldrack, R.A., Feingold, F., Frank, M.J. et al. The Importance of Standards for Sharing of Computational Models and Data. Comput Brain Behav 2, 229–232 (2019). https://doi-org/10.1007/s42113-019-00062-x
  • Esteban, O., Wright, J., Markiewicz, C. J., Thompson, W. H., Goncalves, M., Ciric, R., … Poldrack, R. (2019, December 19). NiPreps: enabling the division of labor in neuroimaging beyond fMRIPrep. Available from: https://doi.org/10.31219/osf.io/ujxp6
  • Esteban O, Markiewicz CJ, Blair RW, Moodie CA, Illkay Isik A, Erramuzpe A, Kent JD, Goncalves M, DuPre E, Snyder M, Oya H, Ghosh SS, Wright J, Durnez J, Poldrack RA, Gorgolewski KJ (2018). fMRIPrep: a robust preprocessing pipeline for functional MRI. Nature Methods. Available from: https://doi.org/10.1038/s41592-018-0235-4
  • Niso G, Gorgolewski KJ, Bock E, Brooks TL, Flandin G, Gramfort A, Henson RN, Jas M, Litvak V, Moreau JT, Oostenveld R, Schoffelen JM, Tadel F, Wexler J, Baillet S (2018). MEG-BIDS, the brain imaging data structure extended to magnetoencephalography. Scientific data. Available from: https://doi.org/10.1038/sdata.2018.110
  • Pernet CR, Appelhoff S, Flandin G, Phillips C, Delorme A, & Oostenveld R (2018). BIDS-EEG: an extension to the Brain Imaging Data Structure (BIDS) Specification for electroencephalography. Available from: https://doi.org/10.31234/osf.io/63a4y
  • Holdgraf C, Appelhoff S, Bickel S, Bouchard K, D’Ambrosio S, David, OD, Dichter B, Flinker A, Foster BL, Gorgolewski KJ, Groen I, Groppe D, Gunduz A, Hamilton L, Honey CJ, Jas M, Knight R, Lachaux JP, Lau JC, Lundstrom BN, Lee-Messer C, Miller KJ, Ojemann JG, Oostenveld R, Petridou N, Piantoni G, Pigorini A, Pouratian N, Ramsey NF, Stolk A, Swann NC, Tadel F, Voytek B, Wandell BA, Winswer J, Zehl L, Hermes, D (2018). BIDS-iEEG: an extension to the brain imaging data structure (BIDS) specification for human intracranial electrophysiology. Available from: https://doi.org/10.31234/osf.io/r7vc2
  • Gorgolewski KJ, Poldrack RA. A Practical Guide for Improving Transparency and Reproducibility in Neuroimaging Research. PLoS Biol [Internet]. 2016 Jul;14(7):e1002506. Available from: http://dx.doi.org/10.1371/journal.pbio.1002506
  • Esteban O, Birman D, Schaer M, Koyejo OO, Poldrack RA, Gorgolewski KJ. MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites. PLoS One [Internet]. 2017 Sep 25;12(9):e0184661. Available from: http://dx.doi.org/10.1371/journal.pone.0184661
  • Gorgolewski KJ, Auer T, Calhoun VD, Craddock RC, Das S, Duff EP, Flandin G, Ghosh SS, Glatard T, Halchenko YO, Handwerker DA, Hanke M, Keator D, Li X, Michael Z, Maumet C, Nichols BN, Nichols TE, Pellman J, Poline J-B, Rokem A, Schaefer G, Sochat V, Triplett W, Turner JA, Varoquaux G, Poldrack RA. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci Data [Internet]. 2016;3:160044. Available from: http://dx.doi.org/10.1038/sdata.2016.44
  • Gorgolewski KJ, Alfaro-Almagro F, Auer T, Bellec P, Capotă M, Mallar Chakravarty M, Churchill NW, Cohen AL, Cameron Craddock R, Devenyi GA, Eklund A, Esteban O, Flandin G, Ghosh SS, Swaroop Guntupalli J, Jenkinson M, Keshavan A, Kiar G, Liem F, Raamana PR, Raffelt D, Steele CJ, Quirion P-O, Smith RE, Strother SC, Varoquaux G, Wang Y, Yarkoni T, Poldrack RA. BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLoS Comput Biol [Internet]. 2017 Mar 9 [cited 2017 Mar 28];13(3):e1005209. Available from: http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005209&type=printable
  • Gorglewski KJ, Varoquaux G, Rivera G, Schwartz Y, Sochat V, Ghosh SS, Maumet C, Nichols TE, Poline J-B, Yarkoni T, Margulies DS, Poldrack RA (2015). NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain. Neuroimage.
    (link: http://www.ncbi.nlm.nih.gov/pubmed/25869863)
  • Gorglewski KJ, Varoquaux G, Rivera G, Schwartz Y, Ghosh SS, Maumet C, Nichols TE, Poldrack RA, Poline J-B, Yarkoni T, Margulies DS (2015). NeuroVault.org: A web-based repository for collecting and sharing unthresholded statistical maps of the human brain. Frontiers in Neuroinformatics.
    (link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392315/)
  • Poldrack RA, Gorgolewski KJ (2015). OpenfMRI: Open sharing of task fMRI data. Neuroimage.
    (link: http://www.ncbi.nlm.nih.gov/pubmed/26048618)
  • Poldrack RA, Poline JB (2015). The publication and reproducibility challenges of shared data. Trends in Cognitive Sciences, 19, 59-61.
    (link: http://www.ncbi.nlm.nih.gov/pubmed/25532702)
  • Gorgolewski K, Poldrack RA (2014). Making big data open: Data sharing in Neuroimaging. Nature Neuroscience, 17, 1510-7.
    (link: http://www.ncbi.nlm.nih.gov/pubmed/25349916)