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Open and reproducible neuroimaging: From study inception to publication.
Niso G, Botvinik-Nezer R, Appelhoff S, De La Vega A, Esteban O, Etzel JA, Finc K, Ganz M, Gau R, Halchenko YO, Herholz P, Karakuzu A, Keator DB, Markiewicz CJ, Maumet C, Pernet CR, Pestilli F, Queder N, Schmitt T, Sójka W, Wagner AS, Whitaker KJ, Rieger JW. Niso G, et al. Among authors: halchenko yo. Neuroimage. 2022 Nov;263:119623. doi: 10.1016/j.neuroimage.2022.119623. Epub 2022 Sep 12. Neuroimage. 2022. PMID: 36100172 Free PMC article. Review.
PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data.
Hanke M, Halchenko YO, Sederberg PB, Olivetti E, Fründ I, Rieger JW, Herrmann CS, Haxby JV, Hanson SJ, Pollmann S. Hanke M, et al. Among authors: halchenko yo. Front Neuroinform. 2009 Feb 4;3:3. doi: 10.3389/neuro.11.003.2009. eCollection 2009. Front Neuroinform. 2009. PMID: 19212459 Free PMC article.
The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments.
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 JB, Rokem A, Schaefer G, Sochat V, Triplett W, Turner JA, Varoquaux G, Poldrack RA. Gorgolewski KJ, et al. Among authors: halchenko yo. Sci Data. 2016 Jun 21;3:160044. doi: 10.1038/sdata.2016.44. Sci Data. 2016. PMID: 27326542 Free PMC article.
A very simple, re-executable neuroimaging publication.
Ghosh SS, Poline JB, Keator DB, Halchenko YO, Thomas AG, Kessler DA, Kennedy DN. Ghosh SS, et al. Among authors: halchenko yo. F1000Res. 2017 Feb 10;6:124. doi: 10.12688/f1000research.10783.2. eCollection 2017. F1000Res. 2017. PMID: 28781753 Free PMC article.
Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.
Kennedy DN, Abraham SA, Bates JF, Crowley A, Ghosh S, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Haselgrove C, Hodge SM, Jarecka D, Kaczmarzyk J, Keator DB, Meyer K, Martone ME, Padhy S, Poline JB, Preuss N, Sincomb T, Travers M. Kennedy DN, et al. Among authors: halchenko yo. Front Neuroinform. 2019 Feb 7;13:1. doi: 10.3389/fninf.2019.00001. eCollection 2019. Front Neuroinform. 2019. PMID: 30792636 Free PMC article.
Analysis of task-based functional MRI data preprocessed with fMRIPrep.
Esteban O, Ciric R, Finc K, Blair RW, Markiewicz CJ, Moodie CA, Kent JD, Goncalves M, DuPre E, Gomez DEP, Ye Z, Salo T, Valabregue R, Amlien IK, Liem F, Jacoby N, Stojić H, Cieslak M, Urchs S, Halchenko YO, Ghosh SS, De La Vega A, Yarkoni T, Wright J, Thompson WH, Poldrack RA, Gorgolewski KJ. Esteban O, et al. Among authors: halchenko yo. Nat Protoc. 2020 Jul;15(7):2186-2202. doi: 10.1038/s41596-020-0327-3. Epub 2020 Jun 8. Nat Protoc. 2020. PMID: 32514178 Free PMC article.
PyBIDS: Python tools for BIDS datasets.
Yarkoni T, Markiewicz CJ, de la Vega A, Gorgolewski KJ, Salo T, Halchenko YO, McNamara Q, DeStasio K, Poline JB, Petrov D, Hayot-Sasson V, Nielson DM, Carlin J, Kiar G, Whitaker K, DuPre E, Wagner A, Tirrell LS, Jas M, Hanke M, Poldrack RA, Esteban O, Appelhoff S, Holdgraf C, Staden I, Thirion B, Kleinschmidt DF, Lee JA, Visconti di Oleggio Castello M, Notter MP, Blair R. Yarkoni T, et al. Among authors: halchenko yo. J Open Source Softw. 2019;4(40):1294. doi: 10.21105/joss.01294. Epub 2019 Aug 12. J Open Source Softw. 2019. PMID: 32775955 Free PMC article. No abstract available.
The Open Brain Consent: Informing research participants and obtaining consent to share brain imaging data.
Bannier E, Barker G, Borghesani V, Broeckx N, Clement P, Emblem KE, Ghosh S, Glerean E, Gorgolewski KJ, Havu M, Halchenko YO, Herholz P, Hespel A, Heunis S, Hu Y, Hu CP, Huijser D, de la Iglesia Vayá M, Jancalek R, Katsaros VK, Kieseler ML, Maumet C, Moreau CA, Mutsaerts HJ, Oostenveld R, Ozturk-Isik E, Pascual Leone Espinosa N, Pellman J, Pernet CR, Pizzini FB, Trbalić AŠ, Toussaint PJ, Visconti di Oleggio Castello M, Wang F, Wang C, Zhu H. Bannier E, et al. Among authors: halchenko yo. Hum Brain Mapp. 2021 May;42(7):1945-1951. doi: 10.1002/hbm.25351. Epub 2021 Feb 1. Hum Brain Mapp. 2021. PMID: 33522661 Free PMC article.
Brainhack: Developing a culture of open, inclusive, community-driven neuroscience.
Gau R, Noble S, Heuer K, Bottenhorn KL, Bilgin IP, Yang YF, Huntenburg JM, Bayer JMM, Bethlehem RAI, Rhoads SA, Vogelbacher C, Borghesani V, Levitis E, Wang HT, Van Den Bossche S, Kobeleva X, Legarreta JH, Guay S, Atay SM, Varoquaux GP, Huijser DC, Sandström MS, Herholz P, Nastase SA, Badhwar A, Dumas G, Schwab S, Moia S, Dayan M, Bassil Y, Brooks PP, Mancini M, Shine JM, O'Connor D, Xie X, Poggiali D, Friedrich P, Heinsfeld AS, Riedl L, Toro R, Caballero-Gaudes C, Eklund A, Garner KG, Nolan CR, Demeter DV, Barrios FA, Merchant JS, McDevitt EA, Oostenveld R, Craddock RC, Rokem A, Doyle A, Ghosh SS, Nikolaidis A, Stanley OW, Uruñuela E; Brainhack Community. Gau R, et al. Neuron. 2021 Jun 2;109(11):1769-1775. doi: 10.1016/j.neuron.2021.04.001. Epub 2021 Apr 30. Neuron. 2021. PMID: 33932337 Free PMC article.
The OpenNeuro resource for sharing of neuroscience data.
Markiewicz CJ, Gorgolewski KJ, Feingold F, Blair R, Halchenko YO, Miller E, Hardcastle N, Wexler J, Esteban O, Goncavles M, Jwa A, Poldrack R. Markiewicz CJ, et al. Among authors: halchenko yo. Elife. 2021 Oct 18;10:e71774. doi: 10.7554/eLife.71774. Elife. 2021. PMID: 34658334 Free PMC article.
59 results