BigBrain References

Posters, Publications, and News involving the BigBrain

  • Publications

    DeKraker J, Lau JC, Ferko KM, Khan AR, Kohler S (2019) Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain. doi: link
    Lau JC, Parrent AG, Demarco J, Gupta G, Kai J, Stanley OW, Kuehn T, Park PJ, Ferko K, Khan AR, Peters TM (2019) A framework for evaluating correspondence between brain images using anatomical fiducials. Hum Brain Mapp. 2019; 40: 4163– 4179. doi: link
    Seidlitz J, Nadig A, Liu S, Bethlehem RAI, Vértes PE, Morgan SE, Váša F, Romero-Garcia R, Lalonde FM, Clasen LS, Blumenthal JD, Paquola C, Bernhardt B, Wagstyl K, Polioudakis D, de la Torre-Ubieta L, Geschwind DH, Han JC, Lee NR, Murphy DG, Bullmore ET, Raznahan A (2019) Transcriptomic and Cellular Decoding of Regional Brain Vulnerability to Neurodevelopmental Disorders. bioRxiv, doi: link
    Irmen F, Horn A, Mosley P, Perry A, Petry-Schmelzer JN, Dafsari HS, Barbe M, Visser-Vandewalle V, Schneider GH, Li N, Kübler D, Wenzel G, Kühn A (2019) Left prefrontal connectivity links subthalamic stimulation with depressive symptoms in Parkinson’s disease. bioRxiv 665976; doi: link
    Horn A, Wenzel G, Irmen F, Huebl J, Li N, Neumann WJ, Krause P, Bohner G, Scheel M, Kühn AA (2019) Deep brain stimulation induced normalization of the human functional connectome in Parkinson’s disease. Brain , awz239, doi: link
    Horn A, Li N, Dembek TA, Kappel A, Boulay C, Ewert S, Tietze A, Husch A, Perera T, Neumann WJ, Reisert M, Si H, Oostenveld R, Rorden C, Yeh FC, Fang Q, Herrington TM, Vorwerk J, Kühn AA (2019) Lead-DBS v2: Towards a comprehensive pipeline for deep brain stimulation imaging. NeuroImage, 184:293-316 doi: link
    Dugré M, Hayot-Sasson M, Glatard T (2019) A performance comparison of Dask and Apache Spark for data-intensive neuroimaging pipelines. arxiv, link
    Hayot-Sasson V, Brown ST, Glatard T (2019) Performance Evaluation of Big Data Processing Strategies for Neuroimaging. arxiv, link
    Xiao Y, Lau JC, Anderson T, DeKraker J, Collins DL, Peters T, Khan AR (2019) Bridging micro and macro: accurate registration of the BigBrain dataset with the MNI PD25 and ICBM152 atlases. bioRxiv 561118; doi: link
    Sitek KR, Gulban OF, Calabrese E, Johnson GA, Lage-Castellanos A, Moerel M, Ghosh SS, De Martino F (2019) Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T. eLife 2019;8:e48932. doi: link
    Wagstyl K, Larocque S, Cucurull G, Lepage C, Cohen JP, Bludau S, Palomero-Gallagher N, Funck T, Spitzer H, Dicksheid T, Fletcher PC, Romero A, Zilles K, Amunts K, Bengio Y, Evans AC (2019) Automated segmentation of cortical layers in BigBrain reveals divergent cortical and laminar thickness gradients in sensory and motor cortices. bioRxiv, doi: link
    DeKraker J, Lau JC, Ferko KM, Khan AR, Köhler S (2019) Hippocampal morphology and cytoarchitecture in the 3D BigBrain. bioRxiv, doi: link
    Paquola C, Vos De Wael R, Wagstyl K,Bethlehem RAI, Hong S-J, Seidlitz J, Bullmore ET, Evans AC, Misic B, Margulies DS, Smallwood J, Bernhardt BC (2019) Microstructural and functional gradients are increasingly dissociated in transmodal cortices. PLoSBiol 17(5):e3000284. doi: link
    Wei Y, Scholtens LH,Turk E, van den Heuvel MP (2019) Multiscale examination of cytoarchitectonic similarity and human brain connectivity, NetworkNeuroscience,3(1), 124–137. doi: link
    Oden L, Schiffer C, Spitzer H, Dickscheid T, Pleiter D (2019) IO Challenges for Human Brain Atlasing Using Deep Learning Methods - An In-Depth Analysis. 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), Pavia, Italy, 2019, pp. 291-298. doi: link
    Iglesias JE, Modat M, Peter L, Stevens A, Annunziata R, Vercauteren T, Lein E, Fischl B, Ourselin S, for the ADNI (2018) Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections. Med Image Analysis, 50:127-144. doi: link
    Maia PD, Pandya S, Torok J, Gupta A, Zeighami Y, Raj A (2018) Heterogeneity of Incipient Atrophy Patterns in Parkinson’s Disease. bioRxiv, doi: link
    Yu Y, Herman P, Rothman D L, Agarwal D, Hyder F (2018) Evaluating the gray and white matter energy budgets of human brain function. ournal of Cerebral Blood Flow & Metabolism, 38(8), 1339–1353. doi: link
    Wagstyl K, Lepage C, Bludau S, Zilles K, Fletcher P, Amunts K, Evans AC (2018) Mapping Cortical Laminar Structure in the 3D BigBrain. Cerebral Cortex (New York, N.Y. : 1991), 28 (7), 2551-2562. doi: link
    Spitzer H, Amunts K, Harmeling S, Dickscheid T (2018) Compact feature representations for human brain cytoarchitecture using self-supervised learning. Medical Imaging with Deep Learning (MIDL 2018, Amsterdam). link
    Spitzer H, Kiwitz K, Amunts K, Harmeling S, Dickscheid T (2018) Improving Cytoarchitectonic Segmentation of Human Brain Areas with Self-supervised Siamese Networks. MICCAI 2018 link
    Gulban OF, Schneider M, Marquardt I, Haast RAM, De Martino F (2018) A scalable method to improve gray matter segmentation at ultra high field MRI. PLoS ONE 13(6): e0198335. doi: link
    Yeh FC, Panesar S, Fernandes D, Meola A, Yoshino M, Fernandez-Miranda JC, Vettel JM, Verstynen T (2018) Population-averaged atlas of the macroscale human structural connectome and its network topology. NeuroImage 178 (2018):57-68 doi: link. Epub 2018 May 24.
    Fournier M, Lewis LB, Evans AC (2017) BigBrain: Automated cortical parcellation and comparison with existing brain atlases. Springer Lecture Notes in Computer Science, Vol. 10081, No. 1, 2017, 14-25. link
    Lambert C, Simon H, Colman J, Barrick TR (2017) Defining thalamic nuclei and topographic connectivity gradients in vivo. NeuroImage 158:466-479. doi: link
    Spitzer H, Amunts K, Harmeling S, Dickscheid T (2017) Parcellation of visual cortex on high-resolution histological brain sections using convolutional neural networks. IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), Melbourne, VIC, 2017, pp. 920-923. doi: link
    Neuro Cloud Consortium: Vogelstein JT, Mensh B, Häusser M, Spruston N, Evans AC, Kording K, Amunts K, Ebell C, Muller J, Telefont M, Hill S, Koushika SP, Calì C, Valdés-Sosa PA, Littlewood PB, Koch C, Saalfeld S, Kepecs A, Peng H, Halchenko YO, Kiar G, Poo MM, Poline JB, Milham MP, Schaffer AP, Gidron R, Okano H, Calhoun VD, Chun M, Kleissas DM, Vogelstein RJ, Perlman E, Burns R, Huganir R, Miller MI (2016) To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery. Neuron. 92(3):622-627. doi: link Beukema P, Yeh FC, Verstynen T (2015) In vivo characterization of the connectivity and subcomponents of the human globus pallidus. NeuroImage 120(2015):382-393 doi: link
    Amunts K, Hawrylycz M, Van Essen D, Van Horn JD, Harel N, Poline JB, De Martino F, Bjaalie JG, Dehaene-Lambertz G, Dehaene S, Valdes-Sosa P, Thirion B, Zilles K, Hill SL, Abrams MB, Tass PA, Vanduffel W, Evans AC, Eickhoff SB (2014) Interoperable atlases of the human brain. Neuroimage, 99: 525-532. doi: link
    Amunts K, Lepage C, Borgeat L, Mohlberg H, Dickscheid T, Rousseau ME, Bludau S, Bazin PL, Lewis LB, Oros-Peusquens AM, Shah NJ, Lippert T, Zilles K, Evans AC (2013) BigBrain: An ultrahigh-resolution 3D human brain model. Science, 340(6139): 1472-1475. link

  • Conference Materials

    Wagstyl, K. et al.: BigBrain: Automated identification of cortical layers in the primary visual cortex, HBM 2017. link
    Lepage, C. et al.: BigBrain: From Artifact Corrections, Alignment, and Optical-Balancing to Segmentation and Surface Extraction, RBIQ/QBIN Toward a super-big brain: promises and pitfalls of microstructural imaging, Montreal, August 2016. link
    Wagstyl, K. et al.: Automated Analysis of Laminar Structure in the Cerebral Cortex, HBM 2016. link
    Lewis, L.B. et al.: BigBrain: Initial Tissue Classification and Surface Extraction, HBM 2014 link
    Bludau, S. et al.: "Two new Cytoarchitectonic Areas of the Human Frontal Pole", OHBM 2012 link
    Lepage, C. et al.: "Automatic Repair of Acquisition Defects in Reconstruction of Histology Sections of a Human Brain", HBM 2010 link

  • News

    Interview with AC Evans for McGill Reporter, Jennifer Morrow, June 26 2019, link
    Interview with K Amunts at PASC17 conference - section on BB, Simone Ulmer, July 26 2019, link
    BRAIN Research: They Wish It Was Only Rocket Science, Geralyn Miller, June 25 2015, link
    Huron Technologies and the BigBrain, Huron Digital Pathology, May 11 2015, link
    Jülich Supercomputing Centre and the BigBrain project, Lenovo Blog, Feb 02 2015, link
    Human Brain in 3-D Detail, Kate McGowan, Jan 2014, link
    Significant Science of 2013: Brain Mapping Gets a Big Boost, Allison Eck, Dec 27 2013, link
    Prof. Evans's Lecture-BigBrain: An ultra-high resolution 3D model of human neuroanatomy, Brainnetome, July 4 2013, link
    An Ultra-High-Resolution, 3D View of the Human Brain, Alzforum, June 21 2013, link
    BigBrain: Ultra-high resolution 3D map of human brain, Kristen Butler, June 21 2013, link
    BigBrain: an ultra-high-resolution 3D roadmap of the human brain, Kurzweil, June 21 2013, link
    Whole human brain mapped in 3D, Helen Shen, June 20 2013, link
    Groundbreaking Brain Atlas Maps Whole Brain at Cellular Level, Becky Lang, June 20 2013, link
    “BigBrain” Project Makes Terabyte Map of a Human Brain, Mia Feldman, June 20 2013, link
    BigBrain: The Best Gray Matter Map Ever Made, William Herkewitz, June 20 2013, link
    Bigbrain: An ultra-high resolution 3-D roadmap of the human brain, American Association for the Advancement of Science, June 20 2013 2013, link
    The 'Google Earth' of 3D Brain Maps is Here, Abby Ohlheiser, June 20 2013, link
    El mapa Big Brain, Memeroteca, June 20 2013, link
    “BigBrain” Model Offers Microscopic Views of Human Brain, Rebecca Voelker, June 20 2013, link
    The Human Brain in Exquisite Detail, Ruth Williams, June 20 2013, link
    A Detailed 3-D Atlas of a Human Brain, Courtney Humphries, June 20 2013, link
    3D map of human brain is the most detailed ever, Sara Reardon, June 20 2013, link
    Scientists create detailed 3-D model of human brain, Melissa Healy, June 20 2013, link
    The Brain: Now in Ultra High-Res 3D, Jesse Emspak, June 20 2013, link
    Ultra-high resolution 3D map of a human brain, The Guarduab, June 20 2013, link

  • Past Events

    BigBrain Workshop 2019 Düsseldorf: AI methods and HPC based processing, 20-21 August 2019. link
    BigBrain Workshop 2017 Montreal : From open data to novel applications, 3 November 2017. link
    BigBrain and its applications, March 31 - April 1, 2015. link

  • Selected Joint Publications

    Wagstyl K, Lepage C, Bludau S, Zilles K, Fletcher PC, Amunts K, Evans AC.v Mapping Cortical Laminar Structure in the 3D BigBrain. Cereb Cortex. 2018 Jul 1;28(7):2551-2562. doi: link
    Nichols TE, Das S, Eickhoff SB, Evans AC, Glatard T, Hanke M, Kriegeskorte N, Milham MP, Poldrack RA, Poline JB, Proal E, Thirion B, Van Essen DC, White T, Yeo BT. (2017) Best practices in data analysis and sharing in neuroimaging using MRI. Nature Neuroscience. 20:299-303. link
    Reid AT, Hoffstaedter F, Gong G, Laird AR, Fox P, Evans AC, Amunts K, Eickhoff SB. (2017) A seed-based cross-modal comparison of brain connectivity measures. Brain Structure and Function. 222(3):1131-1151 doi: link
    Reid AT, Lewis J, Bezgin G, Khundrakpam B, Eickhoff SB, McIntosh AR, Bellec P, Evans AC (2016) A cross-modal, cross-species comparison of connectivity measures in the primate brain. Neuroimage. 125: 311-331. doi: link
    Caspers S, Moebus S, Lux S, Pundt N, Schütz H, Mühleisen TW, Gras V, Eickhoff SB, Romanzetti S, Stöcker T, Stirnberg R, Kirlangic ME, Minnerop M, Pieperhoff P, Mödder U, Das S, Evans AC, Jöckel KH, Erbel R, Cichon S, Nöthen MM, Sturma D, Bauer A, Jon Shah N, Zilles K, Amunts K. Studying variability in human brain aging in a population-based German cohort-rationale and design of 1000BRAINS. Front Aging Neurosci. 2014 Jul 14;6:149. doi: link eCollection 2014.
    Amunts K, Lepage C, Borgeat L, Mohlberg H, Dickscheid T, Rousseau MÉ, Bludau S, Bazin PL, Lewis LB, Oros-Peusquens AM, Shah NJ, Lippert T, Zilles K, Evans AC. BigBrain: an ultrahigh-resolution 3D human brain model. Science. 2013 Jun 21;340(6139):1472-5. doi: link
    Oishi K, Huang H, Yoshioka T, Ying SH, Zee DS, Zilles K, Amunts K, Woods R, Toga AW, Pike GB, Rosa-Neto P, Evans AC, van Zijl PC, Mazziotta JC, Mori S. Superficially located white matter structures commonly seen in the human and the macaque brain with diffusion tensor imaging. Brain Connect. 2011;1(1):37-47. doi: link
    Oishi K, Zilles K, Amunts K, Faria A, Jiang H, Li X, Akhter K, Hua K, Woods R, Toga AW, Pike GB, Rosa-Neto P, Evans A, Zhang J, Huang H, Miller MI, van Zijl PC, Mazziotta J, Mori S. Human brain white matter atlas: identification and assignment of common anatomical structures in superficial white matter. Neuroimage. 2008 Nov 15;43(3):447-57. doi: link Epub 2008 Jul 18.
    Eickhoff SB, Paus T, Caspers S, Grosbras MH, Evans AC, Zilles K, Amunts K. Assignment of functional activations to probabilistic cytoarchitectonic areas revisited. Neuroimage. 2007 Jul 1;36(3):511-21. Epub 2007 Apr 10. Review. doi: link
    Hulshoff Pol HE, Schnack HG, Posthuma D, Mandl RC, Baaré WF, van Oel C, van Haren NE, Collins DL, Evans AC, Amunts K, Bürgel U, Zilles K, de Geus E, Boomsma DI, Kahn RS. Genetic contributions to human brain morphology and intelligence. J Neurosci. 2006 Oct 4;26(40):10235-42. doi: link
    Mazziotta J, Toga A, Evans A, Fox P, Lancaster J, Zilles K, Woods R, Paus T, Simpson G, Pike B, Holmes C, Collins L, Thompson P, MacDonald D, Iacoboni M, Schormann T, Amunts K, Palomero-Gallagher N, Geyer S, Parsons L, Narr K, Kabani N, Le Goualher G, Boomsma D, Cannon T, Kawashima R, Mazoyer B. A probabilistic atlas and reference system for the human brain: International Consortium for Brain Mapping (ICBM). Philos Trans R Soc Lond B Biol Sci. 2001 Aug 29;356(1412):1293-322. doi: link
    Mazziotta J, Toga A, Evans A, Fox P, Lancaster J, Zilles K, Woods R, Paus T, Simpson G, Pike B, Holmes C, Collins L, Thompson P, MacDonald D, Iacoboni M, Schormann T, Amunts K, Palomero-Gallagher N, Geyer S, Parsons L, Narr K, Kabani N, Le Goualher G, Feidler J, Smith K, Boomsma D, Hulshoff Pol H, Cannon T, Kawashima R, Mazoyer B. A four-dimensional probabilistic atlas of the human brain. J Am Med Inform Assoc. 2001 Sep-Oct;8(5):401-30. doi: link
    Neuro Cloud Consortium. Electronic address:; Neuro Cloud Consortium. To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery. Neuron. 2016 Nov 2;92(3):622-627. doi: link
    Reid AT, Hoffstaedter F, Gong G, Laird AR, Fox P, Evans AC, Amunts K, Eickhoff SB. A seed-based cross-modal comparison of brain connectivity measures. Brain Struct Funct. 2017 Apr;222(3):1131-1151. Epub 2016 Jul 2. doi: link
    Lancaster JL, Tordesillas-Gutiérrez D, Martinez M, Salinas F, Evans A, Zilles K, Mazziotta JC, Fox PT. Bias between MNI and Talairach coordinates analyzed using the ICBM-152 brain template. Hum Brain Mapp. 2007 Nov;28(11):1194-205. link

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    Tristan Glatard, Gregory Kiar, Tristan Aumentado-Armstrong, Natacha Beck, Pierre Bellec, Rémi Bernard, Axel Bonnet, Shawn T Brown, Sorina Camarasu-Pop, Frédéric Cervenansky, Samir Das, Rafael Ferreira da Silva, Guillaume Flandin, Pascal Girard, Krzysztof J Gorgolewski, Charles R G Guttmann, Valérie Hayot-Sasson, Pierre-Olivier Quirion, Pierre Rioux, Marc-Étienne Rousseau, Alan C Evans Boutiques: a flexible framework to integrate command-line applications in computing platforms. GigaScience, Volume 7, Issue 5, May 2018, doi: link