opfvta-reexecution/publishing/bibliography.bib

@article{samuel2024,
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  volume = {13},
  ISSN = {2047-217X},
  url = {http://dx.doi.org/10.1093/gigascience/giad113},
  DOI = {10.1093/gigascience/giad113},
  journal = {GigaScience},
  publisher = {Oxford University Press (OUP)},
  author = {Samuel,  Sheeba and Mietchen,  Daniel},
  year = {2024}
}

@manual{git,
  title        = {Git: Fast Version Control System},
  author       = {Linus Torvalds and Junio Hamano},
  year         = {2024},
  note         = {Retrieved from https://git-scm.com/}
}

@article{Ioannidis2005,
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  month = aug,
  pages = {e124}
}

@book{NASrepro,
  title = {Reproducibility and Replicability in Science},
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  DOI = {10.17226/25303},
  publisher = {National Academies Press},
  year = {2019},
  month = sep,
}

@book{datalad,
  doi = {10.21105/joss.03262},
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  year = {2021},
  month = jul,
  publisher = {The Open Journal},
  volume = {6},
  number = {63},
  pages = {3262},
  author = {Yaroslav Halchenko and Kyle Meyer and Benjamin Poldrack and Debanjum Solanky and Adina Wagner and Jason Gors and Dave MacFarlane and Dorian Pustina and Vanessa Sochat and Satrajit Ghosh and Christian M\"{o}nch and Christopher Markiewicz and Laura Waite and Ilya Shlyakhter and Alejandro de la Vega and Soichi Hayashi and Christian H\"{a}usler and Jean-Baptiste Poline and Tobias Kadelka and Kusti Skyt{\'{e}}n and Dorota Jarecka and David Kennedy and Ted Strauss and Matt Cieslak and Peter Vavra and Horea-Ioan Ioanas and Robin Schneider and Mika Pfl\"{u}ger and James Haxby and Simon Eickhoff and Michael Hanke},
  title = {{DataLad}: distributed system for joint management of code,  data,  and their relationship},
  journal = {Journal of Open Source Software}
}

@article{eliferep,
  year = {2019},
  month = feb,
  publisher = {eLife},
  author = {Giuliano Maciocci and Michael Aufreiter and Nokome Bentley},
  url = {https://elifesciences.org/labs/ad58f08d/introducing-elife-s-first-computationally-reproducible-article},
  journal = {editorial},
  title = {Introducing eLife’s first computationally reproducible article},
}


@article{elifeERA,
  url = {https://elifesciences.org/labs/dc5acbde/welcome-to-a-new-era-of-reproducible-publishing},
}

@article{Lasser2020,
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  year = {2020},
  month = aug,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {3},
  number = {1},
  author = {Jana Lasser},
  title = {Creating an executable paper is a journey through Open Science},
  journal = {Communications Physics}
}

@article{pms,
  author       = {Stephen P. Bennett and Christian Faulhammer and Ciaran McCreesh and Ulrich Müller},
  month        = {04},
  year         = {2017},
  title        = {Package Manager Specification},
  language     = {English},
  howpublished = {online},
  organization = {Gentoo Linux},
  url          = {https://projects.gentoo.org/pms/6/pms.html},
  owner        = {chymera},
  timestamp    = {2017.11.05},
}


@article{ng,
  doi = {10.3897/rio.3.e12095},
  url = {https://doi.org/10.3897/rio.3.e12095},
  year = 2017,
  month = feb,
  publisher = {Pensoft Publishers},
  volume = {3},
  pages = {e12095},
  author = {Horea-Ioan Ioanas and Bechara Saab and Markus Rudin},
  title = {Gentoo Linux for Neuroscience --- a replicable, flexible, scalable, rolling-release environment that provides direct access to development software},
  journal = {Research Ideas and Outcomes}
}

@article{portage,
  doi = {10.48550/ARXIV.1610.02742},
  url = {https://arxiv.org/abs/1610.02742},
  author = {Amadio,  Guilherme and Xu,  Benda},
  keywords = {Distributed,  Parallel,  and Cluster Computing (cs.DC),  FOS: Computer and information sciences,  FOS: Computer and information sciences},
  title = {Portage: Bringing Hackers' Wisdom to Science},
  publisher = {arXiv},
  year = {2016},
  copyright = {Creative Commons Zero v1.0 Universal}
}

@article{bash,
  title={What's GNU: Bash-The GNU Shell},
  author={Ramey, Chet},
  journal={Linux Journal},
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  number={4es},
  pages={13--es},
  year={1994},
  publisher={Belltown Media Houston, TX}
}

@book{foss,
  title={Free software, free society: Selected essays of Richard M. Stallman},
  author={Stallman, Richard},
  year={2002},
  publisher={Free Software Foundation},
  ISBN="1882114981",
}

@article{TODO,
  doi = {10.1038/d41586-018-04628-w},
  year = {2018},
  month = apr,
  publisher = {Placeholder for citations},
  volume = {556},
  number = {7701},
  pages = {309--309},
  author = {Placeholder for citations},
  title = {Placeholder for citations},
  journal = {Placeholder for citations},
}

@article{Rougier:2018,
  doi = {10.1038/d41586-018-04628-w},
  year = {2018},
  month = apr,
  publisher = {Springer Nature},
  volume = {556},
  number = {7701},
  pages = {309--309},
  author = {Rougier, Nicolas P. and Hinsen, Konrad},
  title = {Code reviewing puts extra demands on referees },
  journal = {Nature},
}

@article{rpp,
  doi = {https://doi.org/10.1126/science.aac4716},
  author = {Open Science Collaboration},
  year = {2015},
  month = aug,
  volume = {349},
  number = {6251},
  title = {Estimating the reproducibility of psychological science},
  journal = {Science},
}

@article{Science:2018,
  doi = {10.1126/science.359.6377.725},
  author = {Hutson, Matthew},
  url = {http://science.sciencemag.org/content/359/6377/725},
  year = {2018},
  month = feb,
  volume = {359},
  number = {6377},
  title = {Artificial intelligence faces a replication crisis},
  journal = {Science},
}

@Misc{me-gin,
  author =       {Horea-Ioan Ioanas and Austin Macdonald and Yaroslav O. Halchenko},
  title =        {Neuroimaging Article Reexecution and Reproduction Assesment System},
  url =          {https://gin.g-node.org/TheChymera/opfvta-reexecution},
  year =         2024,
  note =         {Apache License, verison 2.0, Accessed: 2024-05-15},
}

@Misc{me,
  author =       {Horea-Ioan Ioanas and Austin Macdonald and Yaroslav O. Halchenko},
  title =        {Neuroimaging Article Reexecution and Reproduction Assesment System},
  url =          {https://github.com/con/opfvta-reexecution},
  year =         2024,
  note =         {Apache License, verison 2.0, Accessed: 2024-05-15},
}

@article{Topalidou:2015,
  author =       {Topalidou, Meropi and Rougier, Nicolas P.},
  title =        {{[Re] Interaction between cognitive and motor cortico-basal
                  ganglia loops during decision making: a computational study}},
  journal =      {ReScience},
  year =         2015,
  volume =       1,
  number =       1,
  doi =          {10.5281/zenodo.27944},
}

@article{Rougier:2017,
  doi =          {10.7717/peerj-cs.142},
  author =       {Nicolas P. Rougier and Konrad Hinsen and Frédéric Alexandre
                  and Thomas Arildsen and Lorena Barba and Fabien
                  C. Y. Benureau and C. Titus Brown and Pierre de Buyl and Ozan
                  Caglayan and Andrew P. Davison and Marc André Delsuc and
                  Georgios Detorakis and Alexandra K. Diem and Damien Drix and
                  Pierre Enel and Benoît Girard and Olivia Guest and Matt
                  G. Hall and Rafael Neto Henriques and Xavier Hinaut and Kamil
                  S Jaron and Mehdi Khamassi and Almar Klein and Tiina Manninen
                  and Pietro Marchesi and Dan McGlinn and Christoph Metzner and
                  Owen L. Petchey and Hans Ekkehard Plesser and Timothée Poisot
                  and Karthik Ram and Yoav Ram and Etienne Roesch and Cyrille
                  Rossant and Vahid Rostami and Aaron Shifman and Joseph
                  Stachelek and Marcel Stimberg and Frank Stollmeier and
                  Federico Vaggi and Guillaume Viejo and Julien Vitay and Anya
                  Vostinar and Roman Yurchak and Tiziano Zito},
  title =        {{Sustainable computational science: the ReScience
                  initiative}},
  journal =      {{PeerJ} Computer Science},
  month =        12,
  volume =       3,
  pages =        {e142},
  year =         2017,
  github =       {https://github.com/ReScience/ReScience-article-2},
  keywords =     {journal},
  tags =         {OS},
}

@article{Margolis2006,
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	year = 2006,
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	publisher = {Wiley},
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	number = {3},
	pages = {907--924},
	author = {Elyssa B. Margolis and Hagar Lock and Gregory O. Hjelmstad and Howard L. Fields},
	title = {The ventral tegmental area revisited: is there an electrophysiological marker for dopaminergic neurons?},
	journal = {The Journal of Physiology}
}

@phdthesis{phd,
	title = {Imaging Monoaminergic Systems and their Pharmacological Control},
	author = {Ioanas, Horea-Ioan},
	year = {2019},
	school = {ETH Zurich}
}

@software{abic_g,
	author = {Tina Segessemann and
	          Markus Rudin and
	          Ioanas, Horea-Ioan},
	title = {ABI Connectivity Data Package Generator},
	month = oct,
	year = 2019,
	publisher = {Zenodo},
	version = {0.1},
	doi = {10.5281/zenodo.3523375},
	url = {https://doi.org/10.5281/zenodo.3523375},
}

@article{abic,
	title = {A mesoscale connectome of the mouse brain},
	author = {Oh, Seung Wook and Harris, Julie A and Ng, Lydia and Winslow, Brent and Cain, Nicholas and Mihalas, Stefan and Wang, Quanxin and Lau, Chris and Kuan, Leonard and Henry, Alex M and others},
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	year = 2014,
	publisher = {Nature Publishing Group},
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	url = {http://www.neuro-s.co.jp/images/product/5-151/5-1515.pdf},
}

@article{rice2016,
	title = {Mapping dopaminergic deficiencies in the substantia nigra/ventral tegmental area in schizophrenia},
	author = {Rice, Matthew W and Roberts, Rosalinda C and Melendez-Ferro, Miguel and Perez-Costas, Emma},
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	volume = {221},
	number = {1},
	pages = {185--201},
	month = jan,
	year = 2016,
	publisher = {Springer},
	doi = {10.1007/s00429-014-0901-y},
}

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	title = {Midbrain dopaminergic neurons (nuclei A8, A9, and A10): three-dimensional reconstruction in the rat},
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	journal = {European Journal of Neuroscience}
}

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	doi = {10.1016/j.tics.2012.07.007},
	url = {https://doi.org/10.1016/j.tics.2012.07.007},
	year = 2012,
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	publisher = {Elsevier {BV}},
	volume = {16},
	number = {9},
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	author = {Mimi Liljeholm and John P. O'Doherty},
	title = {Contributions of the striatum to learning,  motivation,  and performance: an associative account},
	journal = {Trends in Cognitive Sciences}
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@article{Grandjean2014,
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	journal = {NeuroImage},
	year = 2014,
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	month = nov,
	issn = {1095-9572},
	abstract = {Resting state-fMRI (rs-fMRI) in mice allows studying mechanisms underlying functional connectivity (FC) as well as alterations of FC occurring in murine models of neurological diseases. Mouse fMRI experiments are typically carried out under anesthesia to minimize animal movement and potential distress during examination. Yet, anesthesia inevitably affects FC patterns. Such effects have to be understood for proper interpretation of data. We have compared the influence of four commonly used anesthetics on rs-fMRI. Rs-fMRI data acquired under isoflurane, propofol, and urethane presented similar patterns when accounting for anesthesia depth. FC maps displayed bilateral correlation with respect to cortical seeds, but no significant inter-hemispheric striatal connectivity. In contrast, for medetomidine, we detected bilateral striatal but compromised inter-hemispheric cortical connectivity. The spatiotemporal patterns of the rs-fMRI signal have been rationalized considering anesthesia depth and pharmacodynamic properties of the anesthetics. Our results bridge the results from different studies from the burgeoning field of mouse rs-fMRI and offer a framework for understanding the influences of anesthetics on FC patterns. Utilizing this information, we suggest the combined use of medetomidine and isoflurane representing the two proposed classes of anesthetics; the combination of low doses of the two anesthetics retained strong correlations both within cortical and subcortical structures, without the potential seizure-inducing effects of medetomidine, rendering this regimen an attractive anesthesia for rs-fMRI in mice.},
	doi = {10.1016/j.neuroimage.2014.08.043},
	keywords = {Anesthesia, standards; Anesthetics, pharmacology; Animals; Brain, drug effects, physiology; Clinical Protocols; Female; Isoflurane, pharmacology; Magnetic Resonance Imaging; Medetomidine, pharmacology; Mice; Mice, Inbred C57BL; Nerve Net, drug effects, physiology; Propofol, pharmacology; Rest, physiology; Urethane, pharmacology; Anesthesia; Functional connectivity; Mouse; Resting state-fMRI},
}

@article{aowsis,
	title = {An automated open-source workflow for standards-compliant integration of small animal magnetic resonance imaging data},
	author = {Ioanas, Horea-Ioan and Marks, Markus and Garin, Cl{\'e}ment M and Dhenain, Marc and Yanik, Mehmet Fatih and Rudin, Markus},
	journal = {Frontiers in neuroinformatics},
	volume = {14},
	pages = {5},
	year = 2020,
	month = feb,
	publisher = {Frontiers},
	doi = {10.3389/fninf.2020.00005},
}

@article{Brocka2018,
	doi = {10.1016/j.neuroimage.2018.04.059},
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	year = 2018,
	month = aug,
	publisher = {Elsevier {BV}},
	volume = {177},
	pages = {88--97},
	author = {Marta Brocka and Cornelia Helbing and Daniel Vincenz and Thomas Scherf and Dirk Montag and J\"{u}rgen Goldschmidt and Frank Angenstein and Michael Lippert},
	title = {Contributions of dopaminergic and non-dopaminergic neurons to {VTA}-stimulation induced neurovascular responses in brain reward circuits},
	journal = {{NeuroImage}}
}

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	title = {Plasma membrane monoamine transporters: structure,  regulation and function},
	journal = {Nature Reviews Neuroscience}
}

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	publisher = {Elsevier {BV}},
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	number = {1},
	pages = {27--32},
	author = {Xiaoxi Zhuang and Justine Masson and Jay A. Gingrich and Stephen Rayport and Ren{\'{e}} Hen},
	title = {Targeted gene expression in dopamine and serotonin neurons of the mouse brain},
	journal = {Journal of Neuroscience Methods}
}

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	title = {Python for Scientific Computing},
	journal = {Computing in Science {\&} Engineering},
}

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	number = {3},
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	title = {Optogenetic {fMRI} in the mouse hippocampus: Hemodynamic response to brief glutamatergic stimuli},
	journal = {Journal of Cerebral Blood Flow {\&} Metabolism}
}

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	title = {Dopaminergic Loss and Inclusion Body Formation in -Synuclein Mice: Implications for Neurodegenerative Disorders},
	journal = {Science}
}

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}
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}

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	publisher = {Elsevier {BV}},
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	author = {Soghra Akbari Chermahini and Bernhard Hommel},
	title = {The (b)link between creativity and dopamine: Spontaneous eye blink rates predict and dissociate divergent and convergent thinking},
	journal = {Cognition}
}

@article{Salamone1994,
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}

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}
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}

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}

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	title = {{GABAergic} and glutamatergic efferents of the mouse ventral tegmental area},
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}

@misc{opfvta_bidsdata,
        author = {Ioanas, Horea-Ioan and
                Bechara John Saab and
                Rudin, Markus},
        title = {{BIDS Data for "A Whole-Brain Map and Assay Parameter Analysis of Mouse VTA Dopaminergic Activation"}},
        month = jun,
        year = 2019,
        doi = {10.5281/zenodo.3236930},
        url = {https://doi.org/10.5281/zenodo.3236930}
}

@conference{repsep,
        author = {Horea-Ioan Ioanas and Markus Rudin},
        title = {Reproducible Self-Publishing for {P}ython-Based Research},
        year = 2018,
        month = aug,
        publisher = {EuroSciPy},
        url = {https://figshare.com/articles/Reproducible_Self-Publishing_for_Python-Based_Research/7247339},
        doi = {10.6084/m9.figshare.7247339.v1},
}

@article{opfvta,
	title = {Whole-brain opto-fMRI map of mouse VTA dopaminergic activation reflects structural projections with small but significant deviations},
	volume = {12},
	ISSN = {2158-3188},
	url = {http://dx.doi.org/10.1038/s41398-022-01812-5},
	DOI = {10.1038/s41398-022-01812-5},
	number = {1},
	journal = {Translational Psychiatry},
	publisher = {Springer Science and Business Media LLC},
	author = {Ioanas,  Horea-Ioan and Saab,  Bechara John and Rudin,  Markus},
	year = {2022},
	month = feb,
}

@software{mbt05,
  author       = {Ioanas, Horea-Ioan and
                  Segessemann, Tina and
                  Rudin, Markus},
  title        = {"Mouse Brain Atlases" Generator Workflows},
  month        = jan,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {0.5},
  doi          = {10.5281/zenodo.2545838},
  url          = {https://doi.org/10.5281/zenodo.2545838}
}

@software{mbt10,
  author       = {Ioanas, Horea-Ioan and
                  Segessemann, Tina and
                  Halchenko, Yaroslav and
                  Macdonald, Austin and
                  Rudin, Markus},
  title        = {{Mouse Brain Templates — Generator Workflows and Data Links}},
  month        = jan,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {1.0},
  doi          = {10.5281/zenodo.8214739},
  url          = {https://doi.org/10.5281/zenodo.8214739}
}

@article{ants,
	title = {A reproducible evaluation of {ANTs} similarity metric performance in brain image registration},
	author = {Brian B. Avants and Nicholas J. Tustison and Gang Song and Philip A. Cook and Arno Klein and James C. Gee},
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	publisher = {Elsevier {BV}},
	volume = {54},
	number = {3},
	pages = {2033--2044},
	journal = {{NeuroImage}},
}

@article{nipype,
	Title = {Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in {P}ython},
	Author = {
		Gorgolewski, Krzysztof and
		Burns, Christopher D. and
		Madison, Cindeeand
		Clark, Dav and
		Halchenko, Yaroslav O. and
		Waskom, Michael L. and
		Ghosh, Satrajit S.
		},
	Journal = {Front. Neuroinform.},
	Year = {2011},
	Volume = {5},

	ISSN = {1662-5196},
	Owner = {chymera},
	Publisher = {Frontiers Media SA},
	Timestamp = {2015.04.13},
	url = {http://dx.doi.org/10.3389/fninf.2011.00013},
	doi = {10.3389/fninf.2011.00013},
}

@article{fsl,
	Title = {{FSL}},
	Author = {Jenkinson, Mark and Beckmann, Christian F. and Behrens, Timothy E J. and Woolrich, Mark W. and Smith, Stephen M.},
	Journal = {Neuroimage},
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	Month = aug,
	Number = {2},
	Pages = {782--790},
	Volume = {62},
	Abstract = {FSL (the FMRIB Software Library) is a comprehensive library of analysis tools for functional, structural and diffusion MRI brain imaging data, written mainly by members of the Analysis Group, FMRIB, Oxford. For this NeuroImage special issue on "20 years of fMRI" we have been asked to write about the history, developments and current status of FSL. We also include some descriptions of parts of FSL that are not well covered in the existing literature. We hope that some of this content might be of interest to users of FSL, and also maybe to new research groups considering creating, releasing and supporting new software packages for brain image analysis.},
	doi = {10.1016/j.neuroimage.2011.09.015},
	Institution = {FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.},
	Keywords = {Brain Mapping, history/methods; Brain, anatomy /&/ histology/physiology; Diffusion Magnetic Resonance Imaging, history/methods; History, 20th Century; History, 21st Century; Humans; Image Processing, Computer-Assisted, history/methods; Software, history},
	Language = {eng},
	Medline-pst = {ppublish},
	Owner = {chymera},
	Pii = {S1053-8119(11)01060-3},
	Pmid = {21979382},
	Timestamp = {2015.04.13},
	url = {http://dx.doi.org/10.1016/j.neuroimage.2011.09.015},
}

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	title = {{AFNI}: software for analysis and visualization of functional magnetic resonance neuroimages},
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	url = {https://www.sciencedirect.com/science/article/pii/S0010480996900142},
	doi = {10.1006/cbmr.1996.0014},
	publisher = {Elsevier},
}


@article{nilearn,
	doi = {10.3389/fninf.2014.00014},
	url = {https://doi.org/10.3389/fninf.2014.00014},
	year = 2014,
	month = feb,
	publisher = {Frontiers Media {SA}},
	volume = {8},
	author = {Alexandre Abraham and Fabian Pedregosa and Michael Eickenberg and Philippe Gervais and Andreas Mueller and Jean Kossaifi and Alexandre Gramfort and Bertrand Thirion and Gaël Varoquaux},
	title = {Machine learning for neuroimaging with scikit-learn},
	journal = {Frontiers in Neuroinformatics}
}

@misc{samri,
	author = {Horea-Ioan Ioanas and
		Markus Marks and
		Tina Segessemann and
		Dominik Schmidt and
		Florian Aymanns and
		Markus Rudin},
	title = {{SAMRI} --- {S}mall {A}nimal {M}agnetic {R}esonance {I}maging},
	month = jan,
	year = 2019,
	doi = {10.5281/zenodo.3234918},
	url = {https://doi.org/10.5281/zenodo.3234918}
}


@article{irsabi,
	doi = {10.1016/j.neuroimage.2021.118386},
	url = {https://doi.org/10.1016/j.neuroimage.2021.118386},
	year = {2021},
	month = nov,
	publisher = {Elsevier {BV}},
	volume = {241},
	pages = {118386},
	author = {Horea-Ioan Ioanas and Markus Marks and Valerio Zerbi and Mehmet Fatih Yanik and Markus Rudin},
	title = {An optimized registration workflow and standard geometric space for small animal brain imaging}
}

@misc{yoda,
  author       = {Hanke, Michael and {Visconti di Oleggio Castello}, Matteo and Meyer, Kyle and Poldrack, Benjamin and Halchenko, Yaroslav O.},
  title        = {{YODA}: {YODA}’s organigram on data analysis},
  year         = 2018,
  subtype      = {poster},
  howpublished = {Poster presented at the annual meeting of the Organization for Human Brain Mapping,
                  Singapore},
  scholar-time = {2019-03-28T15:34:52.738030},
  url          = {https://github.com/myyoda/poster/blob/master/ohbm2018.pdf},
  eprint       = {https://github.com/myyoda/poster/blob/master/ohbm2018.pdf}
}

@misc{repronim:reprobasics,
  title = {{ReproNim} {R}eproducible {B}asics {M}odule},
  author = {Halchenko, Yaroslav O. and Nastase, Sam and Wagner, Adina and Cheng, Christopher P. and Buccigrossi, Robert and Ghosh, Satrajit and Keator, David and Poline, Jean-Baptiste and Buccigrossi, Robert W. and Bates, Julie},
  year = 2021,
  url = "https://www.repronim.org/module-reproducible-basics/"
}

@article{fair-workflows,
	doi = {10.1162/dint_a_00033},
	url = {https://doi.org/10.1162/dint_a_00033},
	year = 2020,
	month = {jan},
	publisher = {{MIT} Press - Journals},
	volume = {2},
	number = {1-2},
	pages = {108--121},
	author = {Carole Goble and Sarah Cohen-Boulakia and Stian Soiland-Reyes and Daniel Garijo and Yolanda Gil and Michael R. Crusoe and Kristian Peters and Daniel Schober},
	title = {{FAIR} Computational Workflows},
	journal = {Data Intelligence}
}

% I think it is about to be accepted/published?
@article{neurodesk,
	doi = {10.1101/2022.12.23.521691},
	url = {https://doi.org/10.1101/2022.12.23.521691},
	year = 2022,
	month = {dec},
	publisher = {Cold Spring Harbor Laboratory},
	author = {Angela I. Renton and Thanh Thuy Dao and David F. Abbott and Toluwani J Amos and Saskia Bollmann and Andy Botting and Megan E. J. Campbell and Jeryn Chang and Oren Civier and Thomas G. Close and Korbinian Eckstein and Gary F. Egan and Stefanie Evas and Guillaume Flandin and Kelly G. Garner and Marta I. Garrido and Satrajit S Ghosh and Martin Grignard and Anthony J. Hannan and Renzo Huber and Matthew E Hughes and Tom Johnstone and Jakub R. Kaczmarzyk and Lars Kasper and Levin Kuhlmann and Kexin Lou and Paris Lyons and Yorguin-Jose Mantilla-Ramos and Jason B. Mattingley and Jo Morris and Akshaiy Narayanan and Franco Pestilli and Aina Puce and Fernanda L. Ribeiro and Nigel C. Rogasch and Chris Rorden and Mark Schira and Thomas B. Shaw and Benjamin M Slade and Gershon Spitz and Ashley Stewart and Ryan P. Sullivan and David J. White and Xincheng Ye and Judy D. Zhu and Aswin Narayanan and Steffen Bollmann},
	title = {Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging}
}

@misc{neurodocker,
  doi = {10.5281/ZENODO.7929032},
  url = {https://zenodo.org/record/7929032},
  author = {Kaczmarzyk, Jakub and {Satrajit Ghosh} and Gau, Remi and Bollmann, Steffen and Goncalves, Mathias and Halchenko, Yaroslav and Jarecka, Dorota and Wighton, Paul and Notter, Michael and Markiewicz, Chris and Vaillant, Ghislain and {Araikes} and Nielson, Dylan and Cieslak, Matt and Mitchell, Ross and {Sooyoung Ahn} and {Mchlrnwld} and Close, Tom and Rokem, Ariel and Klein, Arno and Torres, Giovanni and Marquardt, Ingo and Kent, James and Mentch, Jeff and {Jennings Zhang} and Flandin, Guillaume and Sassenhagen, Jona and Ferrer, Vicente and {Schahid}},
  title = {ReproNim/neurodocker: 0.9.5},
  publisher = {Zenodo},
  year = {2023},
  copyright = {Open Access}
}

@article{Dar2019,
  doi = {10.1101/619254},
  url = {https://doi.org/10.1101/619254},
  year = {2019},
  month = apr,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Asim H. Dar and Adina S. Wagner and Michael Hanke},
  title = {{REMoDNaV}: Robust Eye-Movement Classification for Dynamic Stimulation}
}

@article{neurolibre,
  title={{NeuroLibre}: A preprint server for full-fledged reproducible neuroscience},
  author={Karakuzu, Agah and DuPre, Elizabeth and Tetrel, Loic and Bermudez, Patrick and Boudreau, Mathieu and Chin, Mary and Poline, Jean-Baptiste and Das, Samir and Bellec, Pierre and Stikov, Nikola},
  publisher={OSF Preprints},
  year={2022}
}

@article{NIDM,
  title = {Sharing brain mapping statistical results with the neuroimaging data model},
  volume = {3},
  ISSN = {2052-4463},
  url = {http://dx.doi.org/10.1038/sdata.2016.102},
  DOI = {10.1038/sdata.2016.102},
  number = {1},
  journal = {Scientific Data},
  publisher = {Springer Science and Business Media LLC},
  author = {Maumet,  Camille and Auer,  Tibor and Bowring,  Alexander and Chen,  Gang and Das,  Samir and Flandin,  Guillaume and Ghosh,  Satrajit and Glatard,  Tristan and Gorgolewski,  Krzysztof J. and Helmer,  Karl G. and Jenkinson,  Mark and Keator,  David B. and Nichols,  B. Nolan and Poline,  Jean-Baptiste and Reynolds,  Richard and Sochat,  Vanessa and Turner,  Jessica and Nichols,  Thomas E.},
  year = {2016},
  month = dec 
}

@article{neurovault,
  title = {NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain},
  volume = {9},
  ISSN = {1662-5196},
  url = {http://dx.doi.org/10.3389/fninf.2015.00008},
  DOI = {10.3389/fninf.2015.00008},
  journal = {Frontiers in Neuroinformatics},
  publisher = {Frontiers Media SA},
  author = {Gorgolewski,  Krzysztof J. and Varoquaux,  Gael and Rivera,  Gabriel and Schwarz,  Yannick and Ghosh,  Satrajit S. and Maumet,  Camille and Sochat,  Vanessa V. and Nichols,  Thomas E. and Poldrack,  Russell A. and Poline,  Jean-Baptiste and Yarkoni,  Tal and Margulies,  Daniel S.},
  year = {2015},
  month = apr
}