@Comment{x-kbibtex-encoding=utf-8}
@Article{HBL+12,
	title = "Decoding Semantics across {fMRI} sessions with Different Stimulus Modalities: A practical {MVPA} Study",
	volume = {6},
	issn = {1662-5196},
	url = {http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00024/full},
	doi = {10.3389/fninf.2012.00024},
	abstract = {Both embodied and symbolic accounts of conceptual organization would predict partial sharing and partial differentiation between the neural activations seen for concepts activated via different stimulus modalities. But cross-participant and cross-session variability in {BOLD} activity patterns makes analyses of such patterns with {MVPA} methods challenging. Here we examine the effect of cross-modal and individual variation on the machine learning analysis of {fMRI} data recorded during a word property generation task. We present the same set of living and non-living concepts (land-mammals, or work tools) to a cohort of Japanese participants in two sessions: the first using auditory presentation of spoken words; the second using visual presentation of words written in Japanese characters. Classification accuracies confirmed that these semantic categories could be detected in single trials, with within-session predictive accuracies of 80-90\%. However cross-session prediction (learning from auditory-task data to classify data from the written-word-task, or vice-versa) suffered from a performance penalty, achieving 65-75\% (still individually significant at p<<0.05). We carried out several follow-on analyses to investigate the reason for this shortfall, concluding that distributional differences in neither time nor space alone could account for it. Rather, combined spatio-temporal patterns of activity need to be identified for successful cross-session learning, and this suggests that feature selection strategies could be modified to take advantage of this.},
	journal = {Frontiers in Neuroinformatics},
	author = {Akama Hiroyuki and Murphy Brian and Na Li and Shimizu Yumiko and Poesio Massimo},
	year = {2012},
	pymvpa-keywords = "pymvpa, fmri"
}

@Article{DTM+11,
	journal = "NeuroImage",
	year = 2011,
	volume = "60",
	pages = "189--203",
	title = "Task-driven {ICA} feature generation for accurate and interpretable
	         prediction using {fMRI}",
	url = "http://www.ncbi.nlm.nih.gov/pubmed/22227050",
	author = "Eugene P. Duff and A. J. Trachtenberg and C. E. Mackay CE and
	           M. A. Howard and F. Wilson and Stephen M. Smith and
	           Mark W. Woolrich",
	journal-impact = "5.895"
}

@Article{ KKO+11,
	Author = "Lisandro Nicolas Kaunitz and Juan Esteban Kamienkowski and Emanuele Olivetti and Brian Murphy and Paolo Avesani and David Paul Melcher",
	Title = "Intercepting the first pass: rapid categorization is suppressed for unseen stimuli",
	Journal = "Frontiers in Perception Science",
	Volume = "2",
	Pages = "198",
	url = "http://www.frontiersin.org/perception_science/10.3389/fpsyg.2011.00198/full",
	year = 2011,
	doi = "10.3389/fpsyg.2011.00198",
	pymvpa-keywords = "pymvpa, eeg"
}

@inproceedings{XLR2012,
	author = {Hao Xu and Alexander Lorbert and Peter J. Ramadge and
	          J. Swaroop Guntupalli and James V. Haxby},
	title = {Regularized hyperalignment of multi-set {fMRI} data},
	year = 2012,
	booktitle = {Proceedings of the 2012 IEEE Signal Processing Workshop},
	address = {Ann Arbor Michigan}
}

@article{GMS+12,
	author = {Gorlin, Scott and Meng, Ming and Sharma, Jitendra and Sugihara, Hiroki and Sur, Mriganka and Sinha, Pawan},
	title = {Imaging prior information in the brain},
	volume = {109},
	number = {20},
	pages = {7935--7940},
	year = {2012},
	doi = {10.1073/pnas.1111224109},
	URL = {http://www.pnas.org/content/109/20/7935.abstract},
	journal = {Proceedings of the National Academy of Sciences}
}

@Article{ CGG+12,
	Author = "Andrew C. Connolly and J. Swaroop Guntupalli and Jason Gors and Michael Hanke and Yaroslav O. Halchenko and Yu-Chien Wu and Hervé Abdi and James V. Haxby",
	Title = "The Representation of Biological Classes in the Human Brain",
	Journal = "Journal of Neuroscience",
	Volume = "32",
	Pages = "2608--2618",
	url = "http://www.jneurosci.org/content/32/8/2608#aff-4",
	year = 2012,
	doi = "10.1523/JNEUROSCI.5547-11.2012",
	journal-impact = "6.908"
}

@Article{ CRK+11,
	Author = "Johan D. Carlin and James B. Rowe and Nikolaus Kriegeskorte and Russell Thompson and Andrew J. Calder",
	Title = "Direction-Sensitive Codes for Observed Head Turns in Human Superior Temporal Sulcus.",
	Journal = "Cerebral Cortex",
	Volume = "",
	Pages = "",
	url = "http://cercor.oxfordjournals.org/content/early/2011/06/27/cercor.bhr061.short",
	year = 2011,
	doi = "10.1093/cercor/bhr061",
	pymvpa-keywords = "pymvpa, fMRI, searchlight",
	journal-impact = "6.544"
}

@Article{ MRH11,
	title = "Dynamic Changes In The Medial Temporal Lobe During Incidental Learning Of Object–Location Associations",
	author = "Anna Manelis and Lynne M. Reder and Stephen José  Hanson",
	journal = "Cerebral Cortex",
	year = "2011",
	journal-impact = "6.544",
	abstract = "The role of the medial temporal lobe (MTL) in associative memory encoding has been the focus of many memory experiments. However, there has been surprisingly little investigation of whether the contributions of different MTL subregions (amygdala, hippocampus [HPC], parahippocampal [PHc], perirhinal cortex [PRc], and temporal polar cortex [TPc]) shift across multiple presentations during associative encoding. We examined this issue using event-related functional magnetic resonance imaging and a multivoxel pattern classification analysis. Subjects performed a visual search task, becoming faster with practice to locate objects whose locations were held constant across trials. The classification analysis implicated right HPC and amygdala early in the task when the speed-up from trial to trial was greatest. The same analysis implicated right PRc and TPc late in learning when speed-up was minimal. These results suggest that associative encoding relies on complex patterns of neural activity in MTL that cannot be expressed by simple increases or decreases of blood oxygenation level—dependent signal during learning. Involvement of MTL subregions during encoding of object–location associations depends on the nature of the learning phase. Right HPC and amygdala support active integration of object and location information, while right PRc and TPc are involved when object and spatial representations become unitized into a single representation.",
	doi = "10.1093/cercor/bhr151",
	pymvpa-keywords = "pymvpa, fMRI"
}

@Comment{   This file is used to autogenerate doc/references.rst   using tools/bib2rst_ref.py .   Due to external dependency on pybliographer (which is   discontinued project), automatic regeneration is not enabled,   thus you are required to run   make references   to regenerate doc/references.rst if you modified this file. }

@Article{ HGF+01,
	Author = "James V. Haxby and M. I. Gobbini and M. L. Furey and A. Ishai and J. L. Schouten and P. Pietrini",
	Title = "Distributed and overlapping representations of faces and objects in ventral temporal cortex.",
	Journal = "Science",
	Volume = "293",
	Pages = "2425–2430",
	year = 2001,
	doi = "10.1126/science.1063736",
	pymvpa-keywords = "split-correlation classifier"
}

@Article{ CPL+06,
	Author = "X. Chen and Francisco Pereira and W. Lee and Stephen Strother and Tom Mitchell",
	Title = "Exploring predictive and reproducible modeling with the single-subject {FIAC} dataset.",
	Journal = "Human Brain Mapping",
	Volume = "27",
	Pages = "452–461",
	url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=16565951",
	year = 2006,
	doi = "10.1002/hbm.20243",
	pymvpa-keywords = "feature selection, feature selection stability",
	pymvpa-summary = "This paper illustrates the necessity to consider the stability or reproducibility of a classifier's feature selection as at least equally important to it's generalization performance."
}

@Article{ LSC+05,
	issn = "1053-8119",
	volume = "26",
	year = "2005",
	journal = "NeuroImage",
	title = "Support vector machines for temporal classification of block design fMRI data.",
	pages = "317–329",
	affiliation = "Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, 30322, USA.",
	author = "Stephen LaConte and Stephen Strother and Vladimir Cherkassky and Jon Anderson and Xiaoping Hu",
	doi = "10.1016/j.neuroimage.2005.01.048",
	pymvpa-summary = "Comprehensive evaluation of preprocessing options with respect to SVM-classifier (and others) performance on block-design fMRI data.",
	pymvpa-keywords = "SVM"
}

@Article{ KGB06,
	issn = "0027-8424",
	volume = "103",
	year = "2006",
	journal = "Proceedings of the National Academy of Sciences of the USA",
	title = "Information-based functional brain mapping.",
	pages = "3863–3868",
	author = "Nikolaus Kriegeskorte and Rainer Goebel and Peter A. Bandettini",
	doi = "10.1073/pnas.0600244103",
	pymvpa-keywords = "searchlight",
	pymvpa-summary = "Paper introducing the searchlight algorithm.",
	affiliation = "Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, Building 10, Room 1D80B, 10 Center Drive MSC 1148, Bethesda, MD 20892-1148, USA. niko@nih.gov"
}

@Article{ KWO11,
	issn = "0956-7976",
	volume = "in press",
	year = "2011",
	journal = "Psychological Science",
	title = "Emergence of perceptual gestalts in the human visual cortex: The case of the configural superiority effect",
	author = "Jonas Kubilius and Johan Wagemans and Hans {Op de Beeck}",
	doi = "10.1177/0956797611417000",
	pymvpa-keywords = "pymvpa, fMRI",
	journal-impact = "4.431"
}

@Article{ HR06,
	issn = "1471-003X",
	volume = "7",
	year = "2006",
	journal = "Nature Reviews Neuroscience",
	title = "Decoding mental states from brain activity in humans.",
	pages = "523–534",
	author = "John-Dylan Haynes and Geraint Rees",
	doi = "10.1038/nrn1931",
	pymvpa-summary = "Review of decoding studies, emphasizing the importance of ethical issues concerning the privacy of personal thought."
}

@Book{ Vap95,
	title = "The Nature of Statistical Learning Theory",
	author = "Vladimir Vapnik",
	publisher = "Springer",
	address = "New York",
	isbn = "0-387-94559-8",
	year = "1995",
	pymvpa-keywords = "support vector machine, SVM"
}

@Article{ KCF+05,
	Author = "B. Krishnapuram and L. Carin and M. A. Figueiredo and A. J. Hartemink",
	Title = "Sparse multinomial logistic regression: fast algorithms and generalization bounds.",
	Journal = "IEEE Transactions on Pattern Analysis and Machine Intelligence",
	Volume = "27",
	Pages = "957–968",
	url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=15943426",
	year = 2005,
	pymvpa-keywords = "sparse multinomial logistic regression, SMLR",
	doi = "10.1109/TPAMI.2005.127"
}

@Article{ EHJ+04,
	title = "Least Angle Regression",
	author = "Bradley Efron and Hastie. Trevor and Iain Johnstone and Robert Tibshirani",
	journal = "Annals of Statistics",
	pages = "407–499",
	volume = "32",
	year = "2004",
	doi = "10.1214/009053604000000067",
	pymvpa-keywords = "least angle regression, LARS"
}

@Article{ HH08,
	issn = "0899-7667",
	volume = "20",
	year = "2008",
	journal = "Neural Computation",
	title = "Brain reading using full brain support vector machines for object recognition: there is no ``face'' identification area.",
	pages = "486–503",
	author = "Stephen José Hanson and Yaroslav O. Halchenko",
	doi = "10.1162/neco.2007.09-06-340",
	pymvpa-keywords = "support vector machine, SVM, feature selection, recursive feature elimination, RFE",
	affiliation = "Rutgers Mind/Brain Analysis Laboratories, Psychology Department, Rutgers University, Newark, NJ 07102, U.S.A. jose@tractatus.rutgers.edu."
}

@Article{ NPD+06,
	issn = "1364-6613",
	volume = "10",
	year = "2006",
	journal = "Trends in Cognitive Science",
	title = "Beyond mind-reading: multi-voxel pattern analysis of fMRI data.",
	pages = "424–430",
	author = "Kenneth A. Norman and Sean M. Polyn and Greg J. Detre and James V. Haxby",
	doi = "10.1016/j.tics.2006.07.005"
}

@Article{ Dem06,
	author = "Janez Demšar",
	title = "Statistical Comparisons of Classifiers over Multiple Data Sets",
	journal = "Journal of Machine Learning Research",
	volume = "7",
	year = "2006",
	issn = "1533-7928",
	pages = "1–30",
	publisher = "MIT Press",
	address = "Cambridge, MA, USA",
	url = "http://portal.acm.org/citation.cfm?id=1248548",
	pymvpa-summary = "This is a review of several classifier benchmark procedures."
}

@Article{ NH02,
	issn = "1065-9471",
	volume = "15",
	number = "1",
	year = "2002",
	Journal = "Human Brain Mapping",
	title = "Nonparametric permutation tests for functional neuroimaging: a primer with examples.",
	pages = "1–25",
	author = "Thomas E Nichols and Andrew P Holmes",
	doi = "10.1002/hbm.1058",
	affiliation = "Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.",
	pymvpa-summary = "Overview of standard nonparametric randomization and permutation testing applied to neuroimaging data (e.g. fMRI)"
}

@Article{ SMM+08,
	volume = "172",
	number = "1",
	year = "2008",
	journal = "Journal of Neuroscience Methods",
	title = "The impact of functional connectivity changes on support vector machines mapping of fMRI data.",
	pages = "94–104",
	doi = "10.1016/j.jneumeth.2008.04.008",
	author = "João Ricardo Sato and Janaina Mourão-Miranda and Maria da Graça {Morais Martin} and Edson Amaro and Pedro Alberto Morettin and Michael John Brammer",
	pymvpa-summary = "Discussion of possible scenarios where univariate and multivariate (SVM) sensitivity maps derived from the same dataset could differ. Including the case were univariate methods would assign a substantially larger score to some features.",
	pymvpa-keywords = "support vector machine, SVM, sensitivity"
}

@Article{ WCW+07,
	issn = "1053-8119",
	volume = "36",
	number = "4",
	year = "2007",
	journal = "NeuroImage",
	title = "Support vector machine learning-based fMRI data group analysis.",
	pages = "1139–51",
	author = "Ze Wang and Anna R. Childress and Jiongjiong Wang and John A. Detre",
	doi = "10.1016/j.neuroimage.2007.03.072",
	pymvpa-keywords = "support vector machine, SVM, group analysis"
}

@Article{ OJA+05,
	title = "Partially Distributed Representations of Objects and Faces in Ventral Temporal Cortex ",
	author = "A. J. O'Toole and F. Jiang and H. Abdi and James V. Haxby",
	journal = "Journal of Cognitive Neuroscience",
	pages = "580–590",
	volume = "17",
	year = "2005",
	doi = "10.1162/0898929053467550"
}

@Article{ OJA+07,
	Author = "A. J. O'Toole and F. Jiang and H. Abdi and N. Penard and J. P. Dunlop and M. A. Parent",
	Title = "Theoretical, statistical, and practical perspectives on pattern-based classification approaches to the analysis of functional neuroimaging data.",
	Journal = "Journal of Cognitive Neuroscience",
	Volume = "19",
	Pages = "1735–1752",
	doi = "10.1162/jocn.2007.19.11.1735",
	year = 2007
}

@Article{ GE03,
	author = "I. Guyon and A. Elisseeff",
	title = "An Introduction to Variable and Feature Selection",
	volume = "3",
	year = "2003",
	pages = "1157–1182",
	journal = "Journal of Machine Learning",
	url = "http://www.jmlr.org/papers/v3/guyon03a.html"
}

@Article{ HMH04,
	Author = "Stephen José Hanson and T. Matsuka and James V. Haxby",
	Title = "Combinatorial codes in ventral temporal lobe for object recognition: {H}axby (2001) revisited: is there a ``face'' area?",
	Journal = "NeuroImage",
	Volume = "23",
	Pages = "156–166",
	year = 2004,
	doi = "10.1016/j.neuroimage.2004.05.020"
}

@Article{ ZH05,
	title = "Regularization and variable selection via the elastic net",
	author = "H. Zou and Trevor Hastie",
	journal = "Journal of the Royal Statistical Society Series B",
	volume = "67",
	number = "2",
	pages = "301–320",
	year = "2005",
	publisher = "Blackwell Synergy",
	pymvpa-keywords = "feature selection, statistical learning",
	url = "http://www-stat.stanford.edu/%7Ehastie/Papers/B67.2%20(2005)%20301-320%20Zou%20%26%20Hastie.pdf"
}

@Article{ MHN+04,
	title = "Learning to Decode Cognitive States from Brain Images",
	author = "Tom Mitchell and Rebecca Hutchinson and Radu S. Niculescu and Francisco Pereira and Xuerui Wang and Marcel Just and Sharlene Newman",
	doi = "10.1023/B:MACH.0000035475.85309.1b",
	journal = "Machine Learning",
	volume = "57",
	pages = "145–175",
	year = "2004"
}

@Article{ PP07,
	issn = "1047-3211",
	volume = "17",
	year = "2007",
	journal = "Cerebral Cortex",
	title = "Decoding near-threshold perception of fear from distributed single-trial brain activation.",
	pages = "691–701",
	author = "Luiz Pessoa and Srikanth Padmala",
	pymvpa-summary = "Analysis of slow event-related fMRI data using patter classification techniques.",
	doi = "10.1093/cercor/bhk020"
}

@Article{ KT05,
	issn = "1097-6256",
	volume = "8",
	year = "2005",
	journal = "Nature Neuroscience",
	title = "Decoding the visual and subjective contents of the human brain.",
	pages = "679–685",
	author = "Yukiyasu Kamitani and Frank Tong",
	pymvpa-summary = "One of the two studies showing the possibility to read out orientation information from visual cortex.",
	doi = "10.1038/nn1444"
}

@Manual{ HHS+latest,
	title = "The PyMVPA Manual",
	author = "Michael Hanke and Yaroslav O. Halchenko and Per B. Sederberg and James M. Hughes",
	address = "Available online at http://www.pymvpa.org/PyMVPA-Manual.pdf"
}

@Article{ HHS+09a,
	title = "PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data",
	author = "Michael Hanke and Yaroslav O. Halchenko and Per B. Sederberg and Stephen José Hanson and James V. Haxby and Stefan Pollmann",
	journal = "Neuroinformatics",
	year = "2009",
	pymvpa-summary = "Introduction into the analysis of fMRI data using PyMVPA.",
	pages = "37–53",
	volume = "7",
	doi = "10.1007/s12021-008-9041-y",
	pymvpa-keywords = "PyMVPA, fMRI",
	journal-impact = "3.054"
}

@Article{ PMB09,
	title = "Machine learning classifiers and f{MRI}: {A} tutorial overview",
	author = "Francisco Pereira and Tom Mitchell and Matthew Botvinick",
	journal = "NeuroImage",
	year = "2009",
	doi = "10.1016/j.neuroimage.2008.11.007",
	url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892746/",
	pages = "199–209",
	volume = "45",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ HHS+09b,
	issn = "1662-5196",
	volume = "3",
	year = "2009",
	journal = "Frontiers in Neuroinformatics",
	title = "PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data.",
	pages = "3",
	author = "Michael Hanke and Yaroslav O. Halchenko and Per B. Sederberg and Emanuele Olivetti and Ingo Fründ and Jochem W. Rieger and Christoph S. Herrmann and James V. Haxby and Stephen José Hanson and Stefan Pollmann",
	doi = "10.3389/neuro.11.003.2009",
	pymvpa-keywords = "PyMVPA, fMRI, EEG, MEG, extracellular recordings",
	pymvpa-summary = "Demonstration of PyMVPA capabilities concerning multi-modal or modality-agnostic data analysis."
}

@Article{ MBK09,
	year = "2009",
	journal = "Social Cognitive and Affective Neuroscience",
	title = "Revealing representational content with pattern-information fMRI–an introductory guide.",
	author = "Marieke Mur and Peter A. Bandettini and Nikolaus Kriegeskorte",
	doi = "10.1093/scan/nsn044",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ JL09,
	title = "OMPC: an open-source MATLAB-to-Python compiler.",
	author = "Peter Jurica and Cees {van Leeuwen}",
	journal = "Frontiers in Neuroinformatics",
	pages = "5",
	volume = "3",
	year = "2009",
	doi = "10.3389/neuro.11.005.2009"
}

@Article{ KFS+09,
	title = "Center-surround patterns emerge as optimal predictors for human saccade targets",
	author = "Wolf Kienzle and Matthias O. Franz and Bernhard Schölkopf and Felix A. Wichmann",
	journal = "Journal of Vision",
	year = "In press",
	pymvpa-summary = "This paper offers an approach to make sense out of feature sensitivities of non-linear classifiers."
}

@Article{ KMB08,
	volume = "2",
	year = "2008",
	journal = "Frontiers in Systems Neuroscience",
	title = "Representational similarity analysis - connecting the branches of systems neuroscience.",
	pages = "4",
	author = "Nikolaus Kriegeskorte and Marieke Mur and Peter A. Bandettini",
	doi = "10.3389/neuro.06.004.2008"
}

@Article{ SET+09,
	title = "Elucidating an MRI-Based Neuroanatomic Biomarker for Psychosis: Classification Analysis Using Probabilistic Brain Atlas and Machine Learning Algorithms",
	author = "Daqiang Sun and Theo G.M. {van Erp} and Paul M. Thompson and Carrie E. Bearden and Melita Daley and Leila Kushan and Molly E. Hardt and Keith H. Nuechterlein and Arthur W. Toga and Tyrone D. Cannon",
	journal = "Biological Psychiatry",
	pages = "1055–1060",
	volume = "66",
	year = "2009",
	doi = "10.1016/j.biopsych.2009.07.019",
	pymvpa-summary = "First published study employing PyMVPA for MRI-based analysis of Psychosis.",
	pymvpa-keywords = "pymvpa, psychosis, MRI",
	journal-impact = "8.926"
}

@Article{ JSW09,
	title = "Does Cognitive Science Need Kernels?",
	volume = "13",
	url = "http://www.sciencedirect.com/science/article/B6VH9-4X4R9BC-1/2/e2e90008d0a8887878c72777462335fd",
	author = "Frank Jäkel and Bernhard Schölkopf and Felix A. Wichmann",
	journal = "Trends in Cognitive Sciences",
	pages = "381–388",
	year = "2009",
	doi = "10.1016/j.tics.2009.06.002",
	pymvpa-keywords = "kernel methods, similarity",
	pymvpa-summary = "A summary of the relationship of machine learning and cognitive science. Moreover it also points out the role of kernel-based methods in this context."
}

@Article{ Ioa05,
	issn = "1549-1676",
	volume = "2",
	number = "8",
	year = "2005",
	month = "Aug",
	journal = "PLoS Med",
	title = "Why most published research findings are false.",
	pages = "e124",
	author = "John P A Ioannidis",
	doi = "10.1371/journal.pmed.0020124",
	pymvpa-keywords = "hypothesis testing",
	pymvpa-summary = "Simulation study speculating that it is more likely for a research claim to be false than true. Along the way the paper highlights aspects to keep in mind while assessing the 'scientific significance' of any given study, such as, viability, reproducibility, and results."
}

@Article{ HHH+10,
	title = "Statistical learning analysis in neuroscience: aiming for transparency.",
	author = "Michael Hanke and Yaroslav O. Halchenko and James V. Haxby and Stefan Pollmann",
	journal = "Frontiers in Neuroscience",
	pages = "38–43",
	volume = "4",
	year = "2010",
	doi = "10.3389/neuro.01.007.2010",
	pymvpa-summary = "Focused review article emphasizing the role of transparency to facilitate adoption and evaluation of statistical learning techniques in neuroimaging research."
}

@Article{ MHH10,
	title = "Implicit memory for object locations depends on reactivation of encoding-related brain regions",
	author = "Anna Manelis and Catherine Hanson and Stephen José Hanson",
	journal = "Human Brain Mapping",
	year = "2010",
	doi = "10.1002/hbm.20992",
	pymvpa-keywords = "pymvpa, implicit memory, fMRI",
	journal-impact = "5.107"
}

@Book{ HTF09,
	title = "The Elements of Statistical Learning: Data Mining, Inference, and Prediction",
	author = "Trevor Hastie and Robert Tibshirani and Jerome H. Friedman",
	publisher = "Springer",
	address = "New York",
	edition = "2",
	year = "2009",
	isbn = "978-0-387-84857-0",
	url = "http://web.stanford.edu/\%7Ehastie/ElemStatLearn/",
	doi = "10.1007/b94608",
	pymvpa-summary = "Excellent summary of virtually all techniques relevant to the field. A free PDF version of this book is available from the authors' website at http://web.stanford.edu/\%7Ehastie/ElemStatLearn/"
}

@Article{ LBB+98,
	title = "Gradient-based learning applied to document recognition",
	author = "Y. Lecun and L. Bottou and Y. Bengio and P. Haffner",
	journal = "Proceedings of the IEEE",
	pages = "2278–2324",
	volume = "86",
	number = "11",
	month = "Nov",
	year = 1998,
	issn = "0018-9219",
	doi = "10.1109/5.726791",
	pymvpa-keywords = "handwritten character recognition, multilayer neural networks, MNIST, statistical learning",
	pymvpa-summary = "Paper introducing Modified NIST (MNIST) dataset for performance comparisons of character recognition performance across a variety of classifiers."
}

@Article{ Coh94,
	title = "The earth is round (p< 0.05)",
	author = "J. Cohen",
	journal = "American Psychologist",
	pages = "997–1003",
	volume = "49",
	number = "12",
	year = "1994",
	url = "http://www.citeulike.org/user/mdreid/article/2643653",
	pymvpa-keywords = "hypothesis testing",
	pymvpa-summary = "Classical critic of null hypothesis significance testing"
}

@Article{ Wri09,
	title = "Ten Statisticians and Their Impacts for Psychologists",
	author = "D.B. Wright",
	journal = "Perspectives on Psychological Science",
	pages = "587–597",
	volume = "4",
	number = "6",
	year = "2009",
	doi = "10.1111/j.1745-6924.2009.01167.x",
	pymvpa-keywords = "statistics, hypothesis testing",
	pymvpa-summary = "Historical excurse into the life of 10 prominent statisticians of XXth century and their scientific contributions."
}

@Book{ Fis25,
	title = "Statistical methods for research workers",
	author = "Ronald A. Fisher",
	year = "1925",
	publisher = "Oliver and Boyd",
	address = "Edinburgh",
	url = "http://psychclassics.yorku.ca/Fisher/Methods/",
	pymvpa-keywords = "statistics, hypothesis testing",
	pymvpa-summary = "One of the 20th century's most influential books on statistical methods, which coined the term 'Test of significance'."
}

@Article{ MKE10,
	title = "Predicting visual stimuli based on activity in auditory cortices.",
	author = "Kaspar Meyer and Jonas T. Kaplan and Ryan Essex and Cecelia Webber and Hanna Damasio and Antonio Damasio",
	journal = "Nature Neuroscience",
	year = "2010",
	doi = "10.1038/nn.2533",
	journal-impact = "14.191"
}

@Article{ VS06,
	title = "Bias in error estimation when using cross-validation for model selection",
	author = "Sudhir Varma and Richard Simon",
	journal = "BMC Bioinformatics",
	pages = "91",
	volume = "7",
	year = "2006",
	issn = "1471-2105",
	abstract = {BACKGROUND: Cross-validation (CV) is an effective method for estimating the prediction error of a classifier. Some recent articles have proposed methods for optimizing classifiers by choosing classifier parameter values that minimize the CV error estimate. We have evaluated the validity of using the CV error estimate of the optimized classifier as an estimate of the true error expected on independent data. RESULTS: We used CV to optimize the classification parameters for two kinds of classifiers; Shrunken Centroids and Support Vector Machines (SVM). Random training datasets were created, with no difference in the distribution of the features between the two classes. Using these "null" datasets, we selected classifier parameter values that minimized the CV error estimate. 10-fold CV was used for Shrunken Centroids while Leave-One-Out-CV (LOOCV) was used for the SVM. Independent test data was created to estimate the true error. With "null" and "non null" (with differential expression between the classes) data, we also tested a nested CV procedure, where an inner CV loop is used to perform the tuning of the parameters while an outer CV is used to compute an estimate of the error. The CV error estimate for the classifier with the optimal parameters was found to be a substantially biased estimate of the true error that the classifier would incur on independent data. Even though there is no real difference between the two classes for the "null" datasets, the CV error estimate for the Shrunken Centroid with the optimal parameters was less than 30\% on 18.5\% of simulated training data-sets. For SVM with optimal parameters the estimated error rate was less than 30\% on 38\% of "null" data-sets. Performance of the optimized classifiers on the independent test set was no better than chance. The nested CV procedure reduces the bias considerably and gives an estimate of the error that is very close to that obtained on the independent testing set for both Shrunken Centroids and SVM classifiers for "null" and "non-null" data distributions. CONCLUSION: We show that using CV to compute an error estimate for a classifier that has itself been tuned using CV gives a significantly biased estimate of the true error. Proper use of CV for estimating true error of a classifier developed using a well defined algorithm requires that all steps of the algorithm, including classifier parameter tuning, be repeated in each CV loop. A nested CV procedure provides an almost unbiased estimate of the true error.},
	url = "http://www.ncbi.nlm.nih.gov/pubmed/16504092",
	doi = "10.1186/1471-2105-7-91",
	affiliation = "Biometric Research Branch, National Cancer Institute, Bethesda, MD, USA. varmas@mail.nih.gov",
	pymvpa-keywords = "statistical learning, model selection, error estimation, hypothesis testing",
	pymvpa-summary = "Demonstration of overfitting and introducing the bias in the error estimation using cross-validation on entire dataset for performing model selection."
}

@Book{ SS01,
	title = "{Learning with Kernels: Support Vector Machines, Regularization}",
	author = "B. Scholkopf and A.J. Smola",
	publisher = "MIT Press",
	address = "Cambridge, MA",
	journal = "Optimization, and Beyond.",
	pages = "2",
	edition = "1",
	month = "December",
	year = "2001",
	isbn = "0-262-19475-9",
	pymvpa-keywords = "statistical learning, kernel methods, error estimation",
	pymvpa-summary = "Good coverage of kernel methods and associated statistical learning aspects (e.g. error bounds)"
}

@Article{ SS09,
	title = "Python in Neuroscience",
	author = "Martin Spacek and Nicholas Swindale",
	journal = "The Neuromorphic Engineer",
	year = "2009",
	doi = "10.2417/1200907.1682",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ GF09,
	url = "http://www.ncbi.nlm.nih.gov/pubmed/19521545",
	volume = "3",
	year = "2009",
	journal = "Front Neuroinformatics",
	title = "OpenElectrophy: An Electrophysiological Data- and Analysis-Sharing Framework.",
	pages = "14",
	author = "Samuel Garcia and Nicolas Fourcaud-Trocmé",
	doi = "10.3389/neuro.11.014.2009",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ Ban09,
	title = "Seven topics in functional magnetic resonance imaging.",
	author = "Peter A Bandettini",
	journal = "Journal of Integrative Neuroscience",
	pages = "371–403",
	volume = "8",
	year = "2009",
	url = "http://www.ncbi.nlm.nih.gov/pubmed/19938211",
	pymvpa-keywords = "pymvpa-reference"
}

@InProceedings{ TRL09,
	title = "Development of an autonomous robot for ground penetrating radar surveys of polar ice",
	booktitle = "The 2009 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)",
	author = "Eric Trautmann and Laura Ray and Jim Lever",
	pages = "1685–1690 ",
	year = "2009",
	doi = "10.1109/IROS.2009.5354290",
	pymvpa-summary = "Study using PyMVPA to perform immobilization detection to improve navigation reliability of an autonomous robot."
}

@InProceedings{ OVG+10,
	title = "Brain Connectivity Analysis by Reduction to Pair Classification",
	booktitle = "The 2nd IAPR International Workshop on Cognitive Information Processing",
	author = "Emanuele Olivetti and Sriharsha Veeramachaneni and Susanne Greiner and Paolo Avesani",
	year = "2010"
}

@Article{ MBL+10,
	title = "Resting developments: a review of fMRI post-processing methodologies for spontaneous brain activity.",
	author = "Daniel S Margulies and Joachim Böttger and Xiangyu Long and Yating Lv and Clare Kelly and Alexander Schäfer and Dirk Goldhahn and Alexander Abbushi and Michael P Milham and Gabriele Lohmann and Arno Villringer",
	journal = "Magnetic Resonance Materials in Physics, Biology and Medicine",
	pages = "289–307",
	volume = "23",
	year = "2010",
	url = "http://www.ncbi.nlm.nih.gov/pubmed/20972883",
	doi = "10.1007/s10334-010-0228-5",
	pymvpa-keywords = "pymvpa-reference"
}

@InProceedings{ LB10,
	title = "An Application of Pattern Matching for the Adjustment of Quality of Service Metrics",
	booktitle = "The International Conference on Emerging Network Intelligence",
	author = "D. Legge and A. Badii",
	volume = "2",
	year = "2010",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ WTB+10,
	title = "Multi-voxel coding of stimuli, rules, and responses in human frontoparietal cortex.",
	author = "Alexandra Woolgar and Russell Thompson and Daniel Bor and John Duncan",
	journal = "NeuroImage",
	year = "2010",
	url = "http://www.ncbi.nlm.nih.gov/pubmed/20406690",
	doi = "10.1016/j.neuroimage.2010.04.035",
	journal-impact = "5.937"
}

@Article{ LaC10,
	title = "Decoding fMRI brain states in real-time.",
	author = "Stephen M Laconte",
	journal = "NeuroImage",
	year = "2010",
	url = "http://www.ncbi.nlm.nih.gov/pubmed/20600972",
	doi = "10.1016/j.neuroimage.2010.06.052",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ Shi10,
	title = "Perspectives on Modeling in Cognitive Science",
	author = "R.M. Shiffrin",
	publisher = "Wiley Online Library",
	journal = "Topics in Cognitive Science",
	pages = "736–750",
	volume = "2",
	year = "2010",
	doi = "10.1111/j.1756-8765.2010.01092.x",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ CAS+10,
	url = "http://www.ncbi.nlm.nih.gov/pubmed/20661296",
	volume = "4:47",
	year = "2010",
	journal = "Frontiers in Human Neuroscience",
	title = "Decoding developmental differences and individual variability in response inhibition through predictive analyses across individuals.",
	author = "Jessica R Cohen and Robert F Asarnow and Fred W Sabb and Robert M Bilder and Susan Y Bookheimer and Barbara J Knowlton and Russell A Poldrack",
	doi = "10.3389/fnhum.2010.00047",
	journal-impact = "2.906"
}

@Article{ HGC+11,
	title = "A Common, High-Dimensional Model of the Representational Space in Human Ventral Temporal Cortex",
	author = "James V. Haxby and J. Swaroop Guntupalli and Andrew C. Connolly and Yaroslav O. Halchenko and Bryan R. Conroy and M. Ida Gobbini and Michael Hanke and Peter J. Ramadge",
	publisher = "Cell Press,",
	journal = "Neuron",
	pages = "404–416",
	volume = "72",
	number = "2",
	month = "Oct",
	year = "2011",
	issn = "0896-6273",
	doi = "10.1016/j.neuron.2011.08.026",
	url = "http://www.cell.com/neuron/abstract/S0896-6273%2811%2900781-1",
	journal-impact = "14.736",
	pymvpa-keywords = "pymvpa, hyperalignment"
}

@InProceedings{ GWC10,
	title = "Scribe Identification in Medieval English Manuscripts",
	booktitle = " Proceedings of the International Conference on Pattern Recognition",
	author = "Tara Gilliam and Richard C. Wilson and John A. Clark",
	year = "2010",
	url = "ftp://ftp.computer.org/press/outgoing/proceedings/juan/icpr10b/data/4109b880.pdf"
}

@Article{ CSM+10,
	url = "http://www.ncbi.nlm.nih.gov/pubmed/20347995",
	year = "2010",
	journal = "NeuroImage",
	title = "Within- and cross-participant classifiers reveal different neural coding of information.",
	author = "John A Clithero and David V Smith and R McKell Carter and Scott A Huettel",
	doi = "10.1016/j.neuroimage.2010.03.057",
	journal-impact = "5.937"
}

@Article{ MKE+11,
	title = "Seeing Touch Is Correlated with Content-Specific Activity in Primary Somatosensory Cortex",
	author = "Kaspar Meyer and Jonas T Kaplan and Ryan Essex and Hanna Damasio and Antonio Damasio",
	journal = "Cerebral Cortex",
	year = "2011",
	url = "http://www.ncbi.nlm.nih.gov/pubmed/21330469",
	doi = "10.1093/cercor/bhq289",
	journal-impact = "6.544"
}

@Article{ SSS+11,
	title = "The integration of negative affect, pain and cognitive control in the cingulate cortex",
	author = "Alexander J Shackman and Tim V Salomons and Heleen A Slagter and Andrew S Fox and Jameel J Winter and Richard J Davidson",
	journal = "Nature Reviews Neuroscience",
	pages = "154–167",
	volume = "12",
	year = "2011",
	url = "http://www.ncbi.nlm.nih.gov/pubmed/21331082",
	doi = "10.1038/nrn2994",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ PSR11,
	issn = "1664-1078",
	volume = "2",
	year = "2011",
	journal = "Front Psychol",
	title = "Single-trial analyses: why bother?",
	pages = "322",
	author = "Cyril R Pernet and Paul Sajda and Guillaume A Rousselet",
	doi = "10.3389/fpsyg.2011.00322",
	affiliation = "Brain Research Imaging Centre, SINAPSE Collaboration, University of Edinburgh Edinburgh, UK.",
	pymvpa-keywords = "pymvpa-reference"
}

@Article{ JP11,
	title = "Analyses of regional-average activation and multivoxel pattern information tell complementary stories",
	author = "K. Jimura and R.A. Poldrack",
	publisher = "Elsevier",
	journal = "Neuropsychologia",
	year = "2011",
	doi = "10.1016/j.neuropsychologia.2011.11.007",
	journal-impact = "3.636"
}

@Article{ CCK+11,
	issn = "1879-0445",
	volume = "21",
	number = "21",
	year = "2011",
	month = "nov",
	journal = "Curr Biol",
	title = "A head view-invariant representation of gaze direction in anterior superior temporal sulcus",
	pages = "1817–21",
	author = "Johan D Carlin and Andrew J Calder and Nikolaus Kriegeskorte and Hamed Nili and James B Rowe",
	doi = "10.1016/j.cub.2011.09.025",
	affiliation = "Medical Research Council Cognition and Brain Sciences Unit, 15 Chaucer Road, Cambridge CB2 7EF, UK.",
	journal-impact = "9.647"
}

@Article{ RC12,
	title = "What makes different people's representations alike: neural similarity-space solves the problem of across-subject f{MRI} decoding",
	author = "Rajeev D.S. Raizada and Andrew C. Connolly",
	journal = "Journal of Cognitive Neuroscience",
	year = "2012",
	volume = "24",
	pages = "868--877",
	url = "http://raizadalab.org/publications.html",
	journal-impact = "4.493"
}

@article{ OWD+11,
author = {Oosterhof, Nikolaas N and Wiestler, Tobias and Downing, Paul E and Diedrichsen, Jörn},
title = {A comparison of volume-based and surface-based multi-voxel pattern analysis.},
journal = {NeuroImage},
year = {2011},
volume = {56},
number = {2},
pages = {593--600},
}


@inproceedings{ OGA2012,
	year =		 {2012},
	isbn =		 {978-3-642-34712-2},
	booktitle =	 {Machine Learning and Interpretation in Neuroimaging},
	volume =		 {7263},
	series =		 {Lecture Notes in Computer Science},
	editor =		 {Langs, Georg and Rish, Irina and Grosse-Wentrup,
	                Moritz and Murphy, Brian},
	doi =			 {10.1007/978-3-642-34713-9_6},
	title =		 {Induction in Neuroscience with Classification:
	                Issues and Solutions},
	publisher =	 {Springer Berlin Heidelberg},
	author =		 {Olivetti, Emanuele and Greiner, Susanne and Avesani,
	                Paolo},
	pages =		 {42-50}
}

@article{PVG+11,
	author = {Pedregosa, Fabian and Varoquaux, Gael and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Edouard},
	title = {Scikit-learn: Machine Learning in Python},
	journal = {Journal of Machine Learning Research},
	volume = {12},
	year = {2011},
	pages = {2825--2830},
	url = {http://dl.acm.org/citation.cfm?id=1953048.2078195},
	pymvpa-keywords = "pymvpa-reference"
}

@article{PB11,
	title={Information mapping with pattern classifiers: a comparative study},
	author={Pereira, Francisco and Botvinick, Matthew},
	journal={Neuroimage},
	volume={56},
	pages={476--496},
	year={2011},
	doi ={10.1016/j.neuroimage.2010.05.026},
	pymvpa-keywords = "pymvpa-reference"
}

@article{VCL11,
	title = "Ubiquity and Specificity of Reinforcement Signals throughout the Human Brain ",
	journal = "Neuron ",
	volume = "72",
	pages = "166--177",
	year = "2011",
	doi = "http://dx.doi.org/10.1016/j.neuron.2011.08.011",
	url = "http://www.sciencedirect.com/science/article/pii/S089662731100732X",
	author = "Timothy J. Vickery and Marvin M. Chun and Daeyeol Lee",
	journal-impact = "14.736"
}

@article{HS11,
	title={High-resolution imaging of the fusiform face area (FFA) using multivariate non-linear classifiers shows diagnosticity for non-face categories},
	author={Hanson, Stephen José  and Schmidt, Arielle},
	journal={NeuroImage},
	volume={54},
	pages={1715--1734},
	year={2011},
	doi = {10.1016/j.neuroimage.2010.08.02},
	pymvpa-keywords = "pymvpa-reference"
}

@article{HRB+11,
	title={Predicting decisions in human social interactions using real-time fMRI and pattern classification},
	author={Hollmann, Maurice and Rieger, Jochem W and Baecke, Sebastian and Lützkendorf, Ralf and Müller, Charles and Adolf, Daniela and Bernarding, Johannes},
	journal={PloS one},
	volume={6},
	pages={e25304},
	year={2011},
	doi = {10.1371/journal.pone.0025304},
	pymvpa-keywords = "pymvpa-reference"
}

@article{EDT+12,
	title={Predicting errors from reconfiguration patterns in human brain networks},
	author={Ekman, Matthias and Derrfuss, Jan and Tittgemeyer, Marc and Fiebach, Christian J},
	journal={Proceedings of the National Academy of Sciences},
	volume={109},
	pages={16714--16719},
	year={2012},
	doi = {10.1073/pnas.1207523109},
	journal-impact = {9.737}
}

@article{CEZ+11,
	title={Rapid transfer of abstract rules to novel contexts in human lateral prefrontal cortex},
	author={Cole, Michael W and Etzel, Joset A and Zacks, Jeffrey M and Schneider, Walter and Braver, Todd S},
	journal={Frontiers in Human Neuroscience},
	volume={5},
	year={2011},
	doi = {10.3389/fnhum.2011.00142},
	journal-impact = {2.906}
}

@article{MSB+12,
	title={Perception of words and pitch patterns in song and speech},
	author={Merrill, Julia and Sammler, Daniela and Bangert, Marc and Goldhahn, Dirk and Lohmann, Gabriele and Turner, Robert and Friederici, Angela D},
	journal={Frontiers in psychology},
	volume={3},
	pages = {76},
	year={2012},
	doi = {10.3389/fpsyg.2012.000}
}

@article{ST12,
	title={Statistical inference and multiple testing correction in classification-based multi-voxel pattern analysis (MVPA): Random permutations and cluster size control},
	author={Stelzer, Johannes and Chen, Yi and Turner, Robert},
	journal={NeuroImage},
	volume = {65},
	pages = {69--82},
	year={2012},
	doi = {10.1016/j.neuroimage.2012.09.063},
	journal-impact = {6.252},
	pymvpa-keywords = "pymvpa-reference"
}

@article{vdL+12,
	title={Appearance matters: neural correlates of food choice and packaging aesthetics},
	author={Van der Laan, Laura N and De Ridder, Denise TD and Viergever, Max A and Smeets, Paul AM},
	journal={PloS one},
	volume={7},
	number={7},
	pages={e41738},
	year={2012},
	doi = {10.1371/journal.pone.0041738},
	journal-impact = {3.730}
}

@article{AVM+12,
	title={mlpy: machine learning Python},
	author={Albanese, Davide and Visintainer, Roberto and Merler, Stefano and Riccadonna, Samantha and Jurman, Giuseppe and Furlanello, Cesare},
	journal={arXiv preprint arXiv:1202.6548},
	year={2012},
	pymvpa-keywords = "pymvpa-reference"
}

@article{CBR+12,
	title={A distinct role of the temporal-parietal junction in predicting socially guided decisions},
	author={Carter, R McKell and Bowling, Daniel L and Reeck, Crystal and Huettel, Scott A},
	journal={Science},
	volume={337},
	number={6090},
	pages={109--111},
	year={2012},
	doi = {10.1126/science.1219681},
	journal-impact = {31.027}
}

@article{KM12,
	title={Multivariate pattern analysis reveals common neural patterns across individuals during touch observation},
	author={Kaplan, Jonas T and Meyer, Kaspar},
	journal={Neuroimage},
	volume={60},
	pages={204--212},
	year={2012},
	doi={10.1016/j.neuroimage.2011.12.059},
	journal-impact = {6.252}
}

@article{JK12,
	title={Improving robot manipulation with data-driven object-centric models of everyday forces},
	author={Jain, Advait and Kemp, Charles C},
	journal={Autonomous Robots},
	pages={1--17},
	year={2012},
	doi={10.1007/s10514-013-9344-1},
	url={http://www.hrl.gatech.edu/pdf/improve_everyday_forces.pdf}
}

@article{SRR+13,
	title={PRoNTo: Pattern Recognition for Neuroimaging Toolbox},
	author={Schrouff, Jessica and Rosa, Maria Joao and Rondina, JM and Marquand, AF and Chu, Carlton and Ashburner, John and Phillips, Christophe and Richiardi, Jonas and Mourão-Miranda, Janaina},
	journal={Neuroinformatics},
	pages={1--19},
	year={2013},
	doi = {10.1007/s12021-013-9178-1},
	pymvpa-keywords = "pymvpa-reference"
}

@article{KKD+12,
	title={Sight and sound converge to form modality-invariant representations in temporoparietal cortex},
	author={Man, Kingson and Kaplan, Jonas T and Damasio, Antonio and Meyer, Kaspar},
	journal={The Journal of Neuroscience},
	volume={32},
	number={47},
	pages={16629--16636},
	year={2012},
	doi = {10.1523/JNEUROSCI.2342-12.2012}
}

@article{SFK+12,
	title={Interpersonal liking modulates motor-related neural regions},
	author={Sobhani, Mona and Fox, Glenn R and Kaplan, Jonas and Aziz-Zadeh, Lisa},
	journal={PloS one},
	volume={7},
	number={10},
	pages={e46809},
	year={2012},
	doi = {10.1371/journal.pone.0046809},
	journal-impact = {3.730}
}

@article{FWJ+12,
	title={Toward Fast Determination of Protein Stability Maps: Experimental and Theoretical Analysis of Mutants of a Nocardiopsis prasina Serine Protease},
	author={Farrell, Damien and Webb, Helen and Johnston, Michael A and Poulsen, Thomas A and O’Meara, Fergal and Christensen, Lars LH and Beier, Lars and Borchert, Torben V and Nielsen, Jens Erik},
	journal={Biochemistry},
	volume={51},
	number={26},
	pages={5339--5347},
	year={2012},
	doi={10.1021/bi201926f},
	journal-impact = {3.377}
}

@article{VCG12,
	title={On the geometric structure of fMRI searchlight-based information maps},
	author={Viswanathan, Shivakumar and Cieslak, Matthew and Grafton, Scott T},
	journal={arXiv preprint arXiv:1210.6317},
	year={2012}
}

@article{LMH+13,
	title={Primary sensory cortices contain distinguishable spatial patterns of activity for each sense},
	author={Liang, M and Mouraux, A and Hu, L and Iannetti, GD},
	journal={Nature communications},
	volume={4},
	year={2013},
	doi={10.1038/ncomms2979},
	pymvpa-keywords = "pymvpa"
}

@article{AHL+13,
	title={Penalized Likelihood Phenotyping: Unifying Voxelwise Analyses and Multi-Voxel Pattern Analyses in Neuroimaging},
	author={Adluru, Nagesh and Hanlon, Bret M and Lutz, Antoine and Lainhart, Janet E and Alexander, Andrew L and Davidson, Richard J},
	journal={Neuroinformatics},
	pages={1--21},
	year={2013},
	doi={10.1007/s12021-012-9175-9},
	pymvpa-keywords = "pymvpa-reference"
}

@article{MRO13,
	title={Category-dependent and category-independent goal-value codes in human ventromedial prefrontal cortex},
	author={McNamee, Daniel and Rangel, Antonio and O'Doherty, John P},
	journal={Nature neuroscience},
	volume={16},
	number={4},
	pages={479--485},
	year={2013},
	doi={10.1038/nn.3337},
	pymvpa-keywords = "pymvpa"
}

@article{MK11,
	title={Cross-Modal Multivariate Pattern Analysis},
	author={Meyer, Kaspar and Kaplan, Jonas T},
	journal={Journal of visualized experiments: JoVE},
	number={57},
	year={2011},
	doi={10.3791/3307},
	pymvpa-keywords = "pymvpa-reference"
}

@article{SPB+13,
	title={Multivoxel Pattern Analysis Reveals Auditory Motion Information in MT+ of Both Congenitally Blind and Sighted Individuals},
	author={Strnad, Lukas and Peelen, Marius V and Bedny, Marina and Caramazza, Alfonso},
	journal={PloS one},
	volume={8},
	number={4},
	pages={e63198},
	year={2013},
	doi={10.1371/journal.pone.0063198},
	pymvpa-keywords = "pymvpa"
}

@article{ARV+13,
	title={7T fMRI reveals feasibility of covert visual attention-based brain--computer interfacing with signals obtained solely from cortical grey matter accessible by subdural surface electrodes},
	author={Andersson, Patrik and Ramsey, Nick F and Viergever, Max A and Pluim, Josien PW},
	journal={Clinical Neurophysiology},
	year={2013},
	pymvpa-keywords = "pymvpa"
}

@article{BHG+13,
	title={Evidence for feature binding in the superior parietal lobule},
	author={Baumgartner, F. and Hanke, M. and Geringswald, F. and Zinke, W. and Speck, O. and Pollmann, S.},
	journal={NeuroImage},
	volume={68},
	pages={173--180},
	year={2013},
	doi={10.1016/j.neuroimage.2012.12.002},
	pymvpa-keywords = "pymvpa"
}

@article{LB13,
	title={Cortical representation of medial axis structure},
	author={Lescroart, Mark D and Biederman, Irving},
	journal={Cerebral Cortex},
	volume={23},
	number={3},
	pages={629--637},
	year={2013},
	doi={10.1093/cercor/bhs046},
	pymvpa-keywords = "pymvpa"
}

@article{SCR+13,
	title={Decoding the anatomical network of spatial attention},
	author={Smith, David V and Clithero, John A and Rorden, Christopher and Karnath, Hans-Otto},
	journal={Proceedings of the National Academy of Sciences},
	volume={110},
	number={4},
	pages={1518--1523},
	year={2013},
	doi={10.1073/pnas.1210126110},
	pymvpa-keywords = "pymvpa"
}

@article{HSN+13,
	title={Imagine all the people: How the brain creates and uses personality models to predict behavior},
	author={Hassabis, Demis and Spreng, R Nathan and Rusu, Andrei A and Robbins, Clifford A and Mar, Raymond A and Schacter, Daniel L},
	journal={Cerebral Cortex},
	year={2013},
	doi={10.1093/cercor/bht042},
	pymvpa-keywords = "pymvpa"
}

@article{KFR+13,
	title={Pattern classification precedes region-average hemodynamic response in early visual cortex},
	author={Kohler, Peter J and Fogelson, Sergey V and Reavis, Eric A and Meng, Ming and Guntupalli, J Swaroop and Hanke, Michael and Halchenko, Yaroslav O and Connolly, Andrew C and Haxby, James V and Tse, Peter U},
	journal={NeuroImage},
	year={2013},
	volume={78},
	pages={249--260},
	doi={10.1016/j.neuroimage.2013.04.019},
	pymvpa-keywords = "pymvpa"
}

@article{MR13,
	author = {Manelis, Anna and Reder, Lynne M.},
	title = {He Who Is Well Prepared Has Half Won The Battle: An fMRI Study of Task Preparation},
	year = {2013},
	doi = {10.1093/cercor/bht262},
	URL = {http://cercor.oxfordjournals.org/content/early/2013/10/02/cercor.bht262.abstract},
	eprint = {http://cercor.oxfordjournals.org/content/early/2013/10/02/cercor.bht262.full.pdf+html},
	journal = {Cerebral Cortex},
	pymvpa-keywords = "pymvpa"
}

@article{ARV+13,
	title={7T fMRI reveals feasibility of covert visual attention-based brain–computer interfacing with signals obtained solely from cortical grey matter accessible by subdural surface electrodes},
	author={Patrik Andersson and Nick F. Ramsey and Max A. Viergever and Josien P.W. Pluim},
	journal={Clinical neurophysiology},
	year={2013},
	volume={124},
	pages={2191--2197},
	doi={10.1016/j.clinph.2013.05.009},
	pymvpa-keywords = "pymvpa"
}

@article{HBI+14,
	title={A high-resolution 7-Tesla fMRI dataset from complex natural stimulation with an audio movie},
	author={Michael Hanke and Florian J. Baumgartner and Pierre Ibe and Falko R. Kaule and Stefan Pollmann and Oliver Speck and Wolf Zinke and Jörg Stadler},
	journal={Scientific Data},
	year={in press},
	URL = {http://www.studyforrest.org},
	pymvpa-keywords = "pymvpa"
}

@article{HSC+14,
	author = {Helfinstein, Sarah M. and Schonberg, Tom and Congdon, Eliza and Karlsgodt, Katherine H. and Mumford, Jeanette A. and Sabb, Fred W. and Cannon, Tyrone D. and London, Edythe D. and Bilder, Robert M. and Poldrack, Russell A.},
	title = {Predicting risky choices from brain activity patterns},
	volume = {111},
	pages = {2470--2475},
	year = {2014},
	doi = {10.1073/pnas.1321728111},
	URL = {http://www.pnas.org/content/111/7/2470.abstract},
	journal = {Proceedings of the National Academy of Sciences},
	pymvpa-keywords = "pymvpa"
}

@article{REA+14,
	author = {Shirley-Ann Rueschemeyer and Matthias Ekman and Markus van Ackeren and James Kilner},
	title = {Observing, Performing, and Understanding Actions: Revisiting the Role of Cortical Motor Areas in Processing of Action Words},
	year = {2014},
	doi = {10.1162/jocn_a_00576},
	journal = {Journal of Cognitive Neuroscience},
	pymvpa-keywords = "pymvpa"
}

@article{HCG14,
	title={Decoding neural representational spaces using multivariate pattern analysis},
	author={Haxby, James V and Connolly, Andrew C and Guntupalli, J Swaroop},
	journal={Annual review of neuroscience},
	volume={37},
	pages={435--456},
	year={2014},
	publisher={Annual Reviews},
	pymvpa-keywords = "pymvpa-reference"
}

@article{GSD+15,
	title={Photometric Redshifts and Model Spectral Energy Distributions of Galaxies From the SDSS-III BOSS DR10 Data},
	author={Greisel, N and Seitz, S and Drory, N and Bender, R and Saglia, RP and Snigula, J},
	journal={arXiv preprint arXiv:1505.01157},
	year={2015},
	URL={http://arxiv.org/abs/1505.01157},
	pymvpa-keywords = "pymvpa"
}

@article{McMLZ+15,
	title={Characterizing the Associative Content of Brain Structures Involved in Habitual and Goal-Directed Actions in Humans: A Multivariate f{MRI} Study},
	author={McNamee, Daniel and Liljeholm, Mimi and Zika, Ondrej and O'Doherty, John P},
	journal={The Journal of Neuroscience},
	volume={35},
	number={9},
	pages={3764--3771},
	year={2015},
	DOI={10.1523/JNEUROSCI.4677-14.2015},
	pymvpa-keywords = "pymvpa"
}


@article{SHA+14,
	title={The Animacy Continuum in the Human Ventral Vision Pathway},
	author={Sha, Long and Haxby, James V and Abdi, Herve and Guntupalli, J Swaroop and Oosterhof, Nikolaas N and Halchenko, Yaroslav O and Connolly, Andrew C},
	year={2014},
	journal={Journal of Cognitive Neuroscience},
	publisher={MIT Press},
	doi={10.1162/jocn_a_00733},
	pymvpa-keywords = "pymvpa"
}


@article{SDV+14,
	doi = {10.1093/cercor/bhu124},
	url = {http://dx.doi.org/10.1093/cercor/bhu124},
	year  = {2014},
	month = {jun},
	publisher = {Oxford University Press ({OUP})},
	author = {M. Schönwiesner and P. Dechent and D. Voit and C. I. Petkov and K. Krumbholz},
	title = {Parcellation of Human and Monkey Core Auditory Cortex with {fMRI} Pattern Classification and Objective Detection of Tonotopic Gradient Reversals},
	journal = {Cerebral Cortex},
	pymvpa-keywords = "pymvpa"
}

@article{KZ14,
	doi = {10.1093/cercor/bhu003},
	url = {http://dx.doi.org/10.1093/cercor/bhu003},
	year  = {2014},
	month = {jan},
	publisher = {Oxford University Press ({OUP})},
	author = {M. E. Klein and R. J. Zatorre},
	title = {Representations of Invariant Musical Categories Are Decodable by Pattern Analysis of Locally Distributed {BOLD} Responses in Superior Temporal and Intraparietal Sulci},
	journal = {Cerebral Cortex},
	pymvpa-keywords = "pymvpa"
}



@article{HS14,
	doi = {10.1002/hipo.22321},
	url = {http://dx.doi.org/10.1002/hipo.22321},
	year  = {2014},
	month = {jul},
	publisher = {Wiley-Blackwell},
	volume = {24},
	number = {11},
	pages = {1394--1403},
	author = {Derek J. Huffman and Craig E.L. Stark},
	title = {Multivariate pattern analysis of the human medial temporal lobe revealed representationally categorical cortex and representationally agnostic hippocampus},
	journal = {Hippocampus},
	pymvpa-keywords = "pymvpa"
}


@article{CIB15,
	doi = {10.1093/cercor/bhv072},
	url = {http://dx.doi.org/10.1093/cercor/bhv072},
	year  = {2015},
	month = {apr},
	publisher = {Oxford University Press ({OUP})},
	author = {M. W. Cole and T. Ito and T. S. Braver},
	title = {The Behavioral Relevance of Task Information in Human Prefrontal Cortex},
	journal = {Cerebral Cortex},
	pymvpa-keywords = "pymvpa"
}



@article{ALR+14,
  doi = {10.1016/j.neuroimage.2013.09.048},
  url = {http://dx.doi.org/10.1016/j.neuroimage.2013.09.048},
  year  = {2014},
  month = {jan},
  publisher = {Elsevier {BV}},
  volume = {84},
  pages = {698--711},
  author = {Brian B. Avants and David J. Libon and Katya Rascovsky and Ashley Boller and Corey T. McMillan and Lauren Massimo and H. Branch Coslett and Anjan Chatterjee and Rachel G. Gross and Murray Grossman},
  title = {Sparse canonical correlation analysis relates network-level atrophy to multivariate cognitive measures in a neurodegenerative population},
  journal = {{NeuroImage}},
  pymvpa-keywords = "pymvpa-reference"
}



@article{SAF+15,
	doi = {10.1016/j.neuroimage.2014.11.014},
	url = {http://dx.doi.org/10.1016/j.neuroimage.2014.11.014},
	year  = {2015},
	month = {jan},
	publisher = {Elsevier {BV}},
	volume = {105},
	pages = {440--451},
	author = {Alexander Schlegel and Prescott Alexander and Sergey V. Fogelson and Xueting Li and Zhengang Lu and Peter J. Kohler and Enrico Riley and Peter U. Tse and Ming Meng},
	title = {The artist emerges: Visual art learning alters neural structure and function},
	journal = {{NeuroImage}},
	pymvpa-keywords = "pymvpa"
}



@article{Kas14,
	doi = {10.1016/j.neunet.2014.01.006},
	url = {http://dx.doi.org/10.1016/j.neunet.2014.01.006},
	year  = {2014},
	month = {apr},
	publisher = {Elsevier {BV}},
	volume = {52},
	pages = {62--76},
	author = {Nikola K. Kasabov},
	title = {{NeuCube}: A spiking neural network architecture for mapping,  learning and understanding of spatio-temporal brain data},
	journal = {Neural Networks},
}

@article{JCS+14,
	doi = {10.3389/fnhum.2014.00339},
	url = {http://dx.doi.org/10.3389/fnhum.2014.00339},
	year  = {2014},
	month = {may},
	publisher = {Frontiers Media {SA}},
	volume = {8},
	author = {Koji Jimura and Fabienne Cazalis and Elena R. S. Stover and Russell A. Poldrack},
	title = {The neural basis of task switching changes with skill acquisition},
	journal = {Front. Hum. Neurosci.},
	pymvpa-keywords = "pymvpa"
}

@article{LMcC14,
	doi = {10.1093/cercor/bhu292},
	url = {http://dx.doi.org/10.1093/cercor/bhu292},
	year  = {2014},
	month = {dec},
	publisher = {Oxford University Press ({OUP})},
	author = {S. M. Lee and G. McCarthy},
	title = {Functional Heterogeneity and Convergence in the Right Temporoparietal Junction},
	journal = {Cerebral Cortex},
	pymvpa-keywords = "pymvpa"
}

@article{WHA14,
	doi = {10.1016/j.neuroimage.2014.05.045},
	url = {http://dx.doi.org/10.1016/j.neuroimage.2014.05.045},
	year  = {2014},
	month = {oct},
	publisher = {Elsevier {BV}},
	volume = {99},
	pages = {402--410},
	author = {David M. Watson and Tom Hartley and Timothy J. Andrews},
	title = {Patterns of response to visual scenes are linked to the low-level properties of the image},
	journal = {{NeuroImage}},
	pymvpa-keywords = "pymvpa"
}

@article{SP14,
	doi = {10.1073/pnas.1404396111},
	url = {http://dx.doi.org/10.1073/pnas.1404396111},
	year  = {2014},
	month = {oct},
	publisher = {Proceedings of the National Academy of Sciences},
	volume = {111},
	number = {44},
	pages = {15845--15850},
	author = {M. L. Schlichting and A. R. Preston},
	title = {Memory reactivation during rest supports upcoming learning of related content},
	journal = {Proceedings of the National Academy of Sciences},
	pymvpa-keywords = "pymvpa"
}

@article{MBT+14,
	doi = {10.1523/jneurosci.2062-14.2014},
	url = {http://dx.doi.org/10.1523/JNEUROSCI.2062-14.2014},
	year  = {2014},
	month = {dec},
	publisher = {Society for Neuroscience},
	volume = {34},
	number = {49},
	pages = {16286--16295},
	author = {M. Mittner and W. Boekel and A. M. Tucker and B. M. Turner and A. Heathcote and B. U. Forstmann},
	title = {When the Brain Takes a Break: A Model-Based Analysis of Mind Wandering},
	journal = {Journal of Neuroscience},
	pymvpa-keywords = "pymvpa"
}

@article{WLM+14,
	doi = {10.1523/jneurosci.0351-14.2014},
	url = {http://dx.doi.org/10.1523/JNEUROSCI.0351-14.2014},
	year  = {2014},
	month = {may},
	publisher = {Society for Neuroscience},
	volume = {34},
	number = {22},
	pages = {7522--7530},
	author = {Q. Wang and S. Luo and J. Monterosso and J. Zhang and X. Fang and Q. Dong and G. Xue},
	title = {Distributed Value Representation in the Medial Prefrontal Cortex during Intertemporal Choices},
	journal = {Journal of Neuroscience},
	pymvpa-keywords = "pymvpa"
}

@article{PLW14,
	doi = {10.1523/jneurosci.2159-13.2014},
	url = {http://dx.doi.org/10.1523/JNEUROSCI.2159-13.2014},
	year  = {2014},
	month = {jan},
	publisher = {Society for Neuroscience},
	volume = {34},
	number = {5},
	pages = {1979--1987},
	author = {C. Parkinson and S. Liu and T. Wheatley},
	title = {A Common Cortical Metric for Spatial,  Temporal,  and Social Distance},
	journal = {Journal of Neuroscience},
	pymvpa-keywords = "pymvpa"
}

@article{KLE+14,
	doi = {10.3389/fnhum.2014.00632},
	url = {http://dx.doi.org/10.3389/fnhum.2014.00632},
	year  = {2014},
	month = {aug},
	publisher = {Frontiers Media {SA}},
	volume = {8},
	author = {Na Yeon Kim and Su Mei Lee and Margret C. Erlendsdottir and Gregory McCarthy},
	title = {Discriminable spatial patterns of activation for faces and bodies in the fusiform gyrus},
	journal = {Front. Hum. Neurosci.},
	pymvpa-keywords = "pymvpa"
}


@article{GM15,
	doi = {10.1016/j.neuroimage.2015.04.006},
	url = {http://dx.doi.org/10.1016/j.neuroimage.2015.04.006},
	year  = {2015},
	month = {apr},
	publisher = {Elsevier {BV}},
	author = {Bingbing Guo and Ming Meng},
	title = {The encoding of category-specific versus nonspecific information in human inferior temporal cortex},
	journal = {{NeuroImage}},
	pymvpa-keywords = "pymvpa"
}

@article{PZB+14,
	doi = {10.1016/j.neuroimage.2014.07.021},
	url = {http://dx.doi.org/10.1016/j.neuroimage.2014.07.021},
	year  = {2014},
	month = {nov},
	publisher = {Elsevier {BV}},
	volume = {101},
	pages = {289--297},
	author = {Stefan Pollmann and Wolf Zinke and Florian Baumgartner and Franziska Geringswald and Michael Hanke},
	title = {The right temporo-parietal junction contributes to visual feature binding},
	journal = {{NeuroImage}},
	pymvpa-keywords = "pymvpa"
}

@article{FKM+14,
	doi = {10.3389/fpsyg.2014.00601},
	url = {http://dx.doi.org/10.3389/fpsyg.2014.00601},
	year  = {2014},
	month = {jun},
	publisher = {Frontiers Media {SA}},
	volume = {5},
	author = {Sergey V. Fogelson and Peter J. Kohler and Kevin J. Miller and Richard Granger and Peter U. Tse},
	title = {Unconscious neural processing differs with method used to render stimuli invisible},
	journal = {Frontiers in Psychology},
	pymvpa-keywords = "pymvpa"
}

@article{PSE14,
	doi = {10.1080/17470919.2014.978026},
	url = {http://dx.doi.org/10.1080/17470919.2014.978026},
	year  = {2014},
	month = {nov},
	publisher = {Informa {UK} Limited},
	volume = {10},
	number = {2},
	pages = {113--125},
	author = {Mark Plitt and Ricky R. Savjani and David M. Eagleman},
	title = {Are corporations people too? The neural correlates of moral judgments about companies and individuals},
	journal = {Social Neuroscience},
	pymvpa-keywords = "pymvpa"
}

@article{KWO14,
	doi = {10.1167/14.9.11},
	url = {http://dx.doi.org/10.1167/14.9.11},
	year  = {2014},
	month = {jul},
	publisher = {Association for Research in Vision and Ophthalmology ({ARVO})},
	volume = {14},
	number = {9},
	pages = {11--11},
	author = {J. Kubilius and J. Wagemans and H. P. Op de Beeck},
	title = {Encoding of configural regularity in the human visual system},
	journal = {Journal of Vision},
	pymvpa-keywords = "pymvpa"
}

@article{HPL+14,
	doi = {10.1007/s10515-014-0157-z},
	url = {http://dx.doi.org/10.1007/s10515-014-0157-z},
	year  = {2014},
	month = {nov},
	publisher = {Springer Science + Business Media},
	volume = {22},
	number = {2},
	pages = {159--197},
	author = {Constance L. Heitmeyer and Marc Pickett and Elizabeth I. Leonard and Myla M. Archer and Indrakshi Ray and David W. Aha and J. Gregory Trafton},
	title = {Building high assurance human-centric decision systems},
	journal = {Autom Softw Eng},
	pymvpa-keywords = "pymvpa"
}

@article{HGH2015,
	doi={10.3389/fninf.2014.00088},
	author={Hebart, M. N. and Görgen, K. and Haynes, J.-D.},
	title={The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data},
	journal={Frontiers in Neuroinformatics},
	volume={8},
	number={88}
}

@article{ GHH+16,
	title = {A Model of Representational Spaces in Human Cortex},
	author = {Guntupalli, J. Swaroop and Hanke, Michael and Halchenko, Yaroslav O. and Connolly, Andrew C. and Ramadge, Peter J. and Haxby, James V.},
	ISSN = {1047-3211, 1460-2199},
	DOI = {10.1093/cercor/bhw068},
	note = {PMID: 26980615},
	journal = {Cerebral Cortex},
	year = {2016},
	month = {Mar},
	pymvpa-keywords = "pymvpa, hyperalignment"
}
