(Meta)Data and workflow management for your most important work and your daily routine (2018) Document |
A Common, High-Dimensional Model of the Representational Space in Human Ventral Temporal Cortex (2011) AcademicArticle |
A communication hub for a decentralized collaboration on studying real-life cognition (2015) AcademicArticle |
A comparison of neuroelectrophysiology databases (2023) AcademicArticle |
A Gaussian Process Model of Human Electrocorticographic DataAuthors:
Jeremy Manning |
A guide to the BRAIN Initiative Cell Census Network data ecosystem (2023) AcademicArticle |
A Model of Representational Spaces in Human Cortex (2016) AcademicArticle |
A multimodal cell census and atlas of the mammalian primary motor cortex (2020) AcademicArticle |
A multimodal fMRI dataset unifying naturalistic processes with a rich array of experimental tasks (2024) AcademicArticle |
A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections using BIDS Apps (2024) AcademicArticle |
A very simple, re-executable neuroimaging publication (2017) AcademicArticleTopics:
Neuroimaging |
Aberrant levels of cortical myelin distinguish individuals with unipolar depression from healthy controls (2021) AcademicArticleAuthors:
Yaroslav Halchenko |
Advanced Image Processing in Magnetic Resonance Imaging: fMRI, MRI, EEG, MEG (2005) BookSectionAuthors:
Yaroslav Halchenko |
Advancing Neuroimaging Research with Predictive Multivariate Pattern Analysis (2010) AcademicArticle |
Align with the NMIND consortium for better neuroimaging (2023) AcademicArticle |
Analysis of task-based functional MRI data preprocessed with fMRIPrep (2020) AcademicArticle |
Application of the Neuroimaging Data Model to Represent and Exchange Primary and Derived Data (2015) Document |
Approach to parallel-hierarchical network learning for real-time image sequence recognition (1999) ArticleAuthors:
Yaroslav Halchenko |
Attention alters animal and action representation in highly-distributed functionally-defined cortical parcels (2015) Document |
Attention locally modulates the discriminability of high-level, task-relevant representations (2014) Document |
Attention selectively reshapes the geometry of distributed semantic representation (2016) AcademicArticle |
Attention selectively reshapes the geometry of distributed semantic representation (2017) AcademicArticle |
Attentional allocation locally warps representational space (2014) Document |
Behaviorally-relevant features of observed actions dominate cortical representational geometry in natural vision (2024) AcademicArticle |
Bottom-up and top-down brain functional connectivity underlying comprehension of everyday visual action (2007) AcademicArticleAuthors:
Yaroslav Halchenko |
Brain reading using full brain support vector machines for object recognition: there is no “face” identification area (2008) AcademicArticleAuthors:
Yaroslav Halchenko |
Brainhack: Developing a culture of open, inclusive, community-driven neuroscience (2021) AcademicArticle |
Bridging the Scientific Knowledge Gap and Reproducibility: A Survey of Provenance, Assertion and Evidence Ontologies (2025) Article |
Clustering cortical searchlights based on shared representational geometry (2015) Document |
Converging catalogues, warehouses, and deployment logistics into a federated 'data distribution' (2014) Document |
Cross-modal searchlight classification: Methodological challenges and recommended solutions (2016) Article |
Dartmouth Brain Imaging Center (DBIC) QA data (weekly QA scans etc.) (2023) DocumentAuthors:
Yaroslav Halchenko |
Data sharing in neuroimaging research (2012) AcademicArticleAuthors:
David Kennedy
Jean-Baptiste Poline
Michael Hanke
Russell Poldrack
Satrajit Ghosh
Yaroslav Halchenko |
DataLad – decentralized data distribution for consumption and sharing of scientific datasets (2016) Document |
DataLad: distributed system for joint management of code, data, and their relationship (2021) AcademicArticle |
Debian Med: Integrated software environment for all medical purposes based on Debian GNU/Linux (2011) Article |
Decoding the Large-Scale Structure of Brain Function by Classifying Mental States Across Individuals (2009) AcademicArticle |
Decoding the neural representation of observed social and nonsocial human actions (2018) Document |
Dense mode clustering in brain maps (2007) AcademicArticleAuthors:
Yaroslav Halchenko |
DICOM datasets for reproducible neuroimaging research across manufacturers and software versions (2025) AcademicArticleAuthors:
Yaroslav Halchenko |
DueCredit - automagically collect citations for software, methods, and data you use (2016) Document |
Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging (2019) AcademicArticle |
Fantastic containers and how to tame them (2019) Document |
Four aspects to make science open "by design" and not as an after-thought (2015) AcademicArticle |
Four aspects to make science open by design and not as an after-thought |
Fusion of Functional Brain Imaging Modalities using L-Norms Signal Reconstruction (2004) ArticleAuthors:
Yaroslav Halchenko |
Fusion of functional brain imaging modalities via linear programming (2004) AcademicArticleAuthors:
Yaroslav Halchenko |
Go Figure: Transparency in neuroscience images preserves context and clarifies interpretation (2025) DocumentAuthors:
Yaroslav Halchenko |
HeuDiConv — flexible DICOM conversion into structureddirectory layouts (2024) AcademicArticle |
How the human brain represents perceived dangerousness or "predacity" of animals (2016) AcademicArticle |
How to make brain imaging research efficient and reproducible: building software and standards (2015) DocumentAuthors:
David Kennedy
Jean-Baptiste Poline
Michael Hanke
Russell Poldrack
Satrajit Ghosh
Yaroslav Halchenko |
HyperTools: a Python Toolbox for Gaining Geometric Insights into High-Dimensional DataAuthors:
Jeremy Manning |
Image Segmentation on the basis of spatial connected features (1998) BookSectionAuthors:
Yaroslav Halchenko |
Improving efficiency in cognitive neuroscience research with NeuroDebian (2010) Document |
In defense of decentralized research data management (2021) AcademicArticle |
Incorrect probabilities in Harvard-Oxford-sub Left hemisphere (2012) DocumentAuthors:
Yaroslav Halchenko |
Investigation of the familiar face recognition model (2012) Document |
IQ in Typical Development: A Mega-Analysis of the Historical Literature (2021) AcademicArticle |
Localizing functional regions of interest based on responses to dynamic naturalistic stimuli (2016) Document |
Method for image coordinate definition on extended laser paths (2000) ArticleAuthors:
Yaroslav Halchenko |
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data (2022) AcademicArticle |
MRS-BIDS, an extension to the Brain Imaging Data Structure for magnetic resonance spectroscopy (2025) AcademicArticle |
multimatch-gaze: The MultiMatch algorithm for gaze path comparison in Python (2019) AcademicArticle |
Narratives: fMRI data for evaluating models of naturalistic language comprehension (2020) AcademicArticle |
NeuroDebian: from disjoint tools and data to robust turnkey platform for neuroimaging and beyond (2013) DocumentAuthors:
Yaroslav Halchenko |
Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging (2024) AcademicArticle |
Neuroimaging article reexecution and reproduction assessment system (2024) AcademicArticle |
Neuroscience Runs on GNU/Linux (2011) AcademicArticle |
NICEMAN: NeuroImaging Computational Environments Manager (2018) Document |
NIDM-Workflow - The Evolution of Provenance in Neuroimaging (2015) Document |
Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python (2011) AcademicArticleTopics:
Neuroimaging |
OME-Zarr: a cloud-optimized bioimaging file format with international community support (2023) AcademicArticle |
OME-Zarr: a cloud-optimized bioimaging file format with international community support (2023) AcademicArticle |
Open and reproducible neuroimaging: from study inception to publication (2022) AcademicArticle |
Open and reproducible neuroimaging: From study inception to publication (11/2) AcademicArticle |
Open is not enough. Let's take the next step: An integrated, community-driven computing platform for neuroscience (2012) AcademicArticle |
Open neuroinformatics infrastructure ecosystem for federated multisite studies (2026) ManuscriptAuthors:
Jean-Baptiste Poline |
Open Neuroscience |
Overview of statistical evaluation techniques adopted by publicly available MVPA toolboxes (2015) DocumentAuthors:
Yaroslav Halchenko |
Pattern classification precedes region-average hemodynamic response in early visual cortex. (2013) AcademicArticle |
Predictive Decoding of Neural Data (2009) ThesisAuthors:
Yaroslav Halchenko |
Prioritized Detection of Personally Familiar Faces (2013) AcademicArticle |
Processing of invisible social cues (2013) AcademicArticle |
Protocol for a machine learning algorithm predicting depressive disorders using the T1w/T2w ratio (2021) AcademicArticleAuthors:
Yaroslav Halchenko |
PyBIDS: Python tools for BIDS datasets (2019) AcademicArticleAuthors:
Adina Wagner
Chris Markiewicz
Jean-Baptiste Poline
John Lee
Matteo Visconti di Oleggio Castello
Michael Hanke
Russell Poldrack
Yaroslav Halchenko |
Pybids: Python tools for manipulation and analysis of BIDS datasets (2018) Document |
PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data (2009) AcademicArticle |
PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data (2009) AcademicArticle |
Quail: A Python toolbox for analyzing and plotting free recall dataAuthors:
Jeremy Manning |
Representation of biological classes in the human brain (2012) AcademicArticle |
ReproIn: automatic generation of shareable, version-controlled BIDS datasets from MR scanners (2018) Document |
Resources for practicing PR4NI – pragmatic cursory overview (2016) DocumentAuthors:
Yaroslav Halchenko |
Scanning parameters for optimal decoding using a 32-channel head coil for fMRI (2011) Document |
SciOps: Achieving Productivity and Reliability in Data-Intensive Research (2024) Manuscript |
Six problems for causal inference from fMRI (2010) AcademicArticle |
Spacetop: A multimodal fMRI dataset unifying naturalistic processes with a rich array of experimental tasks (2025) AcademicArticle |
Statistical learning analysis in neuroscience: aiming for transparency (2010) AcademicArticle |
Structural Equation Modeling of Neuroimaging Data: Exhaustive Search and Markov Chain Monte Carlo (2004) ArticleAuthors:
Yaroslav Halchenko |
TemplateFlow: a community archive of imaging templates and atlases for improved consistency in neuroimaging (2021) AcademicArticle |
TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models (12/2) AcademicArticle |
Temporal dynamics and effective connectivity in the distributed system of familiar face processing (2018) Document |
The “Narratives” fMRI dataset for evaluating models of naturalistic language comprehension (2021) AcademicArticle |
The animacy continuum in the human ventral vision pathway (2015) AcademicArticle |
The best of both worlds: using semantic web with JSON-LD. An example with NIDM-Results & DataLad (2019) Document |
The Brain Imaging Data Structure (BIDS) Specification, Version 1.3.0 (2020) DocumentAuthors:
David Kennedy
Jean-Baptiste Poline
Michael Hanke
Russell Poldrack
Satrajit Ghosh
Vanessa Sochat
Yaroslav Halchenko |
The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments (2016) AcademicArticleAuthors:
Jean-Baptiste Poline
Michael Hanke
Russell Poldrack
Satrajit Ghosh
Vanessa Sochat
Yaroslav Halchenko |
The Brain Imaging Data Structure: a standard for organizing and describing outputs of neuroimaging experiments (2016) AcademicArticleAuthors:
Jean-Baptiste Poline
Michael Hanke
Russell Poldrack
Satrajit Ghosh
Vanessa Sochat
Yaroslav Halchenko |
The impact of shared data in neuroimaging: the case of OpenfMRI.org (2015) Document |
The Individualized Neural Tuning Model: Precise and generalizable cartography of functional architecture in individual brains (2022) AcademicArticle |
The Individualized Neural Tuning Model: Precise and generalizable cartography of functional architecture in individual brains (2023) AcademicArticle |
The model of associative processor for numerical data sorting (1997) BookSectionAuthors:
Yaroslav Halchenko |
The Neural Representation Of Personally Familiar And Unfamiliar Faces In The Distributed System For Face Perception (2017) AcademicArticle |
The Neural Representation Of Personally Familiar And Unfamiliar Faces In The Distributed System For Face Perception (2017) AcademicArticle |
The Open Brain Consent: Informing research participants and obtaining consent to share brain imaging data (2021) AcademicArticle |
The Open Brain Consent: Informing research participants and obtaining consent to share brain imaging data (2020) AcademicArticleAuthors:
Yaroslav Halchenko |
The past, present, and future of the brain imaging data structure (BIDS) (2024) AcademicArticleAuthors:
Chris Markiewicz
Franco Pestilli
Horea-Ioan Ioanas
Jean-Baptiste Poline
Russell Poldrack
Satrajit Ghosh
Yaroslav Halchenko |
The Past, Present, and Future of the Brain Imaging Data Structure (BIDS) (2023) AcademicArticleAuthors:
Chris Markiewicz
Franco Pestilli
Horea-Ioan Ioanas
Jean-Baptiste Poline
Russell Poldrack
Satrajit Ghosh
Yaroslav Halchenko |
The PyMVPA BIDS-App: a robust multivariate pattern analysis pipeline for fMRI data (2023) AcademicArticle |
To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery (2016) AcademicArticle |
Toward standard practices for sharing computer code and programs in neuroscience (2017) AcademicArticle |
Towards standard practices for sharing computer code and programs in neuroscience (2016) AcademicArticle |
Transmodal Analysis of Neural Signals (2013) AcademicArticle |
US-RSE Stories: Open up, Neuroscience! Here comes NeuroDebian (2019) Document |
Variability of the Neuroimaging Results Across OS, and How to Avoid it (2018) Document |
White matter abnormalities in adults with bipolar disorder type-II and unipolar depression (2021) AcademicArticleAuthors:
Yaroslav Halchenko |
Working memory updating in individuals with bipolar and unipolar depression: fMRI study (2022) AcademicArticleAuthors:
Yaroslav Halchenko |
YODA: YODA’s organigram on data analysis (2018) Document |