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