Slides of our talks are also collected on our Talks site. For affiliated faculty and collaborators, only their works joint with CON members are listed.
Papers and reports
- Benchmarking ITU-T T.261 against established codecs on extracellular electrophysiology, with a public comment on DICOM Supplement 253 Projects: DICOM WG-32
- Neurobagel: building an international network for distributed data discovery preprint Projects: Neurobagel
- Behaviorally-relevant features of observed actions dominate cortical representational geometry in natural vision [PREPRINT] [OPENNEURO:ds007942]
- Go figure: transparency in neuroscience images preserves context and clarifies interpretation [PREPRINT]
- STAMPED principles for reproducible research objects preprint Projects: STAMPED Principles
- Nipoppy: A framework for standardizing neuroimaging studies to facilitate international derived-data sharing preprint Projects: Nipoppy
- Eye-Tracking-BIDS: the Brain Imaging Data Structure extended to gaze position and pupil data preprint Projects: BEP020
- MRS-BIDS, an extension to the Brain Imaging Data Structure for magnetic resonance spectroscopy Projects: BIDS
- Spacetop: A multimodal fMRI dataset unifying naturalistic processes with a rich array of experimental tasks [PREPRINT] [OPENNEURO:ds005256]
- DICOM datasets for reproducible neuroimaging research across manufacturers and software versions Projects: DICOM
- Bridging the Scientific Knowledge Gap and Reproducibility: A Survey of Provenance, Assertion and Evidence Ontologies
- Neuroimaging article reexecution and reproduction assessment system Projects: ReproNim
- HeuDiConv — flexible DICOM conversion into structured directory layouts Projects: HeuDiConv
- Proceedings of the OHBM Brainhack 2022
- The past, present, and future of the brain imaging data structure (BIDS) [PREPRINT] Projects: BIDS
- A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections using BIDS Apps [PREPRINT] Projects: DataLad
- Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging
- SciOps: Achieving Productivity and Reliability in Data-Intensive Research preprint
- A comparison of neuroelectrophysiology databases [PREPRINT] Projects: DANDI
- The PyMVPA BIDS-App: a robust multivariate pattern analysis pipeline for fMRI data Projects: BIDS, PyMVPA
- OME-Zarr: a cloud-optimized bioimaging file format with international community support [PREPRINT]
- Align with the NMIND consortium for better neuroimaging
- A guide to the BRAIN Initiative Cell Census Network data ecosystem [PREPRINT]
- The Individualized Neural Tuning Model: Precise and generalizable cartography of functional architecture in individual brains [PREPRINT] Projects: Hyperalignment infrastructure
- Dartmouth Brain Imaging Center (DBIC) QA data (weekly QA scans etc.)
- TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models [PREPRINT]
- Open and reproducible neuroimaging: From study inception to publication [PREPRINT]
- Working memory updating in individuals with bipolar and unipolar depression: fMRI study
- The interaction between depression diagnosis and BMI is related to altered activation pattern in the right inferior frontal gyrus and anterior cingulate cortex during food anticipation [PREPRINT]
- Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data Projects: BIDS
- The Relationship Between Default Mode and Dorsal Attention Networks Is Associated With Depressive Disorder Diagnosis and the Strength of Memory Representations Acquired Prior to the Resting State Scan
- The OpenNeuro resource for sharing of neuroscience data [PREPRINT] Projects: OpenNeuro
- A multimodal cell census and atlas of the mammalian primary motor cortex [PREPRINT]
- The “Narratives” fMRI dataset for evaluating models of naturalistic language comprehension [PREPRINT] [OPENNEURO:ds002345]
- DataLad: distributed system for joint management of code, data, and their relationship Projects: DataLad
- IQ in Typical Development: A Mega-Analysis of the Historical Literature
- White matter abnormalities in adults with bipolar disorder type-II and unipolar depression
- Brainhack: Developing a culture of open, inclusive, community-driven neuroscience [PREPRINT]
- The Open Brain Consent: Informing research participants and obtaining consent to share brain imaging data [PREPRINT] Projects: Open Brain Consent
- In defense of decentralized research data management Projects: DataLad
- Protocol for a machine learning algorithm predicting depressive disorders using the T1w/T2w ratio [OPENNEURO:ds003653]
- Aberrant levels of cortical myelin distinguish individuals with depressive disorders from healthy controls [PREPRINT] [OPENNEURO:ds003653]
- A new virtue of phantom MRI data: explaining variance in human participant data Projects: MRI Phantoms Afterlife
- Analysis of task-based functional MRI data preprocessed with fMRIPrep [PREPRINT]
- The Brain Imaging Data Structure (BIDS) Specification, Version 1.3.0 Projects: BIDS
- SciPy 1.0: fundamental algorithms for scientific computing in Python
- Functional ROI localization in a rich stimuli dataset requires non-GLM style approach (PDF) Projects: Region localization from rich data
- multimatch-gaze: The MultiMatch algorithm for gaze path comparison in Python
- US-RSE Stories: Open up, Neuroscience! Here comes NeuroDebian Projects: NeuroDebian
- PyBIDS: Python tools for BIDS datasets Projects: BIDS
- Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging [PREPRINT] Projects: ReproNim
- Neural Responses to Naturalistic Clips of Behaving Animals in Two Different Task Contexts [PREPRINT] [OPENNEURO:ds000233]
- A very simple, re-executable neuroimaging publication Projects: ReproNim
- Toward standard practices for sharing computer code and programs in neuroscience [PREPRINT]
- The Neural Representation Of Personally Familiar And Unfamiliar Faces In The Distributed System For Face Perception [PREPRINT] [OPENNEURO:ds001297]
- Attention selectively reshapes the geometry of distributed semantic representation [PREPRINT]
- The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments [PREPRINT] Projects: BIDS
- Cross-modal searchlight classification: Methodological challenges and recommended solutions
- A Model of Representational Spaces in Human Cortex Projects: PyMVPA
- How the human brain represents perceived dangerousness or "predacity" of animals
- To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery
- The animacy continuum in the human ventral vision pathway
- Four aspects to make science open "by design" and not as an after-thought
- A communication hub for a decentralized collaboration on studying real-life cognition
- Converging catalogues, warehouses, and deployment logistics into a federated 'data distribution' Projects: DataLad
- Transmodal Analysis of Neural Signals Projects: PyMVPA
- Prioritized Detection of Personally Familiar Faces
- Pattern classification precedes region-average hemodynamic response in early visual cortex.
- Processing of invisible social cues
- NeuroDebian: from disjoint tools and data to robust turnkey platform for neuroimaging and beyond Projects: NeuroDebian
- Representation of biological classes in the human brain [OPENNEURO:ds000241]
- Open is not enough. Let's take the next step: An integrated, community-driven computing platform for neuroscience Projects: NeuroDebian
- Incorrect probabilities in Harvard-Oxford-sub Left hemisphere
- Data sharing in neuroimaging research
- A Common, High-Dimensional Model of the Representational Space in Human Ventral Temporal Cortex Projects: PyMVPA
- Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python Projects: Nipype
- Neuroscience Runs on GNU/Linux Projects: NeuroDebian
- Debian Med: Integrated software environment for all medical purposes based on Debian GNU/Linux Projects: Debian Med
- Advancing Neuroimaging Research with Predictive Multivariate Pattern Analysis Projects: PyMVPA
- Six problems for causal inference from fMRI
- Statistical learning analysis in neuroscience: aiming for transparency Projects: PyMVPA
- Decoding the Large-Scale Structure of Brain Function by Classifying Mental States Across Individuals
- Predictive Decoding of Neural Data Projects: PyMVPA
- PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data Projects: PyMVPA
- PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data Projects: PyMVPA
- Brain reading using full brain support vector machines for object recognition: there is no “face” identification area
- Bottom-up and top-down brain functional connectivity underlying comprehension of everyday visual action
- Dense mode clustering in brain maps
- Advanced Image Processing in Magnetic Resonance Imaging: fMRI, MRI, EEG, MEG
- Structural Equation Modeling of Neuroimaging Data: Exhaustive Search and Markov Chain Monte Carlo
- Fusion of functional brain imaging modalities via linear programming
- Fusion of Functional Brain Imaging Modalities using L-Norms Signal Reconstruction
- Method for image coordinate definition on extended laser paths
- Approach to parallel-hierarchical network learning for real-time image sequence recognition
- Image Segmentation on the basis of spatial connected features
- The model of associative processor for numerical data sorting
Posters
- Beyond the Lab Website: Reusing Structured Research Metadata Across Lab Operations Projects: ORINOCO Lite
- Agent-friendly Provenance Capture with con-duct (PDF) Projects: duct
- STAMPED in Practice: Improving research skills through reproducible experiments (PDF) Projects: STAMPED Principles
- The Ecosystem of Standards in Neuroscience: Which Ones Are For You? Projects: BIDS, DICOM, HED, NIDM, NWB
- DataLad: The Ecosystem for Everyone Projects: DataLad
- The best of both worlds: using semantic web with JSON-LD. An example with NIDM-Results & DataLad Projects: DataLad, NIDM
- Fantastic containers and how to tame them Projects: ReproNim/containers
- YODA: YODA’s organigram on data analysis Projects: DataLad, YODA
- Temporal dynamics and effective connectivity in the distributed system of familiar face processing
- ReproIn: automatic generation of shareable, version-controlled BIDS datasets from MR scanners Projects: HeuDiConv
- Pybids: Python tools for manipulation and analysis of BIDS datasets Projects: BIDS
- NICEMAN: NeuroImaging Computational Environments Manager Projects: ReproMan
- Decoding the neural representation of observed social and nonsocial human actions
- (Meta)Data and workflow management for your most important work and your daily routine Projects: DataLad
- Localizing functional regions of interest based on responses to dynamic naturalistic stimuli Projects: Region localization from rich data
- Finding cortical patches of shared representations: a comparison of clustering algorithms on representational geometries, and the effect of cross-validation to reduce physiological noise Projects: Region localization from rich data
- The impact of shared data in neuroimaging: the case of OpenfMRI.org Projects: OpenfMRI
- NIDM-Workflow - The Evolution of Provenance in Neuroimaging Projects: NIDM
- How to make brain imaging research efficient and reproducible: building software and standards
- Attention alters animal and action representation in highly-distributed functionally-defined cortical parcels
- Application of the Neuroimaging Data Model to Represent and Exchange Primary and Derived Data Projects: NIDM
- Attentional allocation locally warps representational space
- Attention locally modulates the discriminability of high-level, task-relevant representations
- Investigation of the familiar face recognition model Projects: PyMVPA
- NeuroDebian: versatile platform for brain imaging research Projects: NeuroDebian
- Unsupervised brain parcellation from functional neuroimaging data Projects: PyMVPA
- Scanning parameters for optimal decoding using a 32-channel head coil for fMRI
- An integrated community-driven computing platform for neuroscience Projects: NeuroDebian
- Transmodal Analysis of Neural Signals Projects: PyMVPA
- PyMVPA 0.5: A Major Update of the Comprehensive Framework for Statistical Learning Analysis of Neural Data Projects: PyMVPA
- Neural activity localization by predictive mapping between imaging modalities Projects: PyMVPA
- Improving efficiency in cognitive neuroscience research with NeuroDebian Projects: NeuroDebian
- Statistical Learning Analysis in Neuroscience Projects: PyMVPA
Talks
- Reuse, Compose, Extend, Standardize, Automate: Two Decades of RSEing Open (Neuro)Science at CON
- STAMPED principles and their role in the age of AI-driven scientific software development Projects: STAMPED Principles
- Open Neuroscience Infrastructure for Intracranial EEG
- mechababs: STAMPED execution of BIDS Apps at scale Projects: mechababs
- BIDS 2.0 Projects: BIDS 2.0
- Containers: BrainHack 2026 Mashup Projects: ReproNim/containers
- Guidelines for Reproducible Research (BBQS, 2026) (📺 CONTube) Projects: STAMPED Principles
- ReproFlow & YODA: Structure your studies, observable and reproducible they become (📺 CONTube) Projects: STAMPED Principles, YODA
- A few words of intro into AI assisted coding
- distribits 2025: panel discussion with Julia Katharina Pfarr (📺 CONTube) Projects: distribits
- Pragmatic YODA: overview of YODA principles and their wild life encounters (📺 CONTube) Projects: YODA
- A challenge on the way to Neuroscience Nirvana
- SciOps from ReproNim (📺 CONTube) Projects: ReproNim, ReproStim
- DataLad-Registry: Bringing Benefits of Centrality to DataLad (📺 CONTube) Projects: DataLad-Registry
- distribits 2024: questions and panel discussion (📺 CONTube) Projects: DataLad, distribits
- The Brain Imaging Data Structure (BIDS): an open community standard for neuroscience Projects: BIDS
- "What's in the DataLad sandwich" AKA DataLad "ecosystem" (📺 CONTube) Projects: DataLad
- "What's in the DataLad name" AKA How come DataLad? Projects: DataLad
- DANDI components and architecture (📺 CONTube) Projects: DANDI
- BIDS Talk & Q&A for 2024 The Neuro – Irv and Helga Cooper Foundation International Prize (📺 CONTube) Projects: BIDS
- Research Data Management & Data tracking (📺 CONTube) Projects: ReproNim
- ReproCLInic, 2023-07-14: uploading data to NDA (📺 CONTube) Projects: ReproNim
- ReproCLInic, 2023-07-07: several modalities in one BIDS dataset (📺 CONTube) Projects: BIDS, ReproNim
- DANDI: distributed archives for neurophysiology data integration Projects: DANDI
- DANDI: distributed archives for neurophysiology data integration Projects: DANDI
- BIDS 4 DICOM WG-16 Projects: DICOM WG-16
- Building an Archive for Large-scale Neuroscience Data Projects: DANDI
- Towards the Big Data Neuroscience Nirvana
- An Integrated and Trusted Scientific and Statistical Computing Core
- A guide to DANDI, the BRAIN Initiative archive for publishing and sharing neurophysiology data (📺 CONTube) Projects: DANDI
- DataLad - Research Data Management Made Easy (PDF) (📺 CONTube) Projects: DataLad
- ReproMan – Execution and Environment Manager (PDF) (📺 CONTube) Projects: ReproMan
- ABCD-ReproNim course, week 10: instructor Q&A (📺 CONTube) Projects: ReproMan, ReproNim
- Reproducible Execution of Data Collection/Processing (📺 CONTube) Projects: ReproNim
- Version control your data and computation using containers, DataLad and ReproMan, and reproducible they be! (PDF) (📺 CONTube) Projects: ReproNim/containers
- Taking control of your DICOM data: ReproIn/HeuDiConv tools (PDF) (📺 CONTube) Projects: HeuDiConv
- Making science more open and reproducible by design, tools can help (PDF)
- Tales from the CON: A few studies of a curious mind (PDF)
- Open Science Tools from the Center for Open Neuroscience (PDF) (📺 CONTube)
- Tools from Center for Open Neuroscience: be Open by Design (PDF) (📺 CONTube)
- Computational basis (📺 CONTube) Projects: ReproNim
- Variability of the Neuroimaging Results Across OS, and How to Avoid it (PDF) Projects: NeuroDebian
- DataLad (📺 CONTube) Projects: DataLad
- Got Something, Commit Something (PDF) Projects: DataLad
- DataLad -- decentralized data distribution for consumption and sharing of scientific datasets (PDF) Projects: DataLad
- DataLad -- decentralized data distribution for consumption and sharing of scientific datasets (PDF) Projects: DataLad
- DataLad -- Decentralized Distribution and Sharing of Scientific Datasets (PDF) (📺 CONTube) Projects: DataLad
- DataLad -- decentralized data distribution for consumption and sharing of scientific datasets (PDF) Projects: DataLad
- DataLad -- decentralized data distribution for consumption and sharing of scientific datasets (PDF) Projects: DataLad
- Managing data should be as easy as managing code and software (PDF) Projects: DataLad
- Resources for practicing PR4NI – pragmatic cursory overview (PDF) Projects: PyMVPA
- DataLad – decentralized data distribution for consumption and sharing of scientific datasets (PDF) Projects: DataLad
- The road to open neuroscience: from analysis methods to software platforms (PDF)
- DueCredit - automagically collect citations for software, methods, and data you use Projects: DueCredit
- Virtues of cognitive neuroscience: from brain function to software platforms (NeuroDebian) (PDF) (📺 CONTube) Projects: NeuroDebian
- The road to open neuroscience: from analysis methods to software platforms (PDF)
- Overview of statistical evaluation techniques adopted by publicly available MVPA toolboxes (PDF) Projects: PyMVPA
- PyMVPA Workshop 2015 Projects: PyMVPA
- Virtues of cognitive neuroscience: from brain function to software platforms (PDF) Projects: PyMVPA
- Clustering cortical searchlights based on shared representational geometry
- PyMVPA Workshop 2014 Projects: PyMVPA
- "To make a world a better place" or PyMVPA / NeuroDebian / ... (PDF) Projects: PyMVPA
- Fail2Ban -- keep your boxes skiddie-free (PDF) Projects: Fail2Ban
- From statistical learning to an open-source, turnkey platform for neuroimaging (PDF) Projects: PyMVPA
- Open is not enough: benefits from Debian as an integrated, community-driven computing platform (PDF) Projects: Debian
- PyMVPA Course -- Overture (PDF) Projects: PyMVPA
- Applied NeuroDebian: Python in Neuroimaging (PDF) Projects: NeuroDebian
- Debian Med: The ultimate operating system for medicine, pre-clinical research and bio-informatics (PDF) Projects: Debian
- Environments for efficient contemporary research in neuroimaging (PDF) Projects: PyMVPA
- Multivariate analysis strategies of neuroimaging data in PyMVPA (PDF) Projects: PyMVPA
- π's in Debian or Scientific Debian: NumPy, SciPy and beyond (PDF) Projects: Debian
- The virtues and sins of PyMVPA (PDF) Projects: PyMVPA
- More than batteries included: NeuroDebian (PDF) Projects: NeuroDebian
- PsychoPy Workshop: Coding, Git, et al. (PDF) Projects: PsychoPy
- Searchlight whereabouts in PyMVPA (PDF) Projects: PyMVPA
- Debian: The ultimate platform for neuroimaging research (PDF) Projects: NeuroDebian
- Citations infrastructure in Debian (PDF) Projects: Debian
- First PyMVPA Course Ever Projects: PyMVPA
- PyMVPA: Where we are now, and where we are going (PDF) Projects: PyMVPA
- An ecosystem of neuroimaging, statistical learning, and open-source software to make research more efficient, more open, and more fun (PDF) Projects: PyMVPA
- PyMVPA: Fathom Brain Function through Multivariate Pattern Analysis (PDF) Projects: PyMVPA
- Reliable Decoding of Neural Data (PDF) Projects: PyMVPA
- PyMVPA: Fathom Brain Function with Multivariate Pattern Analysis (PDF) Projects: PyMVPA
- Standing on the shoulders of giants: Multivariate pattern analysis in Python (PDF) Projects: PyMVPA
- Modality-independent Analysis Of Neuroimaging Data With PyMVPA (PDF) Projects: PyMVPA
- PyMVPA: A Python toolbox for machine-learning-based fMRI data analysis (PDF) Projects: PyMVPA
- Classifier-based analysis toolbox for Neuroimaging (PDF) Projects: PyMVPA
Datasets
- fMRIPrep Derivatives for SpaceTop
- Behaviorally-relevant features of observed actions dominate cortical representational geometry in natural vision
- MRIQC Derivatives for SpaceTop
- A multimodal fMRI dataset unifying naturalistic processes with a rich array of experimental tasks
- Cortical myelin measured by the T1w/T2w ratio in individuals with depressive disorders and healthy controls
- Narratives
- AK6
- Personally familiar faces
- Neural responses to naturalistic clips of behaving animals in two different task contexts
https://ror.org/04tfhh831