TAPAS: An Open-Source Software Package for Translational Neuromodeling and Computational Psychiatry

Markov chain Monte Carlo methods for hierarchical clustering of dynamic causal models

(2021) Yu Yao et al.   HUMAN BRAIN MAPPING

Realizing the Clinical Potential of Computational Psychiatry: Report From the Banbury Center Meeting, February 2019

(2020) Michael Browning et al.   BIOLOGICAL PSYCHIATRY

GABA-ergic Dynamics in Human Frontotemporal Networks Confirmed by Pharmaco-Magnetoencephalography

(2020) Natalie E. Adams et al.   JOURNAL OF NEUROSCIENCE

Pushing functional MRI spatial and temporal resolution further: High‐density receive arrays combined with shot‐selective 2D CAIPIRINHA for 3D echo‐planar imaging at 7 T

(2020) Arjan D. Hendriks et al.   NMR IN BIOMEDICINE

Predicting individual clinical trajectories of depression with generative embedding

(2020) Stefan Frässle et al.   NeuroImage-Clinical

Atypical processing of uncertainty in individuals at risk for psychosis

(2020) David M. Cole et al.   NeuroImage-Clinical

Remote, Automated, and MRI-Compatible Administration of Interoceptive Inspiratory Resistive Loading

(2020) Sebastian W. Rieger et al.   Frontiers in Human Neuroscience

Ketamine Affects Prediction Errors about Statistical Regularities: A Computational Single-Trial Analysis of the Mismatch Negativity

(2020) Lilian A. Weber et al.   JOURNAL OF NEUROSCIENCE

Whole-brain estimates of directed connectivity for human connectomics

(2020) Stefan Frässle et al.   NEUROIMAGE

New acquisition techniques and their prospects for the achievable resolution of fMRI

(2020) Saskia Bollmann et al.   PROGRESS IN NEUROBIOLOGY

Forging a path to mesoscopic imaging success with ultra-high field functional magnetic resonance imaging

(2020) Kimberly B. Weldon et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cholinergic and dopaminergic effects on prediction error and uncertainty responses during sensory associative learning

(2020) Sandra Iglesias et al.   NEUROIMAGE

Deep neural networks in psychiatry

(2019) Daniel Durstewitz et al.   MOLECULAR PSYCHIATRY

Switch costs in inhibitory control and voluntary behavior: A computational study of the antisaccade task

(2019) Eduardo A. Aponte et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

A dynamical model of the laminar BOLD response

(2019) Martin Havlicek et al.   NEUROIMAGE

Ten simple rules for the computational modeling of behavioral data

(2019) Robert C Wilson et al.   eLife

Machine Learning Approaches for Clinical Psychology and Psychiatry

(2018) Dominic B. Dwyer et al.   Annual Review of Clinical Psychology

Ion channels in EEG: isolating channel dysfunction in NMDA receptor antibody encephalitis

(2018) Mkael Symmonds et al.   BRAIN

Pulse sequences and parallel imaging for high spatiotemporal resolution MRI at ultra-high field

(2018) Benedikt A. Poser et al.   NEUROIMAGE

A method for the dynamic correction of B 0 -related distortions in single-echo EPI at 7 T

(2018) Barbara Dymerska et al.   NEUROIMAGE

Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank

(2018) Fidel Alfaro-Almagro et al.   NEUROIMAGE

A generative model of whole-brain effective connectivity

(2018) Stefan Frässle et al.   NEUROIMAGE

Variational Bayesian inversion for hierarchical unsupervised generative embedding (HUGE)

(2018) Yu Yao et al.   NEUROIMAGE

Inhibition failures and late errors in the antisaccade task: Influence of cue delay

(2018) Eduardo A. Aponte et al.   JOURNAL OF NEUROPHYSIOLOGY

How to control for confounds in decoding analyses of neuroimaging data

(2018) Lukas Snoek et al.   NEUROIMAGE

fMRIPrep: a robust preprocessing pipeline for functional MRI

(2018) Oscar Esteban et al.   NATURE METHODS

Focus of attention modulates the heartbeat evoked potential

(2018) Frederike H. Petzschner et al.   NEUROIMAGE

Maximising BOLD sensitivity through automated EPI protocol optimisation

(2018) Steffen Volz et al.   NEUROIMAGE

The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data

(2017) Lars Kasper et al.   JOURNAL OF NEUROSCIENCE METHODS

KFAS: Exponential Family State Space Models in R

(2017) Jouni Helske   Journal of Statistical Software

Adults with autism overestimate the volatility of the sensory environment

(2017) Rebecca P Lawson et al.   NATURE NEUROSCIENCE

Cleaning up the fMRI time series: Mitigating noise with advanced acquisition and correction strategies

(2017) Molly G. Bright et al.   NEUROIMAGE

The Virtual Epileptic Patient: Individualized whole-brain models of epilepsy spread

(2017) V.K. Jirsa et al.   NEUROIMAGE

Multi-echo fMRI: A review of applications in fMRI denoising and analysis of BOLD signals

(2017) Prantik Kundu et al.   NEUROIMAGE

Cross-validation failure: Small sample sizes lead to large error bars

(2017) Gaël Varoquaux   NEUROIMAGE

Regression DCM for fMRI

(2017) Stefan Frässle et al.   NEUROIMAGE

Assessing and tuning brain decoders: Cross-validation, caveats, and guidelines

(2017) Gaël Varoquaux et al.   NEUROIMAGE

Sources and implications of whole-brain fMRI signals in humans

(2017) Jonathan D. Power et al.   NEUROIMAGE

Computational neuroimaging strategies for single patient predictions

(2017) K.E. Stephan et al.   NEUROIMAGE

Dopamine Neurons Respond to Errors in the Prediction of Sensory Features of Expected Rewards

(2017) Yuji K. Takahashi et al.   NEURON

High-Resolution CBV-fMRI Allows Mapping of Laminar Activity and Connectivity of Cortical Input and Output in Human M1

(2017) Laurentius Huber et al.   NEURON

MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites

(2017) Oscar Esteban et al.   PLoS One

Pavlovian conditioning–induced hallucinations result from overweighting of perceptual priors

(2017) A. R. Powers et al.   SCIENCE

Abnormal Effective Connectivity in the Brain is Involved in Auditory Verbal Hallucinations in Schizophrenia

(2017) Baojuan Li et al.   Neuroscience Bulletin

The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades

(2017) Eduardo A. Aponte et al.   PLoS Computational Biology

Network dynamics during the different stages of hallucinations in schizophrenia

(2016) Stéphanie Lefebvre et al.   HUMAN BRAIN MAPPING

A hierarchical model for integrating unsupervised generative embedding and empirical Bayes

(2016) Sudhir Raman et al.   JOURNAL OF NEUROSCIENCE METHODS

mpdcm: A toolbox for massively parallel dynamic causal modeling

(2016) Eduardo A. Aponte et al.   JOURNAL OF NEUROSCIENCE METHODS

Computational psychiatry as a bridge from neuroscience to clinical applications

(2016) Quentin J M Huys et al.   NATURE NEUROSCIENCE

Profiling neuronal ion channelopathies with non-invasive brain imaging and dynamic causal models: Case studies of single gene mutations

(2016) Jessica R. Gilbert et al.   NEUROIMAGE

The quest for the best: The impact of different EPI sequences on the sensitivity of random effect fMRI group analyses

(2016) Evgeniya Kirilina et al.   NEUROIMAGE

Gradient-based MCMC samplers for dynamic causal modelling

(2016) Biswa Sengupta et al.   NEUROIMAGE

A hemodynamic model for layered BOLD signals

(2016) Jakob Heinzle et al.   NEUROIMAGE

Bayesian model reduction and empirical Bayes for group (DCM) studies

(2016) Karl J. Friston et al.   NEUROIMAGE

The dysconnection hypothesis (2016)

(2016) Karl Friston et al.   SCHIZOPHRENIA RESEARCH

Pharmacological Fingerprints of Contextual Uncertainty

(2016) Louise Marshall et al.   PLOS BIOLOGY

Automated Quality Assessment of Structural Magnetic Resonance Brain Images Based on a Supervised Machine Learning Algorithm

(2016) Ricardo A. Pizarro et al.   Frontiers in Neuroinformatics

The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments

(2016) Krzysztof J. Gorgolewski et al.   Scientific Data

A phenome-wide examination of neural and cognitive function

(2016) R.A. Poldrack et al.   Scientific Data

Predicting the Naturalistic Course of Major Depressive Disorder Using Clinical and Multimodal Neuroimaging Information: A Multivariate Pattern Recognition Study

(2015) Lianne Schmaal et al.   BIOLOGICAL PSYCHIATRY

Computational Psychiatry: towards a mathematically informed understanding of mental illness

(2015) Rick A Adams et al.   JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY

Characterising seizures in anti-NMDA-receptor encephalitis with dynamic causal modelling

(2015) Gerald K. Cooray et al.   NEUROIMAGE

Physiologically informed dynamic causal modeling of fMRI data

(2015) Martin Havlicek et al.   NEUROIMAGE

Gradient-free MCMC methods for dynamic causal modelling

(2015) Biswa Sengupta et al.   NEUROIMAGE

Test-retest reliability of dynamic causal modeling for fMRI

(2015) Stefan Frässle et al.   NEUROIMAGE

Head motion during MRI acquisition reduces gray matter volume and thickness estimates

(2015) Martin Reuter et al.   NEUROIMAGE

Translational Perspectives for Computational Neuroimaging

(2015) Klaas E. Stephan et al.   NEURON

UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age

(2015) Cathie Sudlow et al.   PLOS MEDICINE

Psychiatric Disorders: Diagnosis to Therapy

(2014) John H. Krystal et al.   CELL

Computational approaches to psychiatry

(2014) Klaas Enno Stephan et al.   CURRENT OPINION IN NEUROBIOLOGY

Uncertainty in perception and the Hierarchical Gaussian Filter

(2014) Christoph D. Mathys et al.   Frontiers in Human Neuroscience

Cholinergic Stimulation Enhances Bayesian Belief Updating in the Deployment of Spatial Attention

(2014) S. Vossel et al.   JOURNAL OF NEUROSCIENCE

Recommended implementation of arterial spin-labeled perfusion MRI for clinical applications: A consensus of the ISMRM perfusion study group and the European consortium for ASL in dementia

(2014) David C. Alsop et al.   MAGNETIC RESONANCE IN MEDICINE

Making big data open: data sharing in neuroimaging

(2014) Russell A Poldrack et al.   NATURE NEUROSCIENCE

Computational Psychiatry

(2014) Xiao-Jing Wang et al.   NEURON

New Approaches to Psychiatric Diagnostic Classification

(2014) Michael J. Owen   NEURON

Great Expectations: Using Whole-Brain Computational Connectomics for Understanding Neuropsychiatric Disorders

(2014) Gustavo Deco et al.   NEURON

VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data

(2014) Jean Daunizeau et al.   PLoS Computational Biology

Machine learning for neuroimaging with scikit-learn

(2014) Alexandre Abraham et al.   Frontiers in Neuroinformatics

Massively parallel MRI detector arrays

(2013) Boris Keil et al.   JOURNAL OF MAGNETIC RESONANCE

The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism

(2013) A Di Martino et al.   MOLECULAR PSYCHIATRY

Biophysical network models and the human connectome

(2013) Mark W. Woolrich et al.   NEUROIMAGE

The WU-Minn Human Connectome Project: An overview

(2013) David C. Van Essen et al.   NEUROIMAGE

Resting-state fMRI confounds and cleanup

(2013) Kevin Murphy et al.   NEUROIMAGE

The minimal preprocessing pipelines for the Human Connectome Project

(2013) Matthew F. Glasser et al.   NEUROIMAGE

Methods to detect, characterize, and remove motion artifact in resting state fMRI

(2013) Jonathan D. Power et al.   NEUROIMAGE

Spurious group differences due to head motion in a diffusion MRI study

(2013) Anastasia Yendiki et al.   NEUROIMAGE

Hierarchical Prediction Errors in Midbrain and Basal Forebrain during Sensory Learning

(2013) Sandra Iglesias et al.   NEURON

Noninvasive functional imaging of cerebral blood volume with vascular-space-occupancy (VASO) MRI

(2013) Hanzhang Lu et al.   NMR IN BIOMEDICINE

Elevated Antisaccade Error Rate as an Intermediate Phenotype for Psychosis Across Diagnostic Categories

(2013) James L. Reilly et al.   SCHIZOPHRENIA BULLETIN

Neural masses and fields in dynamic causal modeling

(2013) Rosalyn Moran et al.   Frontiers in Computational Neuroscience

HDDM: Hierarchical Bayesian estimation of the Drift-Diffusion Model in Python

(2013) Thomas V. Wiecki et al.   Frontiers in Neuroinformatics

Abnormalities in fronto-striatal connectivity within language networks relate to differences in grey-matter heterogeneity in Asperger syndrome

(2013) Eugenia Radulescu et al.   NeuroImage-Clinical

Dissecting psychiatric spectrum disorders by generative embedding

(2013) Kay H. Brodersen et al.   NeuroImage-Clinical

Analysing connectivity with Granger causality and dynamic causal modelling

(2012) Karl Friston et al.   CURRENT OPINION IN NEUROBIOLOGY

A systematic review of resting-state functional-MRI studies in major depression

(2012) L. Wang et al.   JOURNAL OF AFFECTIVE DISORDERS

Changes in Auditory Feedback Connections Determine the Severity of Speech Processing Deficits after Stroke

(2012) T. M. Schofield et al.   JOURNAL OF NEUROSCIENCE

Reduced Prefrontal-Parietal Effective Connectivity and Working Memory Deficits in Schizophrenia

(2012) L. Deserno et al.   JOURNAL OF NEUROSCIENCE

Why has it taken so long for biological psychiatry to develop clinical tests and what to do about it?

(2012) S Kapur et al.   MOLECULAR PSYCHIATRY

Early development of arterial spin labeling to measure regional brain blood flow by MRI

(2012) Alan P. Koretsky   NEUROIMAGE

The secret lives of experiments: Methods reporting in the fMRI literature

(2012) Joshua Carp   NEUROIMAGE

FreeSurfer

(2012) Bruce Fischl   NEUROIMAGE

When the world becomes ‘too real’: a Bayesian explanation of autistic perception

(2012) Elizabeth Pellicano et al.   TRENDS IN COGNITIVE SCIENCES

Data sharing in neuroimaging research

(2012) Jean-Baptiste Poline et al.   Frontiers in Neuroinformatics

A Bayesian foundation for individual learning under uncertainty

(2011) Christoph Mathys   Frontiers in Human Neuroscience

From reinforcement learning models to psychiatric and neurological disorders

(2011) Tiago V Maia et al.   NATURE NEUROSCIENCE

The impact of physiological noise correction on fMRI at 7 T

(2011) C. Hutton et al.   NEUROIMAGE

Using pulse oximetry to account for high and low frequency physiological artifacts in the BOLD signal

(2011) Timothy D. Verstynen et al.   NEUROIMAGE

FSL

(2011) Mark Jenkinson et al.   NEUROIMAGE

Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion

(2011) Jonathan D. Power et al.   NEUROIMAGE

Dynamic Causal Models and Physiological Inference: A Validation Study Using Isoflurane Anaesthesia in Rodents

(2011) Rosalyn J. Moran et al.   PLoS One

Individualized prediction of illness course at the first psychotic episode: a support vector machine MRI study

(2011) J. Mourao-Miranda et al.   PSYCHOLOGICAL MEDICINE

Large-scale brain networks and psychopathology: a unifying triple network model

(2011) Vinod Menon   TRENDS IN COGNITIVE SCIENCES

Computational psychiatry

(2011) P. Read Montague et al.   TRENDS IN COGNITIVE SCIENCES

Generative Embedding for Model-Based Classification of fMRI Data

(2011) Kay H. Brodersen et al.   PLoS Computational Biology

Observing the Observer (I): Meta-Bayesian Models of Learning and Decision-Making

(2010) Jean Daunizeau et al.   PLoS One

Observing the Observer (II): Deciding When to Decide

(2010) Jean Daunizeau et al.   PLoS One

Toward New Approaches to Psychotic Disorders: The NIMH Research Domain Criteria Project

(2010) B. N. Cuthbert et al.   SCHIZOPHRENIA BULLETIN

Abnormal Amygdala-Prefrontal Effective Connectivity to Happy Faces Differentiates Bipolar from Major Depression

(2009) Jorge Renner Cardoso de Almeida et al.   BIOLOGICAL PSYCHIATRY

Estimating Bayes factors via thermodynamic integration and population MCMC

(2009) Ben Calderhead et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Automatic quality assessment in structural brain magnetic resonance imaging

(2009) Bénédicte Mortamet et al.   MAGNETIC RESONANCE IN MEDICINE

Bayesian model selection for group studies

(2009) Klaas Enno Stephan et al.   NEUROIMAGE

Effects of model-based physiological noise correction on default mode network anti-correlations and correlations

(2009) Catie Chang et al.   NEUROIMAGE

Understanding why patients with schizophrenia do not perceive the hollow-mask illusion using dynamic causal modelling

(2009) Danai Dima et al.   NEUROIMAGE

Ten simple rules for dynamic causal modeling

(2009) K.E. Stephan et al.   NEUROIMAGE

Dynamic causal modelling: A critical review of the biophysical and statistical foundations

(2009) J. Daunizeau et al.   NEUROIMAGE

A failure to grasp the affective meaning of actions in autism spectrum disorder subjects

(2009) J. Grèzes et al.   NEUROPSYCHOLOGIA

Dysconnection in Schizophrenia: From Abnormal Synaptic Plasticity to Failures of Self-monitoring

(2009) K. E. Stephan et al.   SCHIZOPHRENIA BULLETIN

The free-energy principle: a rough guide to the brain?

(2009) Karl Friston   TRENDS IN COGNITIVE SCIENCES

A review on eye movement studies in childhood and adolescent psychiatry

(2008) Nanda N.J. Rommelse et al.   BRAIN AND COGNITION

Automated quality control of brain MR images

(2008) Elias L. Gedamu et al.   JOURNAL OF MAGNETIC RESONANCE IMAGING

Fronto-cingulate effective connectivity in major depression: A study with fMRI and dynamic causal modeling

(2008) R.G.M. Schlösser et al.   NEUROIMAGE

The respiration response function: The temporal dynamics of fMRI signal fluctuations related to changes in respiration

(2008) Rasmus M. Birn et al.   NEUROIMAGE

Influence of heart rate on the BOLD signal: The cardiac response function

(2008) Catie Chang et al.   NEUROIMAGE

A unified Bayesian framework for MEG/EEG source imaging

(2008) David Wipf et al.   NEUROIMAGE

Physiological noise modelling for spinal functional magnetic resonance imaging studies

(2007) Jonathan C.W. Brooks et al.   NEUROIMAGE