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View article: A probabilistic histological atlas of the human brain for MRI segmentation
A probabilistic histological atlas of the human brain for MRI segmentation Open
In human neuroimaging, brain atlases are essential for segmenting regions of interest (ROIs) and comparing subjects in a common coordinate frame. State-of-the-art atlases derived from histology1-3 provide exquisite three-dimensi…
View article: Deep generative priors for 3D brain analysis
Deep generative priors for 3D brain analysis Open
Diffusion models have recently emerged as powerful generative models in medical imaging. However, it remains a major challenge to combine these data-driven models with domain knowledge to guide brain imaging problems. In neuroimaging, Baye…
View article: Fast segmentation with the NextBrain histological atlas
Fast segmentation with the NextBrain histological atlas Open
Structural brain analysis at the subregion level offers critical insights into healthy aging and neurodegenerative diseases. The NextBrain histological atlas was recently introduced to support such fine-grained investigations, but its exis…
View article: Towards quantitative intensity analysis of conventional T1-weighted images in multiple sclerosis
Towards quantitative intensity analysis of conventional T1-weighted images in multiple sclerosis Open
Conventional T1-weighted (T1w) magnetic resonance imaging (MRI) is commonly used in multiple sclerosis (MS) morphometry and volumetry research. However, arbitrary intensity scales preclude interpretation of signal values across patients, s…
View article: Visualizing cortical laminar architecture in the living human brain using next-generation ultra-high-gradient diffusion MRI
Visualizing cortical laminar architecture in the living human brain using next-generation ultra-high-gradient diffusion MRI Open
View article: Learning to Upscale 3D Segmentations in Neuroimaging
Learning to Upscale 3D Segmentations in Neuroimaging Open
Obtaining high-resolution (HR) segmentations from coarse annotations is a pervasive challenge in computer vision. Applications include inferring pixel-level segmentations from token-level labels in vision transformers, upsampling coarse ma…
View article: End-to-end Cortical Surface Reconstruction from Clinical Magnetic Resonance Images
End-to-end Cortical Surface Reconstruction from Clinical Magnetic Resonance Images Open
Surface-based cortical analysis is valuable for a variety of neuroimaging tasks, such as spatial normalization, parcellation, and gray matter (GM) thickness estimation. However, most tools for estimating cortical surfaces work exclusively …
View article: Reference-Free 3D Reconstruction of Brain Dissection Photographs with Machine Learning
Reference-Free 3D Reconstruction of Brain Dissection Photographs with Machine Learning Open
Correlation of neuropathology with MRI has the potential to transfer microscopic signatures of pathology to invivo scans. Recently, a classical registration method has been proposed, to build these correlations from 3D reconstructed stacks…
View article: Enhancing transcranial ultrasound stimulation planning with MRI-derived skull masks: a comparative analysis with CT-based processing
Enhancing transcranial ultrasound stimulation planning with MRI-derived skull masks: a comparative analysis with CT-based processing Open
Objective. Transcranial ultrasound stimulation (TUS) presents challenges in ultrasound wave transmission through the skull, affecting study outcomes due to aberration and attenuation. While planning strategies incorporating 3D computed tom…
View article: Phase-lag dependent modulation of primary motor cortices connectivity using dual-site tACS: Simulation and preliminary EEG study
Phase-lag dependent modulation of primary motor cortices connectivity using dual-site tACS: Simulation and preliminary EEG study Open
View article: Generating, validating and applying volume conductor models for electric field simulations to determine and optimize the brain regions targeting by transcranial brain stimulation
Generating, validating and applying volume conductor models for electric field simulations to determine and optimize the brain regions targeting by transcranial brain stimulation Open
View article: Ernie Extended - an extended head model to simulate and optimize noninvasive brain stimulation and its implications for extracephalic transcranial electrical stimulation
Ernie Extended - an extended head model to simulate and optimize noninvasive brain stimulation and its implications for extracephalic transcranial electrical stimulation Open
View article: Enhancing Transcranial Ultrasound Stimulation Planning with MRI-Derived Skull Masks: A Comparative Analysis with CT-Based Processing
Enhancing Transcranial Ultrasound Stimulation Planning with MRI-Derived Skull Masks: A Comparative Analysis with CT-Based Processing Open
View article: Fast FEM-based Electric Field Calculations for Transcranial Magnetic Stimulation
Fast FEM-based Electric Field Calculations for Transcranial Magnetic Stimulation Open
Objective To provide a Finite-Element Method (FEM) for rapid, repeated evaluations of the electric field induced by transcranial magnetic stimulation (TMS) in the brain for changing coil positions. Approach Previously, we introduced a firs…
View article: Learn2Synth: Learning Optimal Data Synthesis Using Hypergradients for Brain Image Segmentation
Learn2Synth: Learning Optimal Data Synthesis Using Hypergradients for Brain Image Segmentation Open
Domain randomization through synthesis is a powerful strategy to train networks that are unbiased with respect to the domain of the input images. Randomization allows networks to see a virtually infinite range of intensities and artifacts …
View article: Hierarchical Uncertainty Estimation for Learning-based Registration in Neuroimaging
Hierarchical Uncertainty Estimation for Learning-based Registration in Neuroimaging Open
Over recent years, deep learning based image registration has achieved impressive accuracy in many domains, including medical imaging and, specifically, human neuroimaging with magnetic resonance imaging (MRI). However, the uncertainty est…
View article: Recon-all-clinical: Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI
Recon-all-clinical: Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI Open
Surface-based analysis of the cerebral cortex is ubiquitous in human neuroimaging with MRI. It is crucial for cortical registration, parcellation, and thickness estimation. Traditionally, these analyses require high-resolution, isotropic s…
View article: HEAD AND SHOULDERS - THE IMPACT OF AN EXTENDED HEAD MODEL ON THE SIMULATION AND OPTIMIZATION OF TRANSCRANIAL ELECTRIC STIMULATION
HEAD AND SHOULDERS - THE IMPACT OF AN EXTENDED HEAD MODEL ON THE SIMULATION AND OPTIMIZATION OF TRANSCRANIAL ELECTRIC STIMULATION Open
Electric field calculations are increasingly used for dose characterization of transcranial electrical stimulation (tES), but existing open-source head models are inaccurate for extracephalic montages that include electrodes placed on the …
View article: High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models
High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models Open
Segmentation of brain structures on magnetic resonance imaging (MRI) is a highly relevant neuroimaging topic, as it is a prerequisite for different analyses such as volumetry or shape analysis. Automated segmentation facilitates the study …
View article: High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models
High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models Open
Segmentation of brain structures on magnetic resonance imaging (MRI) is a highly relevant neuroimaging topic, as it is a prerequisite for different analyses such as volumetry or shape analysis. Automated segmentation facilitates the study …
View article: Quantifying White Matter Hyperintensity and Brain Volumes in Heterogeneous Clinical and Low-Field Portable MRI
Quantifying White Matter Hyperintensity and Brain Volumes in Heterogeneous Clinical and Low-Field Portable MRI Open
Brain atrophy and white matter hyperintensity (WMH) are critical neuroimaging features for ascertaining brain injury in cerebrovascular disease and multiple sclerosis. Automated segmentation and quantification is desirable but existing met…
View article: MR imaging of the magnetic fields induced by injected currents can guide improvements of individualized head volume conductor models
MR imaging of the magnetic fields induced by injected currents can guide improvements of individualized head volume conductor models Open
Volume conductor models of the human head are routinely used to estimate the induced electric fields in transcranial brain stimulation (TBS) and for source localization in electro- and magnetoencephalography (EEG and MEG). Magnetic resonan…
View article: Registration by Regression (RbR): a framework for interpretable and flexible atlas registration
Registration by Regression (RbR): a framework for interpretable and flexible atlas registration Open
In human neuroimaging studies, atlas registration enables mapping MRI scans to a common coordinate frame, which is necessary to aggregate data from multiple subjects. Machine learning registration methods have achieved excellent speed and …
View article: Exploring an EM-algorithm for banded regression in computational neuroscience
Exploring an EM-algorithm for banded regression in computational neuroscience Open
Regression is a principal tool for relating brain responses to stimuli or tasks in computational neuroscience. This often involves fitting linear models with predictors that can be divided into groups, such as distinct stimulus feature sub…
View article: Neuroanatomical Predictors of Transcranial Direct Current Stimulation (tDCS)-Induced Modifications in Neurocognitive Task Performance in Typically Developing Individuals
Neuroanatomical Predictors of Transcranial Direct Current Stimulation (tDCS)-Induced Modifications in Neurocognitive Task Performance in Typically Developing Individuals Open
Transcranial direct current stimulation (tDCS) is a noninvasive neuromodulation technique gaining more attention in neurodevelopmental disorders (NDDs). Due to the phenotypic heterogeneity of NDDs, tDCS is unlikely to be equally effective …
View article: P-Count: Persistence-based Counting of White Matter Hyperintensities in Brain MRI
P-Count: Persistence-based Counting of White Matter Hyperintensities in Brain MRI Open
White matter hyperintensities (WMH) are a hallmark of cerebrovascular disease and multiple sclerosis. Automated WMH segmentation methods enable quantitative analysis via estimation of total lesion load, spatial distribution of lesions, and…
View article: PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI
PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI Open
Remarkable progress has been made by data-driven machine-learning methods in the analysis of MRI scans. However, most existing MRI analysis approaches are crafted for specific MR pulse sequences (MR contrasts) and usually require nearly is…
View article: A next-generation, histological atlas of the human brain and its application to automated brain MRI segmentation
A next-generation, histological atlas of the human brain and its application to automated brain MRI segmentation Open
Magnetic resonance imaging (MRI) is the standard tool to image the human brain in vivo . In this domain, digital brain atlases are essential for subject-specific segmentation of anatomical regions of interest (ROIs) and spatial comparison …
View article: H-SynEx: Using synthetic images and ultra-high resolution ex vivo MRI for hypothalamus subregion segmentation
H-SynEx: Using synthetic images and ultra-high resolution ex vivo MRI for hypothalamus subregion segmentation Open
The hypothalamus is a small structure located in the center of the brain and is involved in significant functions such as sleeping, temperature, and appetite control. Various neurological disorders are also associated with hypothalamic abn…
View article: Head and shoulders—The impact of an extended head model on the simulation and optimization of transcranial electric stimulation
Head and shoulders—The impact of an extended head model on the simulation and optimization of transcranial electric stimulation Open
Electric field calculations are increasingly used for dose characterization of transcranial electrical stimulation (tES), but existing open-source head models are inaccurate for extracephalic montages that include electrodes placed on the …