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Found 55 papers, 26 papers with code
Reference-Free 3D Reconstruction of Brain Dissection Photographs with Machine Learning
These photographs bypass the need for exvivo MRI, which is not widely accessible.
A Constrast-Agnostic Method for Ultra-High Resolution Claustrum Segmentation
In this paper, we propose a contrast- and resolution-agnostic method for claustrum segmentation at ultra-high resolution (0. 35 mm isotropic); the method is based on the SynthSeg segmentation framework (Billot et al., 2023), which leverages the use of synthetic training intensity images to achieve excellent generalization.
Hierarchical Uncertainty Estimation for Learning-based Registration in Neuroimaging
Here, we propose a principled way to propagate uncertainties (epistemic or aleatoric) estimated at the level of spatial location by these methods, to the level of global transformation models, and further to downstream tasks.
TV-based Deep 3D Self Super-Resolution for fMRI
While functional Magnetic Resonance Imaging (fMRI) offers valuable insights into cognitive processes, its inherent spatial limitations pose challenges for detailed analysis of the fine-grained functional architecture of the brain.
Recon-all-clinical: Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI
To enable large-scale neuroimaging studies using vast clinical data, we introduce recon-all-clinical, a novel method for cortical reconstruction, registration, parcellation, and thickness estimation in brain MRI scans of any resolution and contrast.
BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023
Pediatric central nervous system tumors are the leading cause of cancer-related deaths in children.
High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models
Here we provide HELM, Hypothalamic ex vivo Label Maps, a dataset composed of label maps built from publicly available ultra-high resolution ex vivo MRI from 10 whole hemispheres, which can be used to develop segmentation methods using synthetic data.
Probabilistic Contrastive Learning with Explicit Concentration on the Hypersphere
Self-supervised contrastive learning has predominantly adopted deterministic methods, which are not suited for environments characterized by uncertainty and noise.
Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge
The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0. 976, 0. 976, and 0. 964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0. 899, 0. 904, and 0. 871, respectively.
Registration by Regression (RbR): a framework for interpretable and flexible atlas registration
In human neuroimaging studies, atlas registration enables mapping MRI scans to a common coordinate frame, which is necessary to aggregate data from multiple subjects.
The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)
Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children.
P-Count: Persistence-based Counting of White Matter Hyperintensities in Brain MRI
White matter hyperintensities (WMH) are a hallmark of cerebrovascular disease and multiple sclerosis.
H-SynEx: Using synthetic images and ultra-high resolution ex vivo MRI for hypothalamus subregion segmentation
Our results show that H-SynEx successfully leverages information from ultra-high resolution scans to segment in vivo from different MRI sequences.
JUMP: A joint multimodal registration pipeline for neuroimaging with minimal preprocessing
We present a pipeline for unbiased and robust multimodal registration of neuroimaging modalities with minimal pre-processing.
Quantifying white matter hyperintensity and brain volumes in heterogeneous clinical and low-field portable MRI
Brain atrophy and white matter hyperintensity (WMH) are critical neuroimaging features for ascertaining brain injury in cerebrovascular disease and multiple sclerosis.
Fully Convolutional Slice-to-Volume Reconstruction for Single-Stack MRI
Here, we propose a SVR method that overcomes the shortcomings of previous work and produces state-of-the-art reconstructions in the presence of extreme inter-slice motion.
Resolution- and Stimulus-agnostic Super-Resolution of Ultra-High-Field Functional MRI: Application to Visual Studies
High-resolution fMRI provides a window into the brain's mesoscale organization.
USLR: an open-source tool for unbiased and smooth longitudinal registration of brain MR
We present USLR, a computational framework for longitudinal registration of brain MRI scans to estimate nonlinear image trajectories that are smooth across time, unbiased to any timepoint, and robust to imaging artefacts.
Diffeomorphic Multi-Resolution Deep Learning Registration for Applications in Breast MRI
In breast surgical planning, accurate registration of MR images across patient positions has the potential to improve the localisation of tumours during breast cancer treatment.
Robust and Generalisable Segmentation of Subtle Epilepsy-causing Lesions: a Graph Convolutional Approach
On a multi-centre dataset of 1015 participants with surface-based features and manual lesion masks from structural MRI data, the proposed GCN achieved an AUC of 0. 74, a significant improvement against a previously used vertex-wise multi-layer perceptron (MLP) classifier (AUC 0. 64).
The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI
Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing.
The Brain Tumor Segmentation (BraTS) Challenge 2023: Glioma Segmentation in Sub-Saharan Africa Patient Population (BraTS-Africa)
Thus, the BraTS-Africa Challenge provides a unique opportunity to include brain MRI glioma cases from SSA in global efforts through the BraTS Challenge to develop and evaluate computer-aided-diagnostic (CAD) methods for the detection and characterization of glioma in resource-limited settings, where the potential for CAD tools to transform healthcare are more likely.
The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)
Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children.
The Brain Tumor Segmentation (BraTS) Challenge: Local Synthesis of Healthy Brain Tissue via Inpainting
The challenge is organized as part of the ASNR-BraTS MICCAI challenge.
The Brain Tumor Segmentation (BraTS) Challenge 2023: Brain MR Image Synthesis for Tumor Segmentation (BraSyn)
In this work, we present the establishment of the Brain MR Image Synthesis Benchmark (BraSyn) in conjunction with the Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2023.
The ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2023: Intracranial Meningioma
Meningiomas are the most common primary intracranial tumor in adults and can be associated with significant morbidity and mortality.
Domain-agnostic segmentation of thalamic nuclei from joint structural and diffusion MRI
Some tools have attempted to incorporate information from diffusion MRI in the segmentation to refine these boundaries, but do not generalise well across diffusion MRI acquisitions.
Cortical analysis of heterogeneous clinical brain MRI scans for large-scale neuroimaging studies
Here we present the first method for cortical reconstruction, registration, parcellation, and thickness estimation for clinical brain MRI scans of any resolution and pulse sequence.
A Domain-specific Perceptual Metric via Contrastive Self-supervised Representation: Applications on Natural and Medical Images
We find that in the natural image domain, CSR behaves on par with the supervised one on several perceptual tests as a metric, and in the medical domain, CSR better quantifies perceptual similarity concerning the experts' ratings.
SVoRT: Iterative Transformer for Slice-to-Volume Registration in Fetal Brain MRI
Experiments with real-world MRI data are also performed to demonstrate the ability of the proposed model to improve the quality of 3D reconstruction under severe fetal motion.
SuperWarp: Supervised Learning and Warping on U-Net for Invariant Subvoxel-Precise Registration
In recent years, learning-based image registration methods have gradually moved away from direct supervision with target warps to instead use self-supervision, with excellent results in several registration benchmarks.
Accurate super-resolution low-field brain MRI
To address this challenge, recent advances in machine learning facilitate the synthesis of higher resolution images derived from one or multiple lower resolution scans.
Supervision by Denoising for Medical Image Segmentation
SUD unifies stochastic averaging and spatial denoising techniques under a spatio-temporal denoising framework and alternates denoising and model weight update steps in an optimization framework for semi-supervision.
The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients
Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance.
Synth-by-Reg (SbR): Contrastive learning for synthesis-based registration of paired images
Nonlinear inter-modality registration is often challenging due to the lack of objective functions that are good proxies for alignment.
SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining
Here we introduce SynthSeg, the first segmentation CNN robust against changes in contrast and resolution.
Volume of hyperintense inflammation (VHI): a deep learning-enabled quantitative imaging biomarker of inflammation load in spondyloarthritis
Short inversion time inversion recovery (STIR) MRI is widely used in clinical practice to identify and quantify inflammation in axial spondyloarthritis.
Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas
The model relies on a spanning tree of latent transforms connecting all the sections and slices of the reference volume, and assumes that the registration between any pair of images can be see as a noisy version of the composition of (possibly inverted) latent transforms connecting the two images.
Uncertainty-Aware Annotation Protocol to Evaluate Deformable Registration Algorithms
In this paper, we introduce a principled strategy for the construction of a gold standard in deformable registration.
Active Annotation of Informative Overlapping Frames in Video Mosaicking Applications
In addition to the efficient construction of a mosaic, our framework provides, as a by-product, ground truth landmark correspondences which can be used for evaluation or learning purposes.
Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast
Most existing algorithms for automatic 3D morphometry of human brain MRI scans are designed for data with near-isotropic voxels at approximately 1 mm resolution, and frequently have contrast constraints as well - typically requiring T1 scans (e. g., MP-RAGE).
DeepReg: a deep learning toolkit for medical image registration
DeepReg (https://github. com/DeepRegNet/DeepReg) is a community-supported open-source toolkit for research and education in medical image registration using deep learning.
3D Reconstruction and Segmentation of Dissection Photographs for MRI-free Neuropathology
NTNC traditionally requires a volumetric MRI scan, acquired either ex vivo or a short time prior to death.
Joint Frequency and Image Space Learning for MRI Reconstruction and Analysis
This is in contrast to most current deep learning approaches for image reconstruction that treat frequency and image space features separately and often operate exclusively in one of the two spaces.
An Auto-Encoder Strategy for Adaptive Image Segmentation
Thus there is a strong need for deep learning-based segmentation tools that do not require heavy supervision and can continuously adapt.
Partial Volume Segmentation of Brain MRI Scans of any Resolution and Contrast
Partial voluming (PV) is arguably the last crucial unsolved problem in Bayesian segmentation of brain MRI with probabilistic atlases.
SynthMorph: learning contrast-invariant registration without acquired images
This approach results in powerful networks that accurately generalize to a broad array of MRI contrasts.
A Learning Strategy for Contrast-agnostic MRI Segmentation
These samples are produced using the generative model of the classical Bayesian segmentation framework, with randomly sampled parameters for appearance, deformation, noise, and bias field.
Ranked #1 on
Brain Segmentation
on Brain MRI segmentation
Unsupervised Deep Learning for Bayesian Brain MRI Segmentation
To develop a deep learning-based segmentation model for a new image dataset (e. g., of different contrast), one usually needs to create a new labeled training dataset, which can be prohibitively expensive, or rely on suboptimal ad hoc adaptation or augmentation approaches.
Joint inference on structural and diffusion MRI for sequence-adaptive Bayesian segmentation of thalamic nuclei with probabilistic atlases
Segmentation of structural and diffusion MRI (sMRI/dMRI) is usually performed independently in neuroimaging pipelines.
Large-scale mammography CAD with Deformable Conv-Nets
State-of-the-art deep learning methods for image processing are evolving into increasingly complex meta-architectures with a growing number of modules.
A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology
In this study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation.
Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections
Here, we overcome this limitation with a probabilistic method that simultaneously solves for registration and synthesis directly on the target images, without any training data.
Part-to-whole Registration of Histology and MRI using Shape Elements
We propose here a novel automatic approach to the joint problem of multimodal registration between histology and MRI, when only a fraction of tissue is available from histology.
Multi-Atlas Segmentation of Biomedical Images: A Survey
Finally, our goal is to also present a perspective on the future of MAS, which, we believe, will be one of the dominant approaches in biomedical image segmentation.
