What matters in reinforcement learning for tractography.

Recently, deep reinforcement learning (RL) has been proposed to learn the tractography procedure and train agents to reconstruct the structure of the white matter without manually curated reference streamlines. While the performances reported were competitive, the proposed framework is complex, and little is still known about the role and impact of its multiple parts. In this work, we thoroughly explore the different components of the proposed framework, such as the choice of the RL algorithm, seeding strategy, the input signal and reward function, and shed light on their impact.

Manifold-aware synthesis of high-resolution diffusion from structural imaging.

The physical and clinical constraints surrounding diffusion-weighted imaging (DWI) often limit the spatial resolution of the produced images to voxels up to eight times larger than those of T1w images. The detailed information contained in accessible high-resolution T1w images could help in the synthesis of diffusion images with a greater level of detail. However, the non-Euclidean nature of diffusion imaging hinders current deep generative models from synthesizing physically plausible images.

DORIS: A diffusion MRI-based 10 tissue class deep learning segmentation algorithm tailored to improve anatomically-constrained tractography.

Modern tractography algorithms such as anatomically-constrained tractography (ACT) are based on segmentation maps of white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF). These maps are generally estimated from a T1-weighted (T1w) image and then registered in diffusion weighted images (DWI) space. Registration of T1w to diffusion space and partial volume estimation are challenging and rarely voxel-perfect.

FIESTA: Autoencoders for accurate fiber segmentation in tractography.

White matter bundle segmentation is a cornerstone of modern tractography to study the brain's structural connectivity in domains such as neurological disorders, neurosurgery, and aging. In this study, we present FIESTA (FIbEr Segmentation in Tractography using Autoencoders), a reliable and robust, fully automated, and easily semi-automatically calibrated pipeline based on deep autoencoders that can dissect and fully populate white matter bundles. This pipeline is built upon previous works that demonstrated how autoencoders can be used successfully for streamline filtering, bundle segmentation, and streamline generation in tractography.

GANs for Medical Image Synthesis: An Empirical Study.

Generative adversarial networks (GANs) have become increasingly powerful, generating mind-blowing photorealistic images that mimic the content of datasets they have been trained to replicate. One recurrent theme in medical imaging, is whether GANs can also be as effective at generating workable medical data, as they are for generating realistic RGB images. In this paper, we perform a multi-GAN and multi-application study, to gauge the benefits of GANs in medical imaging.

Generative Sampling in Bundle Tractography using Autoencoders (GESTA).

Current tractography methods use the local orientation information to propagate streamlines from seed locations. Many such seeds provide streamlines that stop prematurely or fail to map the true white matter pathways because some bundles are "harder-to-track" than others. This results in tractography reconstructions with poor white and gray matter spatial coverage.

TractoInferno - A large-scale, open-source, multi-site database for machine learning dMRI tractography.

TractoInferno is the world's largest open-source multi-site tractography database, including both research- and clinical-like human acquisitions, aimed specifically at machine learning tractography approaches and related ML algorithms. It provides 284 samples acquired from 3 T scanners across 6 different sites. Available data includes T1-weighted images, single-shell diffusion MRI (dMRI) acquisitions, spherical harmonics fitted to the dMRI signal, fiber ODFs, and reference streamlines for 30 delineated bundles generated using 4 tractography algorithms, as well as masks needed to run tractography algorithms.

Echocardiography Segmentation With Enforced Temporal Consistency.

Convolutional neural networks (CNN) have demonstrated their ability to segment 2D cardiac ultrasound images. However, despite recent successes according to which the intra-observer variability on end-diastole and end-systole images has been reached, CNNs still struggle to leverage temporal information to provide accurate and temporally consistent segmentation maps across the whole cycle. Such consistency is required to accurately describe the cardiac function, a necessary step in diagnosing many cardiovascular diseases.

ProstAttention-Net: A deep attention model for prostate cancer segmentation by aggressiveness in MRI scans.

Multiparametric magnetic resonance imaging (mp-MRI) has shown excellent results in the detection of prostate cancer (PCa). However, characterizing prostate lesions aggressiveness in mp-MRI sequences is impossible in clinical practice, and biopsy remains the reference to determine the Gleason score (GS). In this work, we propose a novel end-to-end multi-class network that jointly segments the prostate gland and cancer lesions with GS group grading.

Generative Adversarial Networks in Cardiology.

Generative adversarial networks (GANs) are state-of-the-art neural network models used to synthesise images and other data. GANs brought a considerable improvement to the quality of synthetic data, quickly becoming the standard for data-generation tasks. In this work, we summarise the applications of GANs in the field of cardiology, including generation of realistic cardiac images, electrocardiography signals, and synthetic electronic health records.

Filtering in tractography using autoencoders (FINTA).

Current brain white matter fiber tracking techniques show a number of problems, including: generating large proportions of streamlines that do not accurately describe the underlying anatomy; extracting streamlines that are not supported by the underlying diffusion signal; and under-representing some fiber populations, among others. In this paper, we describe a novel autoencoder-based learning method to filter streamlines from diffusion MRI tractography, and hence, to obtain more reliable tractograms. Our method, dubbed FINTA (Filtering in Tractography using Autoencoders) uses raw, unlabeled tractograms to train the autoencoder, and to learn a robust representation of brain streamlines.

Track-to-Learn: A general framework for tractography with deep reinforcement learning.

Diffusion MRI tractography is currently the only non-invasive tool able to assess the white-matter structural connectivity of a brain. Since its inception, it has been widely documented that tractography is prone to producing erroneous tracks while missing true positive connections. Recently, supervised learning algorithms have been proposed to learn the tracking procedure implicitly from data, without relying on anatomical priors.

Privacy-Net: An Adversarial Approach for Identity-Obfuscated Segmentation of Medical Images.

This paper presents a client/server privacy-preserving network in the context of multicentric medical image analysis. Our approach is based on adversarial learning which encodes images to obfuscate the patient identity while preserving enough information for a target task. Our novel architecture is composed of three components: 1) an encoder network which removes identity-specific features from input medical images, 2) a discriminator network that attempts to identify the subject from the encoded images, 3) a medical image analysis network which analyzes the content of the encoded images (segmentation in our case).

LU-Net: A Multistage Attention Network to Improve the Robustness of Segmentation of Left Ventricular Structures in 2-D Echocardiography.

Segmentation of cardiac structures is one of the fundamental steps to estimate volumetric indices of the heart. This step is still performed semiautomatically in clinical routine and is, thus, prone to interobserver and intraobserver variabilities. Recent studies have shown that deep learning has the potential to perform fully automatic segmentation.

Cardiac Segmentation With Strong Anatomical Guarantees.

Convolutional neural networks (CNN) have had unprecedented success in medical imaging and, in particular, in medical image segmentation. However, despite the fact that segmentation results are closer than ever to the inter-expert variability, CNNs are not immune to producing anatomically inaccurate segmentations, even when built upon a shape prior. In this paper, we present a framework for producing cardiac image segmentation maps that are guaranteed to respect pre-defined anatomical criteria, while remaining within the inter-expert variability.

Free Water in White Matter Differentiates MCI and AD From Control Subjects.

Recent evidence shows that neuroinflammation plays a role in many neurological diseases including mild cognitive impairment (MCI) and Alzheimer's disease (AD), and that free water (FW) modeling from clinically acquired diffusion MRI (DTI-like acquisitions) can be sensitive to this phenomenon. This FW index measures the fraction of the diffusion signal explained by isotropically unconstrained water, as estimated from a bi-tensor model. In this study, we developed a simple but powerful whole-brain FW measure designed for easy translation to clinical settings and potential use as a priori outcome measure in clinical trials.

Tractography and machine learning: Current state and open challenges.

Supervised machine learning (ML) algorithms have recently been proposed as an alternative to traditional tractography methods in order to address some of their weaknesses. They can be path-based and local-model-free, and easily incorporate anatomical priors to make contextual and non-local decisions that should help the tracking process. ML-based techniques have thus shown promising reconstructions of larger spatial extent of existing white matter bundles, promising reconstructions of less false positives, and promising robustness to known position and shape biases of current tractography techniques.

Deep Learning for Segmentation Using an Open Large-Scale Dataset in 2D Echocardiography.

Delineation of the cardiac structures from 2D echocardiographic images is a common clinical task to establish a diagnosis. Over the past decades, the automation of this task has been the subject of intense research. In this paper, we evaluate how far the state-of-the-art encoder-decoder deep convolutional neural network methods can go at assessing 2D echocardiographic images, i.

Automatic classification of tissues on pelvic MRI based on relaxation times and support vector machine.

Tissue segmentation and classification in MRI is a challenging task due to a lack of signal intensity standardization. MRI signal is dependent on the acquisition protocol, the coil profile, the scanner type, etc. While we can compute quantitative physical tissue properties independent of the hardware and the sequence parameters, it is still difficult to leverage these physical properties to segment and classify pelvic tissues.

Convolutional Neural Network With Shape Prior Applied to Cardiac MRI Segmentation.

In this paper, we present a novel convolutional neural network architecture to segment images from a series of short-axis cardiac magnetic resonance slices (CMRI). The proposed model is an extension of the U-net that embeds a cardiac shape prior and involves a loss function tailored to the cardiac anatomy. Since the shape prior is computed offline only once, the execution of our model is not limited by its calculation.

Cortical thickness analysis in operculo-insular epilepsy.

Background: In temporal lobe epilepsy (TLE), advanced neuroimaging techniques reveal anomalies extending beyond the temporal lobe such as thinning of fronto-central cortices. Operculo-insular epilepsy (OIE) is an under-recognized and poorly characterized condition with the potential of mimicking TLE. In this work, we investigated insular and extra-insular cortical thickness (CT) changes in OIE.

Deep Learning Techniques for Automatic MRI Cardiac Multi-Structures Segmentation and Diagnosis: Is the Problem Solved?

Delineation of the left ventricular cavity, myocardium, and right ventricle from cardiac magnetic resonance images (multi-slice 2-D cine MRI) is a common clinical task to establish diagnosis. The automation of the corresponding tasks has thus been the subject of intense research over the past decades. In this paper, we introduce the "Automatic Cardiac Diagnosis Challenge" dataset (ACDC), the largest publicly available and fully annotated dataset for the purpose of cardiac MRI (CMR) assessment.

MIO-TCD: A new benchmark dataset for vehicle classification and localization.

The ability to train on a large dataset of labeled samples is critical to the success of deep learning in many domains. In this paper, we focus on motor vehicle classification and localization from a single video frame and introduce the "MIOvision Traffic Camera Dataset" (MIO-TCD) in this context. MIO-TCD is the largest dataset for motorized traffic analysis to date.

A test-retest study on Parkinson's PPMI dataset yields statistically significant white matter fascicles.

In this work, we propose a diffusion MRI protocol for mining Parkinson's disease diffusion MRI datasets and recover robust disease-specific biomarkers. Using advanced high angular resolution diffusion imaging (HARDI) crossing fiber modeling and tractography robust to partial volume effects, we automatically dissected 50 white matter (WM) fascicles. These fascicles connect deep nuclei (thalamus, putamen, pallidum) to different cortical functional areas (associative, motor, sensorimotor, limbic), basal forebrain and substantia nigra.

Extensive Benchmark and Survey of Modeling Methods for Scene Background Initialization.

Scene background initialization is the process by which a method tries to recover the background image of a video without foreground objects in it. Having a clear understanding about which approach is more robust and/or more suited to a given scenario is of great interest to many end users or practitioners. The aim of this paper is to provide an extensive survey of scene background initialization methods as well as a novel benchmarking framework.