RATNUS: Rapid, Automatic Thalamic Nuclei Segmentation using Multimodal MRI inputs

Accurate segmentation of thalamic nuclei is important for better understanding brain function and improving disease treatment. Traditional segmentation methods often rely on a single T1-weighted image, which has limited contrast in the thalamus. In this work, we introduce RATNUS, which uses synthetic T1-weighted images with many inversion times along with diffusion-derived features to enhance the visibility of nuclei within the thalamus. Using these features, a convolutional neural network is used to segment 13 thalamic nuclei. For comparison with other methods, we introduce a unified nuclei labeling scheme. Our results demonstrate an 87.19% average true positive rate (TPR) against manual labeling. In comparison, FreeSurfer and THOMAS achieve TPRs of 64.25% and 57.64%, respectively, demonstrating the superiority of RATNUS in thalamic nuclei segmentation.

From Registration Uncertainty to Segmentation Uncertainty

Understanding the uncertainty inherent in deep learning-based image registration models has been an ongoing area of research. Existing methods have been developed to quantify both transformation and appearance uncertainties related to the registration process, elucidating areas where the model may exhibit ambiguity regarding the generated deformation. However, our study reveals that neither uncertainty effectively estimates the potential errors when the registration model is used for label propagation. Here, we propose a novel framework to concurrently estimate both the epistemic and aleatoric segmentation uncertainties for image registration. To this end, we implement a compact deep neural network (DNN) designed to transform the appearance discrepancy in the warping into aleatoric segmentation uncertainty by minimizing a negative log-likelihood loss function. Furthermore, we present epistemic segmentation uncertainty within the label propagation process as the entropy of the propagated labels. By introducing segmentation uncertainty along with existing methods for estimating registration uncertainty, we offer vital insights into the potential uncertainties at different stages of image registration. We validated our proposed framework using publicly available datasets, and the results prove that the segmentation uncertainties estimated with the proposed method correlate well with errors in label propagation, all while achieving superior registration performance.

Is Registering Raw Tagged-MR Enough for Strain Estimation in the Era of Deep Learning?

Magnetic Resonance Imaging with tagging (tMRI) has long been utilized for quantifying tissue motion and strain during deformation. However, a phenomenon known as tag fading, a gradual decrease in tag visibility over time, often complicates post-processing. The first contribution of this study is to model tag fading by considering the interplay between $T_1$ relaxation and the repeated application of radio frequency (RF) pulses during serial imaging sequences. This is a factor that has been overlooked in prior research on tMRI post-processing. Further, we have observed an emerging trend of utilizing raw tagged MRI within a deep learning-based (DL) registration framework for motion estimation. In this work, we evaluate and analyze the impact of commonly used image similarity objectives in training DL registrations on raw tMRI. This is then compared with the Harmonic Phase-based approach, a traditional approach which is claimed to be robust to tag fading. Our findings, derived from both simulated images and an actual phantom scan, reveal the limitations of various similarity losses in raw tMRI and emphasize caution in registration tasks where image intensity changes over time.

Efficient Annotation for Medical Image Analysis: A One-Pass Selective Annotation Approach

Annotating biomedical images for supervised learning is a complex and labor-intensive task due to data diversity and its intricate nature. In this paper, we propose an innovative method, the efficient one-pass selective annotation (EPOSA), that significantly reduces the annotation burden while maintaining robust model performance. Our approach employs a variational autoencoder (VAE) to extract salient features from unannotated images, which are subsequently clustered using the DBSCAN algorithm. This process groups similar images together, forming distinct clusters. We then use a two-stage sample selection algorithm, called representative selection (RepSel), to form a selected dataset. The first stage is a Markov Chain Monte Carlo (MCMC) sampling technique to select representative samples from each cluster for annotations. This selection process is the second stage, which is guided by the principle of maximizing intra-cluster mutual information and minimizing inter-cluster mutual information. This ensures a diverse set of features for model training and minimizes outlier inclusion. The selected samples are used to train a VGG-16 network for image classification. Experimental results on the Med-MNIST dataset demonstrate that our proposed EPOSA outperforms random selection and other state-of-the-art methods under the same annotation budget, presenting a promising direction for efficient and effective annotation in medical image analysis.

MomentaMorph: Unsupervised Spatial-Temporal Registration with Momenta, Shooting, and Correction

Tagged magnetic resonance imaging (tMRI) has been employed for decades to measure the motion of tissue undergoing deformation. However, registration-based motion estimation from tMRI is difficult due to the periodic patterns in these images, particularly when the motion is large. With a larger motion the registration approach gets trapped in a local optima, leading to motion estimation errors. We introduce a novel "momenta, shooting, and correction" framework for Lagrangian motion estimation in the presence of repetitive patterns and large motion. This framework, grounded in Lie algebra and Lie group principles, accumulates momenta in the tangent vector space and employs exponential mapping in the diffeomorphic space for rapid approximation towards true optima, circumventing local optima. A subsequent correction step ensures convergence to true optima. The results on a 2D synthetic dataset and a real 3D tMRI dataset demonstrate our method's efficiency in estimating accurate, dense, and diffeomorphic 2D/3D motion fields amidst large motion and repetitive patterns.

A Survey on Deep Learning in Medical Image Registration: New Technologies, Uncertainty, Evaluation Metrics, and Beyond

Over the past decade, deep learning technologies have greatly advanced the field of medical image registration. The initial developments, such as ResNet-based and U-Net-based networks, laid the groundwork for deep learning-driven image registration. Subsequent progress has been made in various aspects of deep learning-based registration, including similarity measures, deformation regularizations, and uncertainty estimation. These advancements have not only enriched the field of deformable image registration but have also facilitated its application in a wide range of tasks, including atlas construction, multi-atlas segmentation, motion estimation, and 2D-3D registration. In this paper, we present a comprehensive overview of the most recent advancements in deep learning-based image registration. We begin with a concise introduction to the core concepts of deep learning-based image registration. Then, we delve into innovative network architectures, loss functions specific to registration, and methods for estimating registration uncertainty. Additionally, this paper explores appropriate evaluation metrics for assessing the performance of deep learning models in registration tasks. Finally, we highlight the practical applications of these novel techniques in medical imaging and discuss the future prospects of deep learning-based image registration.

LitCall: Learning Implicit Topology for CNN-based Aortic Landmark Localization

Landmark detection is a critical component of the image processing pipeline for automated aortic size measurements. Given that the thoracic aorta has a relatively conserved topology across the population and that a human annotator with minimal training can estimate the location of unseen landmarks from limited examples, we proposed an auxiliary learning task to learn the implicit topology of aortic landmarks through a CNN-based network. Specifically, we created a network to predict the location of missing landmarks from the visible ones by minimizing the Implicit Topology loss in an end-to-end manner. The proposed learning task can be easily adapted and combined with Unet-style backbones. To validate our method, we utilized a dataset consisting of 207 CTAs, labeling four landmarks on each aorta. Our method outperforms the state-of-the-art Unet-style architectures (ResUnet, UnetR) in terms of localization accuracy, with only a light (#params=0.4M) overhead. We also demonstrate our approach in two clinically meaningful applications: aortic sub-region division and automatic centerline generation.

DrDisco: Deep Registration for Distortion Correction of Diffusion MRI with single phase-encoding

Diffusion-weighted magnetic resonance imaging (DW-MRI) is a non-invasive way of imaging white matter tracts in the human brain. DW-MRIs are usually acquired using echo-planar imaging (EPI) with high gradient fields, which could introduce severe geometric distortions that interfere with further analyses. Most tools for correcting distortion require two minimally weighted DW-MRI images (B0) acquired with different phase-encoding directions, and they can take hours to process per subject. Since a great amount of diffusion data are only acquired with a single phase-encoding direction, the application of existing approaches is limited. We propose a deep learning-based registration approach to correct distortion using only the B0 acquired from a single phase-encoding direction. Specifically, we register undistorted T1-weighted images and distorted B0 to remove the distortion through a deep learning model. We apply a differentiable mutual information loss during training to improve inter-modality alignment. Experiments on the Human Connectome Project dataset show the proposed method outperforms SyN and VoxelMorph on several metrics, and only takes a few seconds to process one subject.

Label Propagation via Random Walk for Training Robust Thalamus Nuclei Parcellation Model from Noisy Annotations

Data-driven thalamic nuclei parcellation depends on high-quality manual annotations. However, the small size and low contrast changes among thalamic nuclei, yield annotations that are often incomplete, noisy, or ambiguously labelled. To train a robust thalamic nuclei parcellation model with noisy annotations, we propose a label propagation algorithm based on random walker to refine the annotations before model training. A two-step model was trained to generate first the whole thalamus and then the nuclei masks. We conducted experiments on a mild traumatic brain injury~(mTBI) dataset with noisy thalamic nuclei annotations. Our model outperforms current state-of-the-art thalamic nuclei parcellations by a clear margin. We believe our method can also facilitate the training of other parcellation models with noisy labels.

FastCod: Fast Brain Connectivity in Diffusion Imaging

Connectivity information derived from diffusion-weighted magnetic resonance images~(DW-MRIs) plays an important role in studying human subcortical gray matter structures. However, due to the $O(N^2)$ complexity of computing the connectivity of each voxel to every other voxel (or multiple ROIs), the current practice of extracting connectivity information is highly inefficient. This makes the processing of high-resolution images and population-level analyses very computationally demanding. To address this issue, we propose a more efficient way to extract connectivity information; briefly, we consider two regions/voxels to be connected if a white matter fiber streamline passes through them -- no matter where the streamline originates. We consider the thalamus parcellation task for demonstration purposes; our experiments show that our approach brings a 30 to 120 times speedup over traditional approaches with comparable qualitative parcellation results. We also demonstrate high-resolution connectivity features can be super-resolved from low-resolution DW-MRI in our framework. Together, these two innovations enable higher resolution connectivity analysis from DW-MRI. Our source code is availible at jasonbian97.github.io/fastcod.