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. Machine learning registration methods have achieved excellent speed and accuracy but lack interpretability. More recently, keypoint-based methods have been proposed to tackle this issue, but their accuracy is still subpar, particularly when fitting nonlinear transforms. Here we propose Registration by Regression (RbR), a novel atlas registration framework that is highly robust and flexible, conceptually simple, and can be trained with cheaply obtained data. RbR predicts the (x,y,z) atlas coordinates for every voxel of the input scan (i.e., every voxel is a keypoint), and then uses closed-form expressions to quickly fit transforms using a wide array of possible deformation models, including affine and nonlinear (e.g., Bspline, Demons, invertible diffeomorphic models, etc.). Robustness is provided by the large number of voxels informing the registration and can be further increased by robust estimators like RANSAC. Experiments on independent public datasets show that RbR yields more accurate registration than competing keypoint approaches, while providing full control of the deformation model.

Boosting Skull-Stripping Performance for Pediatric Brain Images

Skull-stripping is the removal of background and non-brain anatomical features from brain images. While many skull-stripping tools exist, few target pediatric populations. With the emergence of multi-institutional pediatric data acquisition efforts to broaden the understanding of perinatal brain development, it is essential to develop robust and well-tested tools ready for the relevant data processing. However, the broad range of neuroanatomical variation in the developing brain, combined with additional challenges such as high motion levels, as well as shoulder and chest signal in the images, leaves many adult-specific tools ill-suited for pediatric skull-stripping. Building on an existing framework for robust and accurate skull-stripping, we propose developmental SynthStrip (d-SynthStrip), a skull-stripping model tailored to pediatric images. This framework exposes networks to highly variable images synthesized from label maps. Our model substantially outperforms pediatric baselines across scan types and age cohorts. In addition, the <1-minute runtime of our tool compares favorably to the fastest baselines. We distribute our model at https://w3id.org/synthstrip.

SE-Equivariant and Noise-Invariant 3D Motion Tracking in Medical Images

Rigid motion tracking is paramount in many medical imaging applications where movements need to be detected, corrected, or accounted for. Modern strategies rely on convolutional neural networks (CNN) and pose this problem as rigid registration. Yet, CNNs do not exploit natural symmetries in this task, as they are equivariant to translations (their outputs shift with their inputs) but not to rotations. Here we propose EquiTrack, the first method that uses recent steerable SE(3)-equivariant CNNs (E-CNN) for motion tracking. While steerable E-CNNs can extract corresponding features across different poses, testing them on noisy medical images reveals that they do not have enough learning capacity to learn noise invariance. Thus, we introduce a hybrid architecture that pairs a denoiser with an E-CNN to decouple the processing of anatomically irrelevant intensity features from the extraction of equivariant spatial features. Rigid transforms are then estimated in closed-form. EquiTrack outperforms state-of-the-art learning and optimisation methods for motion tracking in adult brain MRI and fetal MRI time series. Our code is available at github.com/BBillot/equitrack.

Anatomy-aware and acquisition-agnostic joint registration with SynthMorph

Affine image registration is a cornerstone of medical-image processing and analysis. While classical algorithms can achieve excellent accuracy, they solve a time-consuming optimization for every new image pair. Deep-learning (DL) methods learn a function that maps an image pair to an output transform. Evaluating the functions is fast, but capturing large transforms can be challenging, and networks tend to struggle if a test-image characteristic shifts from the training domain, such as the contrast or resolution. A majority of affine methods are also agnostic to the anatomy the user wishes to align; the registration will be inaccurate if algorithms consider all structures in the image. We address these shortcomings with a fast, robust, and easy-to-use DL tool for affine and deformable registration of any brain image without preprocessing, right off the MRI scanner. First, we rigorously analyze how competing architectures learn affine transforms across a diverse set of neuroimaging data, aiming to truly capture the behavior of methods in the real world. Second, we leverage a recent strategy to train networks with wildly varying images synthesized from label maps, yielding robust performance across acquisition specifics. Third, we optimize the spatial overlap of select anatomical labels, which enables networks to distinguish between anatomy of interest and irrelevant structures, removing the need for preprocessing that excludes content that would otherwise reduce the accuracy of anatomy-specific registration. We combine the affine model with prior work on deformable registration and test brain-specific registration across a landscape of MRI protocols unseen at training, demonstrating consistent and improved accuracy compared to existing tools. We distribute our code and tool at https://w3id.org/synthmorph, providing a single complete end-to-end solution for registration of brain MRI.

Data Consistent Deep Rigid MRI Motion Correction

Motion artifacts are a pervasive problem in MRI, leading to misdiagnosis or mischaracterization in population-level imaging studies. Current retrospective rigid intra-slice motion correction techniques jointly optimize estimates of the image and the motion parameters. In this paper, we use a deep network to reduce the joint image-motion parameter search to a search over rigid motion parameters alone. Our network produces a reconstruction as a function of two inputs: corrupted k-space data and motion parameters. We train the network using simulated, motion-corrupted k-space data generated from known motion parameters. At test-time, we estimate unknown motion parameters by minimizing a data consistency loss between the motion parameters, the network-based image reconstruction given those parameters, and the acquired measurements. Intra-slice motion correction experiments on simulated and realistic 2D fast spin echo brain MRI achieve high reconstruction fidelity while retaining the benefits of explicit data consistency-based optimization. Our code is publicly available at https://www.github.com/nalinimsingh/neuroMoCo.

Learning the Effect of Registration Hyperparameters with HyperMorph

We introduce HyperMorph, a framework that facilitates efficient hyperparameter tuning in learning-based deformable image registration. Classical registration algorithms perform an iterative pair-wise optimization to compute a deformation field that aligns two images. Recent learning-based approaches leverage large image datasets to learn a function that rapidly estimates a deformation for a given image pair. In both strategies, the accuracy of the resulting spatial correspondences is strongly influenced by the choice of certain hyperparameter values. However, an effective hyperparameter search consumes substantial time and human effort as it often involves training multiple models for different fixed hyperparameter values and may lead to suboptimal registration. We propose an amortized hyperparameter learning strategy to alleviate this burden by learning the impact of hyperparameters on deformation fields. We design a meta network, or hypernetwork, that predicts the parameters of a registration network for input hyperparameters, thereby comprising a single model that generates the optimal deformation field corresponding to given hyperparameter values. This strategy enables fast, high-resolution hyperparameter search at test-time, reducing the inefficiency of traditional approaches while increasing flexibility. We also demonstrate additional benefits of HyperMorph, including enhanced robustness to model initialization and the ability to rapidly identify optimal hyperparameter values specific to a dataset, image contrast, task, or even anatomical region, all without the need to retrain models. We make our code publicly available at http://hypermorph.voxelmorph.net.

SynthStrip: Skull-Stripping for Any Brain Image

The removal of non-brain signal from magnetic resonance imaging (MRI) data, known as skull-stripping, is an integral component of many neuroimage analysis streams. Despite their abundance, popular classical skull-stripping methods are usually tailored to images with specific acquisition properties, namely near-isotropic resolution and T1-weighted (T1w) MRI contrast, which are prevalent in research settings. As a result, existing tools tend to adapt poorly to other image types, such as stacks of thick slices acquired with fast spin-echo (FSE) MRI that are common in the clinic. While learning-based approaches for brain extraction have gained traction in recent years, these methods face a similar burden, as they are only effective for image types seen during the training procedure. To achieve robust skull-stripping across a landscape of protocols, we introduce SynthStrip, a rapid, learning-based brain-extraction tool. By leveraging anatomical segmentations to generate an entirely synthetic training dataset with anatomies, intensity distributions, and artifacts that far exceed the realistic range of medical images, SynthStrip learns to successfully generalize to a variety of real acquired brain images, removing the need for training data with target contrasts. We demonstrate the efficacy of SynthStrip for a diverse set of image acquisitions and resolutions across subject populations, ranging from newborn to adult. We show substantial improvements in accuracy over popular skull-stripping baselines - all with a single trained model. Our method and labeled evaluation data are available at https://w3id.org/synthstrip.

Rapid head-pose detection for automated slice prescription of fetal-brain MRI

In fetal-brain MRI, head-pose changes between prescription and acquisition present a challenge to obtaining the standard sagittal, coronal and axial views essential to clinical assessment. As motion limits acquisitions to thick slices that preclude retrospective resampling, technologists repeat ~55-second stack-of-slices scans (HASTE) with incrementally reoriented field of view numerous times, deducing the head pose from previous stacks. To address this inefficient workflow, we propose a robust head-pose detection algorithm using full-uterus scout scans (EPI) which take ~5 seconds to acquire. Our ~2-second procedure automatically locates the fetal brain and eyes, which we derive from maximally stable extremal regions (MSERs). The success rate of the method exceeds 94% in the third trimester, outperforming a trained technologist by up to 20%. The pipeline may be used to automatically orient the anatomical sequence, removing the need to estimate the head pose from 2D views and reducing delays during which motion can occur.

HyperMorph: Amortized Hyperparameter Learning for Image Registration

We present HyperMorph, a learning-based strategy for deformable image registration that removes the need to tune important registration hyperparameters during training. Classical registration methods solve an optimization problem to find a set of spatial correspondences between two images, while learning-based methods leverage a training dataset to learn a function that generates these correspondences. The quality of the results for both types of techniques depends greatly on the choice of hyperparameters. Unfortunately, hyperparameter tuning is time-consuming and typically involves training many separate models with various hyperparameter values, potentially leading to suboptimal results. To address this inefficiency, we introduce amortized hyperparameter learning for image registration, a novel strategy to learn the effects of hyperparameters on deformation fields. The proposed framework learns a hypernetwork that takes in an input hyperparameter and modulates a registration network to produce the optimal deformation field for that hyperparameter value. In effect, this strategy trains a single, rich model that enables rapid, fine-grained discovery of hyperparameter values from a continuous interval at test-time. We demonstrate that this approach can be used to optimize multiple hyperparameters considerably faster than existing search strategies, leading to a reduced computational and human burden and increased flexibility. We also show that this has several important benefits, including increased robustness to initialization and the ability to rapidly identify optimal hyperparameter values specific to a registration task, dataset, or even a single anatomical region - all without retraining the HyperMorph model. Our code is publicly available at http://voxelmorph.mit.edu.

Learning Multi-Modal Image Registration without Real Data

We introduce a learning-based strategy for multi-modal registration of images acquired with any modality, without requiring real data during training. While classical registration methods can accurately align multi-modal image pairs, they solve a costly optimization problem for every new pair of images. Learning-based techniques are fast at test time, but can only register images of the specific anatomy and modalities they were trained on. In contrast, our approach leverages a generative model to synthesize label maps and gray-scale images that expose a network to a wide range of anatomy and contrast during training. We demonstrate that this strategy enables robust registration of arbitrary modalities, without the need to retrain for a new modality. Critically, we show that input labels need not be of actual anatomy: training on randomly synthesized shapes, or supervoxels, results in competitive registration performance and makes the network agnostic to anatomy and contrast, all while eradicating the need for real data. We present extensive experiments demonstrating that this strategy enables registration of modalities not seen during training and surpasses the state of art in cross-contrast registration. Our code is integrated with the VoxelMorph library at: http://voxelmorph.csail.mit.edu