Semi-Supervised Medical Image Segmentation via Learning Consistency under Transformations

The scarcity of labeled data often limits the application of supervised deep learning techniques for medical image segmentation. This has motivated the development of semi-supervised techniques that learn from a mixture of labeled and unlabeled images. In this paper, we propose a novel semi-supervised method that, in addition to supervised learning on labeled training images, learns to predict segmentations consistent under a given class of transformations on both labeled and unlabeled images. More specifically, in this work we explore learning equivariance to elastic deformations. We implement this through: 1) a Siamese architecture with two identical branches, each of which receives a differently transformed image, and 2) a composite loss function with a supervised segmentation loss term and an unsupervised term that encourages segmentation consistency between the predictions of the two branches. We evaluate the method on a public dataset of chest radiographs with segmentations of anatomical structures using 5-fold cross-validation. The proposed method reaches significantly higher segmentation accuracy compared to supervised learning. This is due to learning transformation consistency on both labeled and unlabeled images, with the latter contributing the most. We achieve the performance comparable to state-of-the-art chest X-ray segmentation methods while using substantially fewer labeled images.

Automated Estimation of the Spinal Curvature via Spine Centerline Extraction with Ensembles of Cascaded Neural Networks

Scoliosis is a condition defined by an abnormal spinal curvature. For diagnosis and treatment planning of scoliosis, spinal curvature can be estimated using Cobb angles. We propose an automated method for the estimation of Cobb angles from X-ray scans. First, the centerline of the spine was segmented using a cascade of two convolutional neural networks. After smoothing the centerline, Cobb angles were automatically estimated using the derivative of the centerline. We evaluated the results using the mean absolute error and the average symmetric mean absolute percentage error between the manual assessment by experts and the automated predictions. For optimization, we used 609 X-ray scans from the London Health Sciences Center, and for evaluation, we participated in the international challenge "Accurate Automated Spinal Curvature Estimation, MICCAI 2019" (100 scans). On the challenge's test set, we obtained an average symmetric mean absolute percentage error of 22.96.

APIR-Net: Autocalibrated Parallel Imaging Reconstruction using a Neural Network

Deep learning has been successfully demonstrated in MRI reconstruction of accelerated acquisitions. However, its dependence on representative training data limits the application across different contrasts, anatomies, or image sizes. To address this limitation, we propose an unsupervised, auto-calibrated k-space completion method, based on a uniquely designed neural network that reconstructs the full k-space from an undersampled k-space, exploiting the redundancy among the multiple channels in the receive coil in a parallel imaging acquisition. To achieve this, contrary to common convolutional network approaches, the proposed network has a decreasing number of feature maps of constant size. In contrast to conventional parallel imaging methods such as GRAPPA that estimate the prediction kernel from the fully sampled autocalibration signals in a linear way, our method is able to learn nonlinear relations between sampled and unsampled positions in k-space. The proposed method was compared to the start-of-the-art ESPIRiT and RAKI methods in terms of noise amplification and visual image quality in both phantom and in-vivo experiments. The experiments indicate that APIR-Net provides a promising alternative to the conventional parallel imaging methods, and results in improved image quality especially for low SNR acquisitions.

Automated Lesion Detection by Regressing Intensity-Based Distance with a Neural Network

Localization of focal vascular lesions on brain MRI is an important component of research on the etiology of neurological disorders. However, manual annotation of lesions can be challenging, time-consuming and subject to observer bias. Automated detection methods often need voxel-wise annotations for training. We propose a novel approach for automated lesion detection that can be trained on scans only annotated with a dot per lesion instead of a full segmentation. From the dot annotations and their corresponding intensity images we compute various distance maps (DMs), indicating the distance to a lesion based on spatial distance, intensity distance, or both. We train a fully convolutional neural network (FCN) to predict these DMs for unseen intensity images. The local optima in the predicted DMs are expected to correspond to lesion locations. We show the potential of this approach to detect enlarged perivascular spaces in white matter on a large brain MRI dataset with an independent test set of 1000 scans. Our method matches the intra-rater performance of the expert rater that was computed on an independent set. We compare the different types of distance maps, showing that incorporating intensity information in the distance maps used to train an FCN greatly improves performance.

Patient-specific Conditional Joint Models of Shape, Image Features and Clinical Indicators

We propose and demonstrate a joint model of anatomical shapes, image features and clinical indicators for statistical shape modeling and medical image analysis. The key idea is to employ a copula model to separate the joint dependency structure from the marginal distributions of variables of interest. This separation provides flexibility on the assumptions made during the modeling process. The proposed method can handle binary, discrete, ordinal and continuous variables. We demonstrate a simple and efficient way to include binary, discrete and ordinal variables into the modeling. We build Bayesian conditional models based on observed partial clinical indicators, features or shape based on Gaussian processes capturing the dependency structure. We apply the proposed method on a stroke dataset to jointly model the shape of the lateral ventricles, the spatial distribution of the white matter hyperintensity associated with periventricular white matter disease, and clinical indicators. The proposed method yields interpretable joint models for data exploration and patient-specific statistical shape models for medical image analysis.

Automated Image Registration Quality Assessment Utilizing Deep-learning based Ventricle Extraction in Clinical Data

Registration is a core component of many imaging pipelines. In case of clinical scans, with lower resolution and sometimes substantial motion artifacts, registration can produce poor results. Visual assessment of registration quality in large clinical datasets is inefficient. In this work, we propose to automatically assess the quality of registration to an atlas in clinical FLAIR MRI scans of the brain. The method consists of automatically segmenting the ventricles of a given scan using a neural network, and comparing the segmentation to the atlas' ventricles propagated to image space. We used the proposed method to improve clinical image registration to a general atlas by computing multiple registrations and then selecting the registration that yielded the highest ventricle overlap. Methods were evaluated in a single-site dataset of more than 1000 scans, as well as a multi-center dataset comprising 142 clinical scans from 12 sites. The automated ventricle segmentation reached a Dice coefficient with manual annotations of 0.89 in the single-site dataset, and 0.83 in the multi-center dataset. Registration via age-specific atlases could improve ventricle overlap compared to a direct registration to the general atlas (Dice similarity coefficient increase up to 0.15). Experiments also showed that selecting scans with the registration quality assessment method could improve the quality of average maps of white matter hyperintensity burden, instead of using all scans for the computation of the white matter hyperintensity map. In this work, we demonstrated the utility of an automated tool for assessing image registration quality in clinical scans. This image quality assessment step could ultimately assist in the translation of automated neuroimaging pipelines to the clinic.

Weakly Supervised Object Detection with 2D and 3D Regression Neural Networks

Weakly supervised detection methods can infer the location of target objects in an image without requiring location or appearance information during training. We propose a weakly supervised deep learning method for the detection of objects that appear at multiple locations in an image. The method computes attention maps using the last feature maps of an encoder-decoder network optimized only with global labels: the number of occurrences of the target object in an image. In contrast with previous approaches, attention maps are generated at full input resolution thanks to the decoder part. The proposed approach is compared to multiple state-of-the-art methods in two tasks: the detection of digits in MNIST-based datasets, and the real life application of detection of enlarged perivascular spaces -- a type of brain lesion -- in four brain regions in a dataset of 2202 3D brain MRI scans. In MNIST-based datasets, the proposed method outperforms the other methods. In the brain dataset, several weakly supervised detection methods come close to the human intrarater agreement in each region. The proposed method reaches the lowest number of false positive detections in all brain regions at the operating point, while its average sensitivity is similar to that of the other best methods.

Event-Based Modeling with High-Dimensional Imaging Biomarkers for Estimating Spatial Progression of Dementia

Event-based models (EBM) are a class of disease progression models that can be used to estimate temporal ordering of neuropathological changes from cross-sectional data. Current EBMs only handle scalar biomarkers, such as regional volumes, as inputs. However, regional aggregates are a crude summary of the underlying high-resolution images, potentially limiting the accuracy of EBM. Therefore, we propose a novel method that exploits high-dimensional voxel-wise imaging biomarkers: n-dimensional discriminative EBM (nDEBM). nDEBM is based on an insight that mixture modeling, which is a key element of conventional EBMs, can be replaced by a more scalable semi-supervised support vector machine (SVM) approach. This SVM is used to estimate the degree of abnormality of each region which is then used to obtain subject-specific disease progression patterns. These patterns are in turn used for estimating the mean ordering by fitting a generalized Mallows model. In order to validate the biomarker ordering obtained using nDEBM, we also present a framework for Simulation of Imaging Biomarkers' Temporal Evolution (SImBioTE) that mimics neurodegeneration in brain regions. SImBioTE trains variational auto-encoders (VAE) in different brain regions independently to simulate images at varying stages of disease progression. We also validate nDEBM clinically using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). In both experiments, nDEBM using high-dimensional features gave better performance than state-of-the-art EBM methods using regional volume biomarkers. This suggests that nDEBM is a promising approach for disease progression modeling.

3D Regression Neural Network for the Quantification of Enlarged Perivascular Spaces in Brain MRI

Enlarged perivascular spaces (EPVS) in the brain are an emerging imaging marker for cerebral small vessel disease, and have been shown to be related to increased risk of various neurological diseases, including stroke and dementia. Automatic quantification of EPVS would greatly help to advance research into its etiology and its potential as a risk indicator of disease. We propose a convolutional network regression method to quantify the extent of EPVS in the basal ganglia from 3D brain MRI. We first segment the basal ganglia and subsequently apply a 3D convolutional regression network designed for small object detection within this region of interest. The network takes an image as input, and outputs a quantification score of EPVS. The network has significantly more convolution operations than pooling ones and no final activation, allowing it to span the space of real numbers. We validated our approach using a dataset of 2000 brain MRI scans scored visually. Experiments with varying sizes of training and test sets showed that a good performance can be achieved with a training set of only 200 scans. With a training set of 1000 scans, the intraclass correlation coefficient (ICC) between our scoring method and the expert's visual score was 0.74. Our method outperforms by a large margin - more than 0.10 - four more conventional automated approaches based on intensities, scale-invariant feature transform, and random forest. We show that the network learns the structures of interest and investigate the influence of hyper-parameters on the performance. We also evaluate the reproducibility of our network using a set of 60 subjects scanned twice (scan-rescan reproducibility). On this set our network achieves an ICC of 0.93, while the intrarater agreement reaches 0.80. Furthermore, the automatic EPVS scoring correlates similarly to age as visual scoring.