KEYWORDS: Image segmentation, Magnetic resonance imaging, Voxels, Deep learning, Thalamus, White matter, Data modeling, Visualization, Realistic image synthesis
T1-weighted (T1w) magnetic resonance (MR) neuroimages are usually acquired with an inversion time that nulls the cerebrospinal fluid—i.e., CSFn MPRAGE images—but are rarely acquired with the white matter nulled—i.e., WMn images. Since WMn images can be useful in highlighting thalamic nuclei, we develop a method to synthesize these images from other images that are often acquired. We propose a two-part model, with a deep learning based encoder and a decoder based on an imaging equation which governs the acquisition of our T1w images. This model can be trained on a subset of the dataset where the WMn MPRAGE images are available. Our model takes image contrasts that are often acquired (e.g., CSFn MPRAGE) as input, and generates WMn MPRAGE images as output, along with two quantitative parameter maps as intermediate results. After training, our model is able to generate a synthetic WMn MPRAGE image for any given subject. Our model results have high signal-to-noise ratio and are visually almost identical to the ground truth images. Furthermore, downstream thalamic nuclei segmentation on synthetic WMn MPRAGE images are consistent with ground truth WMn MPRAGE images.
White matter lesion (WML) segmentation applied to magnetic resonance imaging (MRI) scans of people with multiple sclerosis has been an area of extensive research in recent years. As with most tasks in medical imaging, deep learning (DL) methods have proven very effective and have quickly replaced existing methods. Despite the improvement offered by these networks, there are still shortcomings with these DL approaches. In this work, we compare several DL algorithms, as well as methods for ensembling the results of those algorithms, for performing MS lesion segmentation. An ensemble approach is shown to best estimate total WML and has the highest agreement with manual delineations.
The cranial meninges are membranes enveloping the brain. The space between these membranes contains mainly cerebrospinal fluid. It is of interest to study how the volumes of this space change with respect to normal aging. In this work, we propose to combine convolutional neural networks (CNNs) with nested topology-preserving geometric deformable models (NTGDMs) to reconstruct meningeal surfaces from magnetic resonance (MR) images. We first use CNNs to predict implicit representations of these surfaces then refine them with NTGDMs to achieve sub-voxel accuracy while maintaining spherical topology and the correct anatomical ordering. MR contrast harmonization is used to match the contrasts between training and testing images. We applied our algorithm to a subset of healthy subjects from the Baltimore Longitudinal Study of Aging for demonstration purposes and conducted longitudinal statistical analysis of the intracranial volume (ICV) and subarachnoid space (SAS) volume. We found a statistically significant decrease in the ICV and an increase in the SAS volume with respect to normal aging.
KEYWORDS: Image segmentation, Thalamus, Convolutional neural networks, Medical imaging, Visualization, Traumatic brain injury, Super resolution, Magnetism, Magnetic resonance imaging, Image processing algorithms and systems
Thalamus segmentation plays an important role in studies that are related to neural system diseases. Existing thalamus segmentation algorithms use traditional image processing techniques on magnetic resonance images (MRI), which suffer from accuracy and efficiency. In recent years, deep convolutional neural networks (CNN) have been able to outperform many conventional algorithms in medical imaging tasks. We propose segmenting the thalamus using a 3D CNN that takes an MPRAGE image and a set of feature images derived from a diffusion tensor image (DTI). Experimental results demonstrate that using CNNs to segment the thalamus can improve accuracy and efficiency on various datasets.
Convolutional neural networks (CNNs) have been successfully applied to human brain segmentation. To in- corporate the left and right symmetry property of the brain into a network architecture, we propose a 3D left-right-reflection equivariant network to segment the anatomical structures of the brain. We extended previous group convolutions to account for left-right paired labels in the delineation. The proposed networks were compared with conventional networks trained with left-right reflection data augmentation in several tasks, showing improved performance. This is also the first work to extend reflection-equivariant CNNs to left-right paired labels in the human brain.
Automatic and accurate cerebellum parcellation has long been a challenging task due to the relative surface complexity and large anatomical variation of the human cerebellum. An inaccurate segmentation will inevitably bias further studies. In this paper we present an automatic approach for the quality control of cerebellum parcellation based on shape analysis in a hierarchical structure. We assume that the overall shape variation of a segmented structure comes from both population and segmentation variation. In this hierarchical structure, the higher level shape mainly captures the population variation of the human cerebellum, while the lower level shape captures both population and segmentation variation. We use a partial least squares regression to combine the lower level and higher level shape information. By compensating for population variation, we show that the estimated segmentation variation is highly correlated with the accuracy of the cerebellum parcellation results, which not only provides a confidence measurement of the cerebellum parcellation, but also gives some clues about when a segmentation software may fail in real scenarios.
To better understand cerebellum-related diseases and functional mapping of the cerebellum, quantitative measurements of cerebellar regions in magnetic resonance (MR) images have been studied in both clinical and neurological studies. Such studies have revealed that different spinocerebellar ataxia (SCA) subtypes have different patterns of cerebellar atrophy and that atrophy of different cerebellar regions is correlated with specific functional losses. Previous methods to automatically parcellate the cerebellum, that is, to identify its sub-regions, have been largely based on multi-atlas segmentation. Recently, deep convolutional neural network (CNN) algorithms have been shown to have high speed and accuracy in cerebral sub-cortical structure segmentation from MR images. In this work, two three-dimensional CNNs were used to parcellate the cerebellum into 28 regions. First, a locating network was used to predict a bounding box around the cerebellum. Second, a parcellating network was used to parcellate the cerebellum using the entire region within the bounding box. A leave-one-out cross validation of fifteen manually delineated images was performed. Compared with a previously reported state-ofthe-art algorithm, the proposed algorithm shows superior Dice coefficients. The proposed algorithm was further applied to three MR images of a healthy subject and subjects with SCA6 and SCA8, respectively. A Singularity container of this algorithm is publicly available.
The cerebellum plays an important role in both motor control and cognitive functions. Several methods to automatically segment different regions of the cerebellum have been recently proposed. Usually, the performance of the segmentation algorithms is evaluated by comparing with expert delineations. However, this is a laboratory approach and is not applicable in real scenarios where expert delineations are not available. In this paper, we propose a method that can automatically detect cerebellar lobule segmentation outliers. Instead of only evaluating the final segmentation result, the intermediate output of each segmentation step is evaluated and considered using a Hidden Markov Model (HMM) to produce a global segmentation assessment. For each intermediate step, a state-of-the-art image classification model Bag-of-Words" (BoW) is applied to quantize features of segmentation results, which then serves as observations of the trained HMM. Experiments show that the proposed method achieves both a high accuracy on predicting Dice of upcoming segmentation steps, and a high sensitivity to outlier detection.
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