Accurate personalized survival prediction for amyotrophic lateral sclerosis patients.

Amyotrophic Lateral Sclerosis (ALS) is a rapidly progressive neurodegenerative disease. Accurately predicting the survival time for ALS patients can help patients and clinicians to plan for future treatment and care. We describe the application of a machine-learned tool that incorporates clinical features and cortical thickness from brain magnetic resonance (MR) images to estimate the time until a composite respiratory failure event for ALS patients, and presents the prediction as individual survival distributions (ISDs). These ISDs provide the probability of survival (none of the respiratory failures) at multiple future time points, for each individual patient. Our learner considers several survival prediction models, and selects the best model to provide predictions. We evaluate our learned model using the mean absolute error margin (MAE-margin), a modified version of mean absolute error that handles data with censored outcomes. We show that our tool can provide helpful information for patients and clinicians in planning future treatment.

Effects of MRI scanner manufacturers in classification tasks with deep learning models.

Deep learning has become a leading subset of machine learning and has been successfully employed in diverse areas, ranging from natural language processing to medical image analysis. In medical imaging, researchers have progressively turned towards multi-center neuroimaging studies to address complex questions in neuroscience, leveraging larger sample sizes and aiming to enhance the accuracy of deep learning models. However, variations in image pixel/voxel characteristics can arise between centers due to factors including differences in magnetic resonance imaging scanners. Such variations create challenges, particularly inconsistent performance in machine learning-based approaches, often referred to as domain shift, where the trained models fail to achieve satisfactory or improved results when confronted with dissimilar test data. This study analyzes the performance of multiple disease classification tasks using multi-center MRI data obtained from three widely used scanner manufacturers (GE, Philips, and Siemens) across several deep learning-based networks. Furthermore, we investigate the efficacy of mitigating scanner vendor effects using ComBat-based harmonization techniques when applied to multi-center datasets of 3D structural MR images. Our experimental results reveal a substantial decline in classification performance when models trained on one type of scanner manufacturer are tested with data from different manufacturers. Moreover, despite applying ComBat-based harmonization, the harmonized images do not demonstrate any noticeable performance enhancement for disease classification tasks.

DSMRI: Domain Shift Analyzer for Multi-Center MRI Datasets.

In medical research and clinical applications, the utilization of MRI datasets from multiple centers has become increasingly prevalent. However, inherent variability between these centers presents challenges due to domain shift, which can impact the quality and reliability of the analysis. Regrettably, the absence of adequate tools for domain shift analysis hinders the development and validation of domain adaptation and harmonization techniques. To address this issue, this paper presents a novel Domain Shift analyzer for MRI (DSMRI) framework designed explicitly for domain shift analysis in multi-center MRI datasets. The proposed model assesses the degree of domain shift within an MRI dataset by leveraging various MRI-quality-related metrics derived from the spatial domain. DSMRI also incorporates features from the frequency domain to capture low- and high-frequency information about the image. It further includes the wavelet domain features by effectively measuring the sparsity and energy present in the wavelet coefficients. Furthermore, DSMRI introduces several texture features, thereby enhancing the robustness of the domain shift analysis process. The proposed framework includes visualization techniques such as t-SNE and UMAP to demonstrate that similar data are grouped closely while dissimilar data are in separate clusters. Additionally, quantitative analysis is used to measure the domain shift distance, domain classification accuracy, and the ranking of significant features. The effectiveness of the proposed approach is demonstrated using experimental evaluations on seven large-scale multi-site neuroimaging datasets.

SF2Former: Amyotrophic lateral sclerosis identification from multi-center MRI data using spatial and frequency fusion transformer.

Amyotrophic Lateral Sclerosis (ALS) is a complex neurodegenerative disorder characterized by motor neuron degeneration. Significant research has begun to establish brain magnetic resonance imaging (MRI) as a potential biomarker to diagnose and monitor the state of the disease. Deep learning has emerged as a prominent class of machine learning algorithms in computer vision and has shown successful applications in various medical image analysis tasks. However, deep learning methods applied to neuroimaging have not achieved superior performance in classifying ALS patients from healthy controls due to insignificant structural changes correlated with pathological features. Thus, a critical challenge in deep models is to identify discriminative features from limited training data. To address this challenge, this study introduces a framework called SF2Former, which leverages the power of the vision transformer architecture to distinguish ALS subjects from the control group by exploiting the long-range relationships among image features. Additionally, spatial and frequency domain information is combined to enhance the network's performance, as MRI scans are initially captured in the frequency domain and then converted to the spatial domain. The proposed framework is trained using a series of consecutive coronal slices and utilizes pre-trained weights from ImageNet through transfer learning. Finally, a majority voting scheme is employed on the coronal slices of each subject to generate the final classification decision. The proposed architecture is extensively evaluated with multi-modal neuroimaging data (i.e., T1-weighted, R2*, FLAIR) using two well-organized versions of the Canadian ALS Neuroimaging Consortium (CALSNIC) multi-center datasets. The experimental results demonstrate the superiority of the proposed strategy in terms of classification accuracy compared to several popular deep learning-based techniques.

Blind Image Deconvolution Using Variational Deep Image Prior.

Conventional deconvolution methods utilize hand-crafted image priors to constrain the optimization. While deep-learning-based methods have simplified the optimization by end-to-end training, they fail to generalize well to blurs unseen in the training dataset. Thus, training image-specific models is important for higher generalization. Deep image prior (DIP) provides an approach to optimize the weights of a randomly initialized network with a single degraded image by maximum a posteriori (MAP), which shows that the architecture of a network can serve as the hand-crafted image prior. Unlike conventional hand-crafted image priors, which are obtained through statistical methods, finding a suitable network architecture is challenging due to the unclear relationship between images and their corresponding architectures. As a result, the network architecture cannot provide enough constraint for the latent sharp image. This paper proposes a new variational deep image prior (VDIP) for blind image deconvolution, which exploits additive hand-crafted image priors on latent sharp images and approximates a distribution for each pixel to avoid suboptimal solutions. Our mathematical analysis shows that the proposed method can better constrain the optimization. The experimental results further demonstrate that the generated images have better quality than that of the original DIP on benchmark datasets.

Retinal blood vessel segmentation from fundus image using an efficient multiscale directional representation technique Bendlets.

The improper circulation of blood flow inside the retinal vessel is the primary source of most of the optical disorders including partial vision loss and blindness. Accurate blood vessel segmentation of the retinal image is utilized for biometric identification, computer-assisted laser surgical procedure, automatic screening, and diagnosis of ophthalmologic diseases like Diabetic retinopathy, Age-related macular degeneration, Hypertensive retinopathy, and so on. Proper identification of retinal blood vessels at its early stage assists medical experts to take expedient treatment procedures which could mitigate potential vision loss. This paper presents an efficient retinal blood vessel segmentation approach where a 4-D feature vector is constructed by the outcome of Bendlet transform, which can capture directional information much more efficiently than the traditional wavelets. Afterward, a bunch of ensemble classifiers is applied to find out the best possible result of whether a pixel falls inside a vessel or non-vessel segment. The detailed and comprehensive experiments operated on two benchmark and publicly available retinal color image databases (DRIVE and STARE) prove the effectiveness of the proposed approach where the average accuracy for vessel segmentation accomplished approximately 95%. Furthermore, in comparison with other promising works on the aforementioned databases demonstrates the enhanced performance and robustness of the proposed method.