Joint MRI T1 Unenhancing and Contrast-enhancing Multiple Sclerosis Lesion Segmentation with Deep Learning in OPERA Trials

Multi-Omic characterization of the effects of Ocrelizumab in patients with relapsing-remitting multiple sclerosis

The study examined changes in the plasma proteome, metabolome, and lipidome of N = 14 patients with relapsing-remitting multiple sclerosis (RRMS) initiating treatment with ocrelizumab, assayed at baseline, 6 months, and 12 months. Analyses of >4000 circulating biomarkers identified depletion of B-cell associated proteins as the early effect observed following ocrelizumab (OCR) initiation, accompanied by the reduction in plasma abundance of cytokines and cytotoxic proteins, markers of neuronaxonal damage, and biologically active lipids including ceramides and lysophospholipids, at 6 months. B-cell depletion was accompanied by decreases in B-cell receptor and cytokine signaling but a pronounced increase in circulating plasma B-cell activating factor (BAFF). This was followed by an upregulation of a number of signaling and metabolic pathways at 12 months. Patients with higher baseline brain MRI lesion load demonstrated both higher levels of cytotoxic and structural proteins in plasma at baseline and more pronounced biomarker change trajectories over time. Digital cytometry identified a putative increase in myeloid cells and a pro-inflammatory subset of T-cells. Therapeutic effects of ocrelizumab extend beyond CD20-mediated B-cell lysis and implicate metabolic reprogramming, juxtaposing the early normalization of immune activation, cytokine signaling and metabolite and lipid turnover in periphery with changes in the dynamics of immune cell activation or composition. We identify BAFF increase following CD20 depletion as a tentative compensatory mechanism that contributes to the reconstitution of targeted B-cells, necessitating further research.

RIDGE: Reproducibility, Integrity, Dependability, Generalizability, and Efficiency Assessment of Medical Image Segmentation Models

Deep learning techniques hold immense promise for advancing medical image analysis, particularly in tasks like image segmentation, where precise annotation of regions or volumes of interest within medical images is crucial but manually laborious and prone to interobserver and intraobserver biases. As such, deep learning approaches could provide automated solutions for such applications. However, the potential of these techniques is often undermined by challenges in reproducibility and generalizability, which are key barriers to their clinical adoption. This paper introduces the RIDGE checklist, a comprehensive framework designed to assess the Reproducibility, Integrity, Dependability, Generalizability, and Efficiency of deep learning-based medical image segmentation models. The RIDGE checklist is not just a tool for evaluation but also a guideline for researchers striving to improve the quality and transparency of their work. By adhering to the principles outlined in the RIDGE checklist, researchers can ensure that their developed segmentation models are robust, scientifically valid, and applicable in a clinical setting.

Consensus of algorithms for lesion segmentation in brain MRI studies of multiple sclerosis

Segmentation of multiple sclerosis (MS) lesions on brain MRI scans is crucial for diagnosis, disease and treatment monitoring but is a time-consuming task. Despite several automated algorithms have been proposed, there is still no consensus on the most effective method. Here, we applied a consensus-based framework to improve lesion segmentation on T1-weighted and FLAIR scans. The framework is designed to combine publicly available state-of-the-art deep learning models, by running multiple segmentation tasks before merging the outputs of each algorithm. To assess the effectiveness of the approach, we applied it to MRI datasets from two different centers, including a private and a public dataset, with 131 and 30 MS patients respectively, with manually segmented lesion masks available. No further training was performed for any of the included algorithms. Overlap and detection scores were improved, with Dice increasing by 4-8% and precision by 3-4% respectively for the private and public dataset. High agreement was obtained between estimated and true lesion load (ρ = 0.92 and ρ = 0.97) and count (ρ = 0.83 and ρ = 0.94). Overall, this framework ensures accurate and reliable results, exploiting complementary features and overcoming some of the limitations of individual algorithms.

Contrast-Enhancing Lesion Segmentation in Multiple Sclerosis: A Deep Learning Approach Validated in a Multicentric Cohort

The detection of contrast-enhancing lesions (CELs) is fundamental for the diagnosis and monitoring of patients with multiple sclerosis (MS). This task is time-consuming and suffers from high intra- and inter-rater variability in clinical practice. However, only a few studies proposed automatic approaches for CEL detection. This study aimed to develop a deep learning model that automatically detects and segments CELs in clinical Magnetic Resonance Imaging (MRI) scans. A 3D UNet-based network was trained with clinical MRI from the Swiss Multiple Sclerosis Cohort. The dataset comprised 372 scans from 280 MS patients: 162 showed at least one CEL, while 118 showed no CELs. The input dataset consisted of T1-weighted before and after gadolinium injection, and FLuid Attenuated Inversion Recovery images. The sampling strategy was based on a white matter lesion mask to confirm the existence of real contrast-enhancing lesions. To overcome the dataset imbalance, a weighted loss function was implemented. The Dice Score Coefficient and True Positive and False Positive Rates were 0.76, 0.93, and 0.02, respectively. Based on these results, the model developed in this study might well be considered for clinical decision support.

Detection of diffusely abnormal white matter in multiple sclerosis on multiparametric brain MRI using semi-supervised deep learning

In addition to focal lesions, diffusely abnormal white matter (DAWM) is seen on brain MRI of multiple sclerosis (MS) patients and may represent early or distinct disease processes. The role of MRI-observed DAWM is understudied due to a lack of automated assessment methods. Supervised deep learning (DL) methods are highly capable in this domain, but require large sets of labeled data. To overcome this challenge, a DL-based network (DAWM-Net) was trained using semi-supervised learning on a limited set of labeled data for segmentation of DAWM, focal lesions, and normal-appearing brain tissues on multiparametric MRI. DAWM-Net segmentation performance was compared to a previous intensity thresholding-based method on an independent test set from expert consensus (N = 25). Segmentation overlap by Dice Similarity Coefficient (DSC) and Spearman correlation of DAWM volumes were assessed. DAWM-Net showed DSC > 0.93 for normal-appearing brain tissues and DSC > 0.81 for focal lesions. For DAWM-Net, the DAWM DSC was 0.49 ± 0.12 with a moderate volume correlation (ρ = 0.52, p < 0.01). The previous method showed lower DAWM DSC of 0.26 ± 0.08 and lacked a significant volume correlation (ρ = 0.23, p = 0.27). These results demonstrate the feasibility of DL-based DAWM auto-segmentation with semi-supervised learning. This tool may facilitate future investigation of the role of DAWM in MS.

Clinical applications of deep learning in neuroinflammatory diseases: A scoping review

BACKGROUND

Deep learning (DL) is an artificial intelligence technology that has aroused much excitement for predictive medicine due to its ability to process raw data modalities such as images, text, and time series of signals.

OBJECTIVES

Here, we intend to give the clinical reader elements to understand this technology, taking neuroinflammatory diseases as an illustrative use case of clinical translation efforts. We reviewed the scope of this rapidly evolving field to get quantitative insights about which clinical applications concentrate the efforts and which data modalities are most commonly used.

METHODS

We queried the PubMed database for articles reporting DL algorithms for clinical applications in neuroinflammatory diseases and the radiology.healthairegister.com website for commercial algorithms.

RESULTS

The review included 148 articles published between 2018 and 2024 and five commercial algorithms. The clinical applications could be grouped as computer-aided diagnosis, individual prognosis, functional assessment, the segmentation of radiological structures, and the optimization of data acquisition. Our review highlighted important discrepancies in efforts. The segmentation of radiological structures and computer-aided diagnosis currently concentrate most efforts with an overrepresentation of imaging. Various model architectures have addressed different applications, relatively low volume of data, and diverse data modalities. We report the high-level technical characteristics of the algorithms and synthesize narratively the clinical applications. Predictive performances and some common a priori on this topic are finally discussed.

CONCLUSION

The currently reported efforts position DL as an information processing technology, enhancing existing modalities of paraclinical investigations and bringing perspectives to make innovative ones actionable for healthcare.

AI-based detection of contrast-enhancing MRI lesions in patients with multiple sclerosis

BACKGROUND

Contrast-enhancing (CE) lesions are an important finding on brain magnetic resonance imaging (MRI) in patients with multiple sclerosis (MS) but can be missed easily. Automated solutions for reliable CE lesion detection are emerging; however, independent validation of artificial intelligence (AI) tools in the clinical routine is still rare.

METHODS

A three-dimensional convolutional neural network for CE lesion segmentation was trained externally on 1488 datasets of 934 MS patients from 81 scanners using concatenated information from FLAIR and T1-weighted post-contrast imaging. This externally trained model was tested on an independent dataset comprising 504 T1-weighted post-contrast and FLAIR image datasets of MS patients from clinical routine. Two neuroradiologists (R1, R2) labeled CE lesions for gold standard definition in the clinical test dataset. The algorithmic output was evaluated on both patient- and lesion-level.

RESULTS

On a patient-level, recall, specificity, precision, and accuracy of the AI tool to predict patients with CE lesions were 0.75, 0.99, 0.91, and 0.96. The agreement between the AI tool and both readers was within the range of inter-rater agreement (Cohen's kappa; AI vs. R1: 0.69; AI vs. R2: 0.76; R1 vs. R2: 0.76). On a lesion-level, false negative lesions were predominately found in infratentorial location, significantly smaller, and at lower contrast than true positive lesions (p < 0.05).

CONCLUSIONS

AI-based identification of CE lesions on brain MRI is feasible, approaching human reader performance in independent clinical data and might be of help as a second reader in the neuroradiological assessment of active inflammation in MS patients.

CRITICAL RELEVANCE STATEMENT

Al-based detection of contrast-enhancing multiple sclerosis lesions approaches human reader performance, but careful visual inspection is still needed, especially for infratentorial, small and low-contrast lesions.

Use of "Diagnostic Yield" in Imaging Research Reports: Results from Articles Published in Two General Radiology Journals

OBJECTIVE

"Diagnostic yield," also referred to as the detection rate, is a parameter positioned between diagnostic accuracy and diagnosis-related patient outcomes in research studies that assess diagnostic tests. Unfamiliarity with the term may lead to incorrect usage and delivery of information. Herein, we evaluate the level of proper use of the term "diagnostic yield" and its related parameters in articles published in Radiology and Korean Journal of Radiology (KJR).

MATERIALS AND METHODS

Potentially relevant articles published since 2012 in these journals were identified using MEDLINE and PubMed Central databases. The initial search yielded 239 articles. We evaluated whether the correct definition and study setting of "diagnostic yield" or "detection rate" were used and whether the articles also reported companion parameters for false-positive results. We calculated the proportion of articles that correctly used these parameters and evaluated whether the proportion increased with time (2012-2016 vs. 2017-2022).

RESULTS

Among 39 eligible articles (19 from Radiology and 20 from KJR), 17 (43.6%; 11 from Radiology and 6 from KJR) correctly defined "diagnostic yield" or "detection rate." The remaining 22 articles used "diagnostic yield" or "detection rate" with incorrect meanings such as "diagnostic performance" or "sensitivity." The proportion of correctly used diagnostic terms was higher in the studies published in Radiology than in those published in KJR (57.9% vs. 30.0%). The proportion improved with time in Radiology (33.3% vs. 80.0%), whereas no improvement was observed in KJR over time (33.3% vs. 27.3%). The proportion of studies reporting companion parameters was similar between journals (72.7% vs. 66.7%), and no considerable improvement was observed over time.

CONCLUSION

Overall, a minority of articles accurately used "diagnostic yield" or "detection rate." Incorrect usage of the terms was more frequent without improvement over time in KJR than in Radiology. Therefore, improvements are required in the use and reporting of these parameters.