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The Developing Human Connectome Project (dHCP) aims to explore developmental patterns of the human brain during the perinatal period. An automated processing pipeline has been developed to extract high-quality cortical surfaces from structural brain magnetic resonance (MR) images for the dHCP neonatal dataset. However, the current implementation of the pipeline requires more than 6.5 h to process a single MRI scan, making it expensive for large-scale neuroimaging studies. In this paper, we propose a fast deep learning (DL) based pipeline for dHCP neonatal cortical surface reconstruction, incorporating DL-based brain extraction, cortical surface reconstruction and spherical projection, as well as GPU-accelerated cortical surface inflation and cortical feature estimation. We introduce a multiscale deformation network to learn diffeomorphic cortical surface reconstruction end-to-end from T2-weighted brain MRI. A fast unsupervised spherical mapping approach is integrated to minimize metric distortions between cortical surfaces and projected spheres. The entire workflow of our DL-based dHCP pipeline completes within only 24 s on a modern GPU, which is nearly 1000 times faster than the original dHCP pipeline. The qualitative assessment demonstrates that for 82.5% of the test samples, the cortical surfaces reconstructed by our DL-based pipeline achieve superior (54.2%) or equal (28.3%) surface quality compared to the original dHCP pipeline., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Purpose: To develop and validate a data acquisition scheme combined with a motion-resolved reconstruction and dictionary-matching-based parameter estimation to enable free-breathing isotropic resolution self-navigated whole-liver simultaneous water-specific T 1 ( wT 1 ) and T 2 ( wT 2 ) mapping for the characterization of diffuse and oncological liver diseases., Methods: The proposed data acquisition consists of a magnetization preparation pulse and a two-echo gradient echo readout with a radial stack-of-stars trajectory, repeated with different preparations to achieve different T 1 and T 2 contrasts in a fixed acquisition time of 6 min. Regularized reconstruction was performed using self-navigation to account for motion during the free-breathing acquisition, followed by water-fat separation. Bloch simulations of the sequence were applied to optimize the sequence timing for B 1 insensitivity at 3 T, to correct for relaxation-induced blurring, and to map T 1 and T 2 using a dictionary. The proposed method was validated on a water-fat phantom with varying relaxation properties and in 10 volunteers against imaging and spectroscopy reference values. The performance and robustness of the proposed method were evaluated in five patients with abdominal pathologies., Results: Simulations demonstrate good B 1 insensitivity of the proposed method in measuring T 1 and T 2 values. The proposed method produces co-registered wT 1 and wT 2 maps with a good agreement with reference methods (phantom: wT 1 = 1 . 02 wT 1,ref - 8 . 93 ms , R 2 = 0 . 991 ; wT 2 = 1 . 03 wT 2,ref + 0 . 73 ms , R 2 = 0 . 995 ). The proposed wT 1 and wT 2 mapping exhibits good repeatability and can be robustly performed in patients with pathologies., Conclusions: The proposed method allows whole-liver wT 1 and wT 2 quantification with high accuracy at isotropic resolution in a fixed acquisition time during free-breathing., (© 2024 The Author(s). NMR in Biomedicine published by John Wiley & Sons Ltd.)

Parkinson's disease (PD) is a prevalent neurological disorder characterized by progressive dopaminergic neuron loss, leading to both motor and non-motor symptoms. Early and accurate diagnosis is challenging due to the subtle and variable nature of early symptoms. This study aims to address these diagnostic challenges by proposing a novel method, Localized Region Extraction and Multi-Modal Fusion (LRE-MMF), designed to enhance diagnostic accuracy through the integration of structural MRI (sMRI) and resting-state functional MRI (rs-fMRI) data. The LRE-MMF method utilizes the complementary strengths of sMRI and rs-fMRI: sMRI provides detailed anatomical information, while rs-fMRI captures functional connectivity patterns. We applied this approach to a dataset consisting of 20 PD patients and 20 healthy controls (HC), all scanned with a 3 T MRI. The primary objective was to determine whether the integration of sMRI and rs-fMRI through the LRE-MMF method improves the classification accuracy between PD and HC subjects. LRE-MMF involves the division of imaging data into localized regions, followed by feature extraction and dimensionality reduction using Principal Component Analysis (PCA). The resulting features were fused and processed through a neural network to learn high-level representations. The model achieved an accuracy of 75 %, with a precision of 0.8125, recall of 0.65, and an AUC of 0.8875. The validation accuracy curves indicated good generalization, with significant brain regions identified, including the caudate, putamen, thalamus, supplementary motor area, and precuneus, as per the AAL atlas. These results demonstrate the potential of the LRE-MMF method for improving early diagnosis and understanding of PD by effectively utilizing both sMRI and rs-fMRI data. This approach could contribute to the development of more accurate diagnostic tools., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Schizophrenia is a persistent neurological disorder profoundly affecting cognitive, emotional, and behavioral functions, prominently characterized by delusions, hallucinations, disordered speech, and abnormal motor activity. These symptoms often present diagnostic challenges due to their overlap with other forms of psychosis. Therefore, the implementation of automated diagnostic methodologies is imperative. This research leverages Functional Magnetic Resonance Imaging (fMRI), a neuroimaging modality capable of delineating functional activations across diverse brain regions. Furthermore, the utilization of evolving machine learning techniques for fMRI data analysis has significantly progressive. Here, our study stands as a novel attempt, focusing on the comprehensive assessment of both classical and atypical symptoms of schizophrenia. We aim to uncover associated changes in brain functional activity. Our study encompasses two distinct fMRI datasets (1.5T and 3T), each comprising 34 schizophrenia patients for the 1.5T dataset and 25 schizophrenia patients for the 3T dataset, along with an equal number of healthy controls. Machine learning algorithms are applied to assess data subsets, enabling an in-depth evaluation of the current functional condition concerning symptom impact. The identified voxels contribute to determining the brain regions most influenced by each symptom, as quantified by symptom intensity. This rigorous approach has yielded various new findings while maintaining an impressive classification accuracy rate of 97 %. By elucidating variations in activation patterns across multiple brain regions in individuals with schizophrenia, this study contributes to the understanding of functional brain changes associated with the disorder. The insights gained may inform differential clinical interventions and provide a means of assessing symptom severity accurately, offering new avenues for the management of schizophrenia., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Robustness of deep learning segmentation models is crucial for their safe incorporation into clinical practice. However, these models can falter when faced with distributional changes. This challenge is evident in magnetic resonance imaging (MRI) scans due to the diverse acquisition protocols across various domains, leading to differences in image characteristics such as textural appearances. We posit that the restricted anatomical differences between subjects could be harnessed to refine the latent space into a set of shape components. The learned set then aims to encompass the relevant anatomical shape variation found within the patient population. We explore this by utilising multiple MRI sequences to learn texture invariant and shape equivariant features which are used to construct a shape dictionary using vector quantisation. We investigate shape equivariance to a number of different types of groups. We hypothesise and prove that the greater the group order, i.e., the denser the constraint, the better becomes the model robustness. We achieve shape equivariance either with a contrastive based approach or by imposing equivariant constraints on the convolutional kernels. The resulting shape equivariant dictionary is then sampled to compose the segmentation output. Our method achieves state-of-the-art performance for the task of single domain generalisation for prostate and cardiac MRI segmentation. Code is available at https://github.com/AinkaranSanthi/A_Geometric_Perspective_For_Robust_Segmentation., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Ainkaran Santhirasekaram reports financial support was provided by Imperial College London. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2024. Published by Elsevier B.V. All rights reserved.)

Background: Schizophrenia is a complex and disabling mental disorder that represents one of the most important challenges for neuroimaging research. There were many attempts to understand these basic mechanisms behind the disorder, yet we know very little. By employing machine learning techniques with age-matched samples from the auditory oddball task using multi-site functional magnetic resonance imaging (fMRI) data, this study aims to address these challenges., Methods: The study employed a three-stage model to gain a better understanding of the neurobiology underlying schizophrenia and techniques that could be applied for diagnosis. At first, we constructed four-level hierarchical sets from each fMRI volume of 34 schizophrenia patients (SZ) and healthy controls (HC) individually in terms of hemisphere, gyrus, lobes, and Brodmann areas. Second, we employed statistical methods, namely, t -tests and Pearson's correlation, to assess the group differences in cortical activation. Finally, we assessed the predictive power of the brain regions for machine learning algorithms using K-nearest Neighbor (KNN), Naive Bayes, Decision Tree (DT), Random Forest (RF), Support Vector Machines (SVMs), and Extreme Learning Machine (ELM)., Results: Our investigation depicts promising results, obtaining an accuracy of up to 84% when applying Pearson's correlation-selected features at lobes and Brodmann region level (81% for Gyrus), as well as Hemispheres involving different stages. Thus, the results of our study were consistent with previous studies that have revealed some functional abnormalities in several brain regions. We also discovered the involvement of other brain regions which were never sufficiently studied in previous literature, such as the posterior lobe (posterior cerebellum), Pyramis, and Brodmann Area 34., Conclusions: We present a unique and comprehensive approach to investigating the neurological basis of schizophrenia in this study. By bridging the gap between neuroimaging and computable analysis, we aim to improve diagnostic accuracy in patients with schizophrenia and identify potential prognostic markers for disease progression., (© 2024 The Author(s). Published by IMR Press.)

Through the application of machine learning algorithms to neuroimaging data the brain age methodology was shown to provide a useful individual-level biological age prediction and identify key brain regions responsible for the prediction. In this study, we present the methodology of constructing a rhesus macaque brain age model using a machine learning algorithm and discuss the key predictive brain regions in comparison to the human brain, to shed light on cross-species primate similarities and differences. Structural information of the brain (e.g., parcellated volumes) from brain magnetic resonance imaging of 43 rhesus macaques were used to develop brain atlas-based features to build a brain age model that predicts biological age. The best-performing model used 22 selected features and achieved an R 2 of 0.72. We also identified interpretable predictive brain features including Right Fronto-orbital Cortex, Right Frontal Pole, Right Inferior Lateral Parietal Cortex, and Bilateral Posterior Central Operculum. Our findings provide converging evidence of the parallel and comparable brain regions responsible for both non-human primates and human biological age prediction., Competing Interests: Declaration of Competing Interest The authors declare there is no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Sex-specific abdominal organ volume and proton density fat fraction (PDFF) in people with obesity during a weight loss intervention was assessed with automated multiorgan segmentation of quantitative water-fat MRI. An nnU-Net architecture was employed for automatic segmentation of abdominal organs, including visceral and subcutaneous adipose tissue, liver, and psoas and erector spinae muscle, based on quantitative chemical shift-encoded MRI and using ground truth labels generated from participants of the Lifestyle Intervention (LION) study. Each organ's volume and fat content were examined in 127 participants (73 female and 54 male participants; body mass index, 30-39.9 kg/m 2 ) and in 81 (54 female and 32 male participants) of these participants after an 8-week formula-based low-calorie diet. Dice scores ranging from 0.91 to 0.97 were achieved for the automatic segmentation. PDFF was found to be lower in visceral adipose tissue compared with subcutaneous adipose tissue in both male and female participants. Before intervention, female participants exhibited higher PDFF in subcutaneous adipose tissue (90.6% vs 89.7%; P < .001) and lower PDFF in liver (8.6% vs 13.3%; P < .001) and visceral adipose tissue (76.4% vs 81.3%; P < .001) compared with male participants. This relation persisted after intervention. As a response to caloric restriction, male participants lost significantly more visceral adipose tissue volume (1.76 L vs 0.91 L; P < .001) and showed a higher decrease in subcutaneous adipose tissue PDFF (2.7% vs 1.5%; P < .001) than female participants. Automated body composition analysis on quantitative water-fat MRI data provides new insights for understanding sex-specific metabolic response to caloric restriction and weight loss in people with obesity. Keywords: Obesity, Chemical Shift-encoded MRI, Abdominal Fat Volume, Proton Density Fat Fraction, nnU-Net ClinicalTrials.gov registration no. NCT04023942 Supplemental material is available for this article. Published under a CC BY 4.0 license.

Purpose: To estimate pixel-wise predictive uncertainty for deep learning-based MR image reconstruction and to examine the impact of domain shifts and architecture robustness., Methods: Uncertainty prediction could provide a measure for robustness of deep learning (DL)-based MR image reconstruction from undersampled data. DL methods bear the risk of inducing reconstruction errors like in-painting of unrealistic structures or missing pathologies. These errors may be obscured by visual realism of DL reconstruction and thus remain undiscovered. Furthermore, most methods are task-agnostic and not well calibrated to domain shifts. We propose a strategy that estimates aleatoric (data) and epistemic (model) uncertainty, which entails training a deep ensemble (epistemic) with nonnegative log-likelihood (aleatoric) loss in addition to the conventional applied losses terms. The proposed procedure can be paired with any DL reconstruction, enabling investigations of their predictive uncertainties on a pixel level. Five different architectures were investigated on the fastMRI database. The impact on the examined uncertainty of in-distributional and out-of-distributional data with changes to undersampling pattern, imaging contrast, imaging orientation, anatomy, and pathology were explored., Results: Predictive uncertainty could be captured and showed good correlation to normalized mean squared error. Uncertainty was primarily focused along the aliased anatomies and on hyperintense and hypointense regions. The proposed uncertainty measure was able to detect disease prevalence shifts. Distinct predictive uncertainty patterns were observed for changing network architectures., Conclusion: The proposed approach enables aleatoric and epistemic uncertainty prediction for DL-based MR reconstruction with an interpretable examination on a pixel level., (© 2024 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.)

Cardiac magnetic resonance imaging (CMR) has emerged as a valuable diagnostic tool for cardiac diseases. However, a significant drawback of CMR is its slow imaging speed, resulting in low patient throughput and compromised clinical diagnostic quality. The limited temporal resolution also causes patient discomfort and introduces artifacts in the images, further diminishing their overall quality and diagnostic value. There has been growing interest in deep learning-based CMR imaging algorithms that can reconstruct high-quality images from highly under-sampled k-space data. However, the development of deep learning methods requires large training datasets, which have so far not been made publicly available for CMR. To address this gap, we released a dataset that includes multi-contrast, multi-view, multi-slice and multi-coil CMR imaging data from 300 subjects. Imaging studies include cardiac cine and mapping sequences. The 'CMRxRecon' dataset contains raw k-space data and auto-calibration lines. Our aim is to facilitate the advancement of state-of-the-art CMR image reconstruction by introducing standardized evaluation criteria and making the dataset freely accessible to the research community., (© 2024. The Author(s).)

In recent years, Artificial Intelligence has been used to assist healthcare professionals in detecting and diagnosing neurodegenerative diseases. In this study, we propose a methodology to analyze functional Magnetic Resonance Imaging signals and perform classification between Parkinson's disease patients and healthy participants using Machine Learning algorithms. In addition, the proposed approach provides insights into the brain regions affected by the disease. The functional Magnetic Resonance Imaging from the PPMI and 1000-FCP datasets were pre-processed to extract time series from 200 brain regions per participant, resulting in 11,600 features. Causal Forest and Wrapper Feature Subset Selection algorithms were used for dimensionality reduction, resulting in a subset of features based on their heterogeneity and association with the disease. We utilized Logistic Regression and XGBoost algorithms to perform PD detection, achieving 97.6% accuracy, 97.5% F 1 score, 97.9% precision, and 97.7%recall by analyzing sets with fewer than 300 features in a population including men and women. Finally, Multiple Correspondence Analysis was employed to visualize the relationships between brain regions and each group (women with Parkinson, female controls, men with Parkinson, male controls). Associations between the Unified Parkinson's Disease Rating Scale questionnaire results and affected brain regions in different groups were also obtained to show another use case of the methodology. This work proposes a methodology to (1) classify patients and controls with Machine Learning and Causal Forest algorithm and (2) visualize associations between brain regions and groups, providing high-accuracy classification and enhanced interpretability of the correlation between specific brain regions and the disease across different groups.

The use of synthetic CT (sCT) in the radiotherapy workflow would reduce costs and scan time while removing the uncertainties around working with both MR and CT modalities. The performance of deep learning (DL) solutions for sCT generation is steadily increasing, however most proposed methods were trained and validated on private datasets of a single contrast from a single scanner. Such solutions might not perform equally well on other datasets, limiting their general usability and therefore value. Additionally, functional evaluations of sCTs such as dosimetric comparisons with CT-based dose calculations better show the impact of the methods, but the evaluations are more labor intensive than pixel-wise metrics. To improve the generalization of an sCT model, we propose to incorporate a pre-trained DL model to pre-process the input MR images by generating artificial proton density, T1 and T2 maps (i.e. contrast-independent quantitative maps), which are then used for sCT generation. Using a dataset of only T2w MR images, the robustness towards input MR contrasts of this approach is compared to a model that was trained using the MR images directly. We evaluate the generated sCTs using pixel-wise metrics and calculating mean radiological depths, as an approximation of the mean delivered dose. On T2w images acquired with the same settings as the training dataset, there was no significant difference between the performance of the models. However, when evaluated on T1w images, and a wide range of other contrasts and scanners from both public and private datasets, our approach outperforms the baseline model. Using a dataset of T2w MR images, our proposed model implements synthetic quantitative maps to generate sCT images, improving the generalization towards other contrasts. Our code and trained models are publicly available., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: [All model evaluations were performed using Hero Imaging, NONPI Medical AB, where Attila Simkó is an employee, Tommy Löfstedt, Anders Garpebring, Tufve Nyholm and Joakim Jonsson are co-founders.], (Copyright © 2023 The Author(s). Published by Elsevier GmbH.. All rights reserved.)

Automated segmentation of brain white matter lesions is crucial for both clinical assessment and scientific research in multiple sclerosis (MS). Over a decade ago, we introduced an engineered lesion segmentation tool, LST. While recent lesion segmentation approaches have leveraged artificial intelligence (AI), they often remain proprietary and difficult to adopt. As an open-source tool, we present LST-AI, an advanced deep learning-based extension of LST that consists of an ensemble of three 3D U-Nets. LST-AI explicitly addresses the imbalance between white matter (WM) lesions and non-lesioned WM. It employs a composite loss function incorporating binary cross-entropy and Tversky loss to improve segmentation of the highly heterogeneous MS lesions. We train the network ensemble on 491 MS pairs of T1-weighted and FLAIR images, collected in-house from a 3T MRI scanner, and expert neuroradiologists manually segmented the utilized lesion maps for training. LST-AI also includes a lesion location annotation tool, labeling lesions as periventricular, infratentorial, and juxtacortical according to the 2017 McDonald criteria, and, additionally, as subcortical. We conduct evaluations on 103 test cases consisting of publicly available data using the Anima segmentation validation tools and compare LST-AI with several publicly available lesion segmentation models. Our empirical analysis shows that LST-AI achieves superior performance compared to existing methods. Its Dice and F1 scores exceeded 0.62, outperforming LST, SAMSEG (Sequence Adaptive Multimodal SEGmentation), and the popular nnUNet framework, which all scored below 0.56. Notably, LST-AI demonstrated exceptional performance on the MSSEG-1 challenge dataset, an international WM lesion segmentation challenge, with a Dice score of 0.65 and an F1 score of 0.63-surpassing all other competing models at the time of the challenge. With increasing lesion volume, the lesion detection rate rapidly increased with a detection rate of >75% for lesions with a volume between 10 mm 3 and 100 mm 3 . Given its higher segmentation performance, we recommend that research groups currently using LST transition to LST-AI. To facilitate broad adoption, we are releasing LST-AI as an open-source model, available as a command-line tool, dockerized container, or Python script, enabling diverse applications across multiple platforms., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Alzheimer's is a degenerative brain cell disease that affects around 5.8 million people globally. The progressive neurodegenerative disease known as Alzheimer's Disease (AD), affects the frontal cortex, the part of the brain in charge of memory, language, and cognition. As a result, researchers are utilizing a variety of machine-learning techniques to create an automated method for AD detection. The massive data collected during ROI and biomarker identification takes longer to handle using current methods. This study uses metaheuristic-tuned deep learning to detect the AD-affected region. The research utilizes advanced deep learning and image processing techniques to enhance early and accurate diagnosis of Alzheimer's disease, potentially enhancing patient outcomes and prompt therapy. The capacity of deep neural networks to extract complex patterns from magnetic resonance imaging (MRI) scans makes them indispensable in the diagnosis of AD since they allow the detection of minor aberrations and complex alterations in brain structure and composition. An adaptive histogram approach processes the collected photographs, and a weighted median filter is used in place of the noisy pixels. The next step is to identify the issue region using a deep convolution network-based clustering segmentation process. A correlated information theory approach is used to extract various textural and statistical features from the separated regions. Lastly, the selected features are probed by the fly-optimized densely linked convolution neural networks. The method surpasses state-of-the-art techniques in sensitivity (15.52%), specificity (15.62%), accuracy (9.01%), error rate (11.29%), and F-measure (10.52%) for recognizing AD-impacted regions in MRI scans using the Kaggle dataset., Competing Interests: The authors have no relevant financial or non-financial interests to disclose.

Nuclear magnetic resonance (NMR) spectral analysis of biofluids can be a time-consuming process, requiring the expertise of a trained operator. With NMR becoming increasingly popular in the field of metabolomics, there is a growing need to change this paradigm and to automate the process. Here we introduce MagMet, an online web server, that automates the processing and quantification of 1D 1 H NMR spectra from biofluids-specifically, human serum/plasma metabolites, including those associated with inborn errors of metabolism (IEM). MagMet uses a highly efficient data processing procedure that performs automatic Fourier Transformation, phase correction, baseline optimization, chemical shift referencing, water signal removal, and peak picking/peak alignment. MagMet then uses the peak positions, linewidth information, and J-couplings from its own specially prepared standard metabolite reference spectral NMR library of 85 serum/plasma compounds to identify and quantify compounds from experimentally acquired NMR spectra of serum/plasma. MagMet employs linewidth adjustment for more consistent quantification of metabolites from higher field instruments and incorporates a highly efficient data processing procedure for more rapid and accurate detection and quantification of metabolites. This optimized algorithm allows the MagMet webserver to quickly detect and quantify 58 serum/plasma metabolites in 2.6 min per spectrum (when processing a dataset of 50-100 spectra). MagMet's performance was also assessed using spectra collected from defined mixtures (simulating other biofluids), with >100 previously measured plasma spectra, and from spiked serum/plasma samples simulating known IEMs. In all cases, MagMet performed with precision and accuracy matching the performance of human spectral profiling experts. MagMet is available at http://magmet.ca., (© 2023 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.)

Purpose: During the acquisition of MRI data, patient-, sequence-, or hardware-related factors can introduce artefacts that degrade image quality. Four of the most significant tasks for improving MRI image quality have been bias field correction, super-resolution, motion-, and noise correction. Machine learning has achieved outstanding results in improving MR image quality for these tasks individually, yet multi-task methods are rarely explored., Methods: In this study, we developed a model to simultaneously correct for all four aforementioned artefacts using multi-task learning. Two different datasets were collected, one consisting of brain scans while the other pelvic scans, which were used to train separate models, implementing their corresponding artefact augmentations. Additionally, we explored a novel loss function that does not only aim to reconstruct the individual pixel values, but also the image gradients, to produce sharper, more realistic results. The difference between the evaluated methods was tested for significance using a Friedman test of equivalence followed by a Nemenyi post-hoc test., Results: Our proposed model generally outperformed other commonly-used correction methods for individual artefacts, consistently achieving equal or superior results in at least one of the evaluation metrics. For images with multiple simultaneous artefacts, we show that the performance of using a combination of models, trained to correct individual artefacts depends heavily on the order that they were applied. This is not an issue for our proposed multi-task model. The model trained using our novel convolutional loss function always outperformed the model trained with a mean squared error loss, when evaluated using Visual Information Fidelity, a quality metric connected to perceptual quality., Conclusion: We trained two models for multi-task MRI artefact correction of brain, and pelvic scans. We used a novel loss function that significantly improves the image quality of the outputs over using mean squared error. The approach performs well on real world data, and it provides insight into which artefacts it detects and corrects for. Our proposed model and source code were made publicly available., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Objectives: The UK Biobank (UKBB) and German National Cohort (NAKO) are among the largest cohort studies, capturing a wide range of health-related data from the general population, including comprehensive magnetic resonance imaging (MRI) examinations. The purpose of this study was to demonstrate how MRI data from these large-scale studies can be jointly analyzed and to derive comprehensive quantitative image-based phenotypes across the general adult population., Materials and Methods: Image-derived features of abdominal organs (volumes of liver, spleen, kidneys, and pancreas; volumes of kidney hilum adipose tissue; and fat fractions of liver and pancreas) were extracted from T1-weighted Dixon MRI data of 17,996 participants of UKBB and NAKO based on quality-controlled deep learning generated organ segmentations. To enable valid cross-study analysis, we first analyzed the data generating process using methods of causal discovery. We subsequently harmonized data from UKBB and NAKO using the ComBat approach for batch effect correction. We finally performed quantile regression on harmonized data across studies providing quantitative models for the variation of image-derived features stratified for sex and dependent on age, height, and weight., Results: Data from 8791 UKBB participants (49.9% female; age, 63 ± 7.5 years) and 9205 NAKO participants (49.1% female, age: 51.8 ± 11.4 years) were analyzed. Analysis of the data generating process revealed direct effects of age, sex, height, weight, and the data source (UKBB vs NAKO) on image-derived features. Correction of data source-related effects resulted in markedly improved alignment of image-derived features between UKBB and NAKO. Cross-study analysis on harmonized data revealed comprehensive quantitative models for the phenotypic variation of abdominal organs across the general adult population., Conclusions: Cross-study analysis of MRI data from UKBB and NAKO as proposed in this work can be helpful for future joint data analyses across cohorts linking genetic, environmental, and behavioral risk factors to MRI-derived phenotypes and provide reference values for clinical diagnostics., Competing Interests: Conflicts of interest and sources of funding: none declared., (Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc.)

While NMR-based metabolomics is only about 20 years old, NMR has been a key part of metabolic and metabolism studies for &gt;40 years. Historically, metabolic researchers used NMR because of its high level of reproducibility, superb instrument stability, facile sample preparation protocols, inherently quantitative character, non-destructive nature, and amenability to automation. In this chapter, we provide a short history of NMR-based metabolomics. We then provide a detailed description of some of the practical aspects of performing NMR-based metabolomics studies including sample preparation, pulse sequence selection, and spectral acquisition and processing. The two different approaches to metabolomics data analysis, targeted vs. untargeted, are briefly outlined. We also describe several software packages to help users process NMR spectra obtained via these two different approaches. We then give several examples of useful or interesting applications of NMR-based metabolomics, ranging from applications to drug toxicology, to identifying inborn errors of metabolism to analyzing the contents of biofluids from dairy cattle. Throughout this chapter, we will highlight the strengths and limitations of NMR-based metabolomics. Additionally, we will conclude with descriptions of recent advances in NMR hardware, methodology, and software and speculate about where NMR-based metabolomics is going in the next 5-10 years., (© 2022. The Author(s), under exclusive license to Springer Nature Switzerland AG.)

Introduction: Whole-body MRI (WB-MRI) is recommended by the National Institute of Clinical Excellence as the first-line imaging tool for diagnosis of multiple myeloma. Reporting WB-MRI scans requires expertise to interpret and can be challenging for radiologists who need to meet rapid turn-around requirements. Automated computational tools based on machine learning (ML) could assist the radiologist in terms of sensitivity and reading speed and would facilitate improved accuracy, productivity and cost-effectiveness. The MALIMAR study aims to develop and validate a ML algorithm to increase the diagnostic accuracy and reading speed of radiological interpretation of WB-MRI compared with standard methods., Methods and Analysis: This phase II/III imaging trial will perform retrospective analysis of previously obtained clinical radiology MRI scans and scans from healthy volunteers obtained prospectively to implement training and validation of an ML algorithm. The study will comprise three project phases using approximately 633 scans to (1) train the ML algorithm to identify active disease, (2) clinically validate the ML algorithm and (3) determine change in disease status following treatment via a quantification of burden of disease in patients with myeloma. Phase 1 will primarily train the ML algorithm to detect active myeloma against an expert assessment ('reference standard'). Phase 2 will use the ML output in the setting of radiology reader study to assess the difference in sensitivity when using ML-assisted reading or human-alone reading. Phase 3 will assess the agreement between experienced readers (with and without ML) and the reference standard in scoring both overall burden of disease before and after treatment, and response., Ethics and Dissemination: MALIMAR has ethical approval from South Central-Oxford C Research Ethics Committee (REC Reference: 17/SC/0630). IRAS Project ID: 233501. CPMS Portfolio adoption (CPMS ID: 36766). Participants gave informed consent to participate in the study before taking part. MALIMAR is funded by National Institute for Healthcare Research Efficacy and Mechanism Evaluation funding (NIHR EME Project ID: 16/68/34). Findings will be made available through peer-reviewed publications and conference dissemination., Trial Registration Number: NCT03574454., Competing Interests: Competing interests: AR receives honoraria for educational lecture at Garmisch International Symposium, has an unpaid role on the European Society of Radiology Board of Directors and receives travel cost support where necessary. BG receives grants from other entities; EU commission and UKRI London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare, is a Scientific advisor for Kheiron Medical Technologies (January 2018–September 2021) and receives stock options as part of standard employment packages from both Kheiron Medical Technologies and HeartFlow. EA has a patent pending for Machine Learning in Alzheimer’s disease and has a role on the scientific advisory board for Radiopharm Theranostics Limited. MK receives grants from both Myeloma UK and Celgene/BMS, and consulting fees or payments from AbbVie, BMS/Celgene, Janssen, GSK, Karyopharm, Takeda and Seagen. CM & DK receive additional funding as a co-investigator on a radiology NIHR study and is part of the joint venture Celescan with the Royal Marsden, The Institute of Cancer Research and Sopra Steria. TB receives additional funding from CRUK grant funding (NCITA) and NIHR (HTA) and receives honoraria from Bayer., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Introduction: European Association of Urology and UK National Institute for Health and Care Excellence guidelines recommend that all men with suspicions of prostate cancer should undergo prebiopsy contrast enhanced, that is, multiparametric prostate MRI. Subsequent prostate biopsies should also be performed if MRI is positive, that is, Prostate Imaging-Reporting and Data System (PI-RADS) scores 3-5. However, several retrospective post hoc analyses have shown that this approach still leads to many unnecessary biopsy procedures. For example, 88%-96% of men with PI-RADS, three findings are still diagnosed with clinically non-significant prostate cancer or no cancer at all., Methods and Analysis: This is a prospective, randomised, controlled, multicentre trial, being conducted in Finland, to demonstrate non-inferiority in clinically significant cancer detection rates among men undergoing prostate biopsies post-MRI and men undergoing prostate biopsies post-MRI only after a shared decision based on individualised risk estimation. Men without previous diagnosis of prostate cancer and with abnormal digital rectal examination findings and/or prostate-specific antigen between 2.5 ug/L and 20.0 ug/L are included. We aim to recruit 830 men who are randomised at a 1:1 ratio into control (all undergo biopsies after MRI) and intervention arms (the decision to perform biopsies is based on risk estimation and shared decision-making). The primary outcome of the study is the proportion of men with clinically significant prostate cancer (Gleason 4+3 prostate cancer or higher). We will also compare the overall biopsy rate, benign biopsy rate and the detection of non-significant prostate cancer between the two study groups., Ethics and Dissemination: The study (protocol V.2.0, 4 January 2021) was approved by the Ethics Committee of the Hospital District of Southwest Finland (IORG number: 0001744, IBR number: 00002216; trial number: 99/1801/2019). Participants are required to provide written informed consent. Full reports of this study will be submitted to peer-reviewed journals, mainly urology and radiology., Trial Registration Number: NCT04287088; the study is registered at ClinicalTrials.gov., Competing Interests: Competing interests: PT reports representation as a member of the Data Management Committee in the ProScreen trial. AV is named as a co-inventor on US patent number: 9 672 329 for a statistical method to predict the result of prostate biopsy. Patent has been commercialised and will receive royalties from clinical use. AV is also a co-inventor of the 4kscore, a commercially available reflex test for predicting prostate biopsy. He may receive royalties from sales of the test. He owns stock options in Opko, which offers the test. Otherwise, no competing interest was declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Autism Spectrum Disorder (ASD) diagnosis is still based on behavioral criteria through a lengthy and time-consuming process. Much effort is being made to identify brain imaging biomarkers and develop tools that could facilitate its diagnosis. In particular, using Machine Learning classifiers based on resting-state fMRI (rs-fMRI) data is promising, but there is an ongoing need for further research on their accuracy and reliability. Therefore, we conducted a systematic review and meta-analysis to summarize the available evidence in the literature so far. A bivariate random-effects meta-analytic model was implemented to investigate the sensitivity and specificity across the 55 studies that offered sufficient information for quantitative analysis. Our results indicated overall summary sensitivity and specificity estimates of 73.8% and 74.8%, respectively. SVM stood out as the most used classifier, presenting summary estimates above 76%. Studies with bigger samples tended to obtain worse accuracies, except in the subgroup analysis for ANN classifiers. The use of other brain imaging or phenotypic data to complement rs-fMRI information seems promising, achieving higher sensitivities when compared to rs-fMRI data alone (84.7% versus 72.8%). Finally, our analysis showed AUC values between acceptable and excellent. Still, given the many limitations indicated in our study, further well-designed studies are warranted to extend the potential use of those classification algorithms to clinical settings., (© 2022. The Author(s).)

Developmental delays in infanthood often persist, turning into life-long difficulties, and coming at great cost for the individual and community. By examining the developing brain and its relation to developmental outcomes we can start to elucidate how the emergence of brain circuits is manifested in variability of infant motor, cognitive and behavioural capacities. In this study, we examined if cortical structural covariance at birth, indexing coordinated development, is related to later infant behaviour. We included 193 healthy term-born infants from the Developing Human Connectome Project (dHCP). An individual cortical connectivity matrix derived from morphological and microstructural features was computed for each subject (morphometric similarity networks, MSNs) and was used as input for the prediction of behavioural scores at 18 months using Connectome-Based Predictive Modeling (CPM). Neonatal MSNs successfully predicted social-emotional performance. Predictive edges were distributed between and within known functional cortical divisions with a specific important role for primary and posterior cortical regions. These results reveal that multi-modal neonatal cortical profiles showing coordinated maturation are related to developmental outcomes and that network organization at birth provides an early infrastructure for future functional skills., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Measurement of cardiac structure and function from images (e.g. volumes, mass and derived parameters such as left ventricular (LV) ejection fraction [LVEF]) guides care for millions. This is best assessed using cardiovascular magnetic resonance (CMR), but image analysis is currently performed by individual clinicians, which introduces error. We sought to develop a machine learning algorithm for volumetric analysis of CMR images with demonstrably better precision than human analysis., Methods: A fully automated machine learning algorithm was trained on 1923 scans (10 scanner models, 13 institutions, 9 clinical conditions, 60,000 contours) and used to segment the LV blood volume and myocardium. Performance was quantified by measuring precision on an independent multi-site validation dataset with multiple pathologies with n = 109 patients, scanned twice. This dataset was augmented with a further 1277 patients scanned as part of routine clinical care to allow qualitative assessment of generalization ability by identifying mis-segmentations. Machine learning algorithm ('machine') performance was compared to three clinicians ('human') and a commercial tool (cvi42, Circle Cardiovascular Imaging)., Findings: Machine analysis was quicker (20 s per patient) than human (13 min). Overall machine mis-segmentation rate was 1 in 479 images for the combined dataset, occurring mostly in rare pathologies not encountered in training. Without correcting these mis-segmentations, machine analysis had superior precision to three clinicians (e.g. scan-rescan coefficients of variation of human vs machine: LVEF 6.0% vs 4.2%, LV mass 4.8% vs. 3.6%; both P < 0.05), translating to a 46% reduction in required trial sample size using an LVEF endpoint., Conclusion: We present a fully automated algorithm for measuring LV structure and global systolic function that betters human performance for speed and precision., (© 2022. The Author(s).)

Many previous intervention studies have used functional magnetic resonance imaging (fMRI) data to predict the antidepressant response of patients with major depressive disorder (MDD); however, practical constraints have limited many of those attempts to small, single centre studies which may not adequately reflect how these models will generalize when used in clinical practice. Not only does the act of collecting data at multiple sites generally increase sample sizes (a critical point in machine learning development) it also generates a more heterogeneous dataset due to systematic differences in scanners at different sites, and geographical differences in patient populations. As part of the Canadian Biomarker Integration Network in Depression (CAN-BIND-1) study, 144 MDD patients from six sites underwent resting state fMRI prior to starting escitalopram treatment, and again two weeks after the start. Here, we consider ways to use machine learning techniques to produce models that can predict response (measured at eight weeks after initiation), based on various parcellations, functional connectivity (FC) metrics, dimensionality reduction algorithms, and base learners, and also whether to use scans from one or both time points. Models that use only baseline (pre-treatment) or only week 2 (early-response) whole-brain FC features consistently failed to perform significantly better than default models. Utilizing the change in FC between these two time points, however, yielded significant results, with the best performing analytical pipeline achieving 69.6% (SD 10.8) accuracy. These results appear contrary to findings from many smaller single-site studies, which report substantially higher predictive accuracies from models trained on only baseline resting state FC features, suggesting these models may not generalize well beyond data used for development. Further, these results indicate the potential value of collecting data both before and shortly after treatment initiation., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Purpose: To introduce a novel deep learning-based approach for fast and high-quality dynamic multicoil MR reconstruction by learning a complementary time-frequency domain network that exploits spatiotemporal correlations simultaneously from complementary domains., Theory and Methods: Dynamic parallel MR image reconstruction is formulated as a multivariable minimization problem, where the data are regularized in combined temporal Fourier and spatial (x-f) domain as well as in spatiotemporal image (x-t) domain. An iterative algorithm based on variable splitting technique is derived, which alternates among signal de-aliasing steps in x-f and x-t spaces, a closed-form point-wise data consistency step and a weighted coupling step. The iterative model is embedded into a deep recurrent neural network which learns to recover the image via exploiting spatiotemporal redundancies in complementary domains., Results: Experiments were performed on two datasets of highly undersampled multicoil short-axis cardiac cine MRI scans. Results demonstrate that our proposed method outperforms the current state-of-the-art approaches both quantitatively and qualitatively. The proposed model can also generalize well to data acquired from a different scanner and data with pathologies that were not seen in the training set., Conclusion: The work shows the benefit of reconstructing dynamic parallel MRI in complementary time-frequency domains with deep neural networks. The method can effectively and robustly reconstruct high-quality images from highly undersampled dynamic multicoil data ( 16 × and 24 × yielding 15 s and 10 s scan times respectively) with fast reconstruction speed (2.8 seconds). This could potentially facilitate achieving fast single-breath-hold clinical 2D cardiac cine imaging., (© 2021 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.)

Introduction: The dynamic nature and complexity of the cellular events that take place during the last trimester of pregnancy make the developing cortex particularly vulnerable to perturbations. Abrupt interruption to normal gestation can lead to significant deviations to many of these processes, resulting in atypical trajectory of cortical maturation in preterm birth survivors., Methods: We sought to first map typical cortical micro- and macrostructure development using invivo MRI in a large sample of healthy term-born infants scanned after birth (n = 259). Then we offer a comprehensive characterization of the cortical consequences of preterm birth in 76 preterm infants scanned at term-equivalent age (37-44 weeks postmenstrual age). We describe the group-average atypicality, the heterogeneity across individual preterm infants, and relate individual deviations from normative development to age at birth and neurodevelopment at 18 months., Results: In the term-born neonatal brain, we observed heterogeneous and regionally specific associations between age at scan and measures of cortical morphology and microstructure, including rapid surface expansion, greater cortical thickness, lower cortical anisotropy and higher neurite orientation dispersion. By term-equivalent age, preterm infants had on average increased cortical tissue water content and reduced neurite density index in the posterior parts of the cortex, and greater cortical thickness anteriorly compared to term-born infants. While individual preterm infants were more likely to show extreme deviations (over 3.1 standard deviations) from normative cortical maturation compared to term-born infants, these extreme deviations were highly variable and showed very little spatial overlap between individuals. Measures of regional cortical development were associated with age at birth, but not with neurodevelopment at 18 months., Conclusion: We showed that preterm birth alters cortical micro- and macrostructural maturation near the time of full-term birth. Deviations from normative development were highly variable between individual preterm infants., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

The success of deep learning in recent years has arguably been driven by the availability of large datasets for training powerful predictive algorithms. In medical applications however, the sensitive nature of the data limits the collection and exchange of large-scale datasets. Privacy-preserving and collaborative learning systems can enable the successful application of machine learning in medicine. However, collaborative protocols such as federated learning require the frequent transfer of parameter updates over a network. To enable the deployment of such protocols to a wide range of systems with varying computational performance, efficient deep learning architectures for resource-constrained environments are required. Here we present MoNet, a small, highly optimized neural-network-based segmentation algorithm leveraging efficient multi-scale image features. MoNet is a shallow, U-Net-like architecture based on repeated, dilated convolutions with decreasing dilation rates. We apply and test our architecture on the challenging clinical tasks of pancreatic segmentation in computed tomography (CT) images as well as brain tumor segmentation in magnetic resonance imaging (MRI) data. We assess our model's segmentation performance and demonstrate that it provides performance on par with compared architectures while providing superior out-of-sample generalization performance, outperforming larger architectures on an independent validation set, while utilizing significantly fewer parameters. We furthermore confirm the suitability of our architecture for federated learning applications by demonstrating a substantial reduction in serialized model storage requirement as a surrogate for network data transfer. Finally, we evaluate MoNet's inference latency on the central processing unit (CPU) to determine its utility in environments without access to graphics processing units. Our implementation is publicly available as free and open-source software., Competing Interests: The authors have declared that no competing interests exist.

Computational fluid dynamics (CFD) simulations of respiratory airflow have the potential to change the clinical assessment of regional airway function in health and disease, in pulmonary medicine and otolaryngology. For example, in diseases where multiple sites of airway obstruction occur, such as obstructive sleep apnea (OSA), CFD simulations can identify which sites of obstruction contribute most to airway resistance and may therefore be candidate sites for airway surgery. The main barrier to clinical uptake of respiratory CFD to date has been the difficulty in validating CFD results against a clinical gold standard. Invasive instrumentation of the upper airway to measure respiratory airflow velocity or pressure can disrupt the airflow and alter the subject's natural breathing patterns. Therefore, in this study, we instead propose phase contrast (PC) velocimetry magnetic resonance imaging (MRI) of inhaled hyperpolarized 129Xe gas as a non-invasive reference to which airflow velocities calculated via CFD can be compared. To that end, we performed subject-specific CFD simulations in airway models derived from 1H MRI, and using respiratory flowrate measurements acquired synchronously with MRI. Airflow velocity vectors calculated by CFD simulations were then qualitatively and quantitatively compared to velocity maps derived from PC velocimetry MRI of inhaled hyperpolarized 129Xe gas. The results show both techniques produce similar spatial distributions of high velocity regions in the anterior-posterior and foot-head directions, indicating good qualitative agreement. Statistically significant correlations and low Bland-Altman bias between the local velocity values produced by the two techniques indicates quantitative agreement. This preliminary in vivo comparison of respiratory airway CFD and PC MRI of hyperpolarized 129Xe gas demonstrates the feasibility of PC MRI as a technique to validate respiratory CFD and forms the basis for further comprehensive validation studies. This study is therefore a first step in the pathway towards clinical adoption of respiratory CFD., Competing Interests: Drs Hui Wang and Guruprasad Krishnamoorthy are employees of Philips. Philips did not fund this study, nor did they have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript other than the roles of these authors as articulated in the ‘author contributions’ section. These conflicts do not alter our adherence to PLOS ONE policies on sharing data and materials. No other competing interests exist.

A prominent cognitive aspect of anxiety is dysregulation of emotional interpretation of facial expressions, associated with neural activity from the amygdala and prefrontal cortex. We report machine learning analysis of fMRI results supporting a key role for a third area, the temporal pole (TP) for childhood anxiety in this context. This finding is based on differential fMRI responses to emotional faces (angry versus fearful faces) in children with one or more of generalized anxiety, separation anxiety, and social phobia (n = 22) compared with matched controls (n = 23). In our machine learning (Adaptive Boosting) model, the right TP distinguished anxious from control children (accuracy = 81%). Involvement of the TP as significant for neurocognitive aspects of pediatric anxiety is a novel finding worthy of further investigation., (© 2021. The Author(s).)

Similarity analysis is one of the crucial steps in most fMRI studies. Representational Similarity Analysis (RSA) can measure similarities of neural signatures generated by different cognitive states. This paper develops Deep Representational Similarity Learning (DRSL), a deep extension of RSA that is appropriate for analyzing similarities between various cognitive tasks in fMRI datasets with a large number of subjects, and high-dimensionality - such as whole-brain images. Unlike the previous methods, DRSL is not limited by a linear transformation or a restricted fixed nonlinear kernel function - such as Gaussian kernel. DRSL utilizes a multi-layer neural network for mapping neural responses to linear space, where this network can implement a customized nonlinear transformation for each subject separately. Furthermore, utilizing a gradient-based optimization in DRSL can significantly reduce runtime of analysis on large datasets because it uses a batch of samples in each iteration rather than all neural responses to find an optimal solution. Empirical studies on multi-subject fMRI datasets with various tasks - including visual stimuli, decision making, flavor, and working memory - confirm that the proposed method achieves superior performance to other state-of-the-art RSA algorithms.

Background: Dixon cardiac magnetic resonance fingerprinting (MRF) has been recently introduced to simultaneously provide water T 1 , water T 2 , and fat fraction (FF) maps., Purpose: To assess Dixon cardiac MRF repeatability in healthy subjects and its clinical feasibility in a cohort of patients with cardiovascular disease., Population: T1MES phantom, water-fat phantom, 11 healthy subjects and 19 patients with suspected cardiovascular disease., Study Type: Prospective., Field Strength/sequence: 1.5T, inversion recovery spin echo (IRSE), multiecho spin echo (MESE), modified Look-Locker inversion recovery (MOLLI), T 2 gradient spin echo (T 2 -GRASE), 6-echo gradient rewound echo (GRE), and Dixon cardiac MRF., Assessment: Dixon cardiac MRF precision was assessed through repeated scans against conventional MOLLI, T 2 -GRASE, and PDFF in phantom and 11 healthy subjects. Dixon cardiac MRF native T 1 , T 2 , FF, postcontrast T 1 and synthetic extracellular volume (ECV) maps were assessed in 19 patients in comparison to conventional sequences. Measurements in patients were performed in the septum and in late gadolinium enhanced (LGE) areas and assessed using mean value distributions, correlation, and Bland-Altman plots. Image quality and diagnostic confidence were assessed by three experts using 5-point scoring scales., Statistical Tests: Paired Wilcoxon rank signed test and paired t-tests were applied. Statistical significance was indicated by *(P < 0.05)., Results: Dixon cardiac MRF showed good overall precision in phantom and in vivo. Septal average repeatability was ~23 msec for T 1 , ~2.2 msec for T 2 , and ~1% for FF. Biases in healthy subjects/patients were measured at +37 msec*/+60 msec* and -8.8 msec*/-8 msec* when compared to MOLLI and T 2 -GRASE, respectively. No statistically significant differences in postcontrast T 1 (P = 0.17) and synthetic ECV (P = 0.19) measurements were observed in patients., Data Conclusion: Dixon cardiac MRF attained good overall precision in phantom and healthy subjects, while providing coregistered T 1 , T 2 , and fat fraction maps in a single breath-hold scan with similar or better image quality than conventional methods in patients., Level of Evidence: 2., Technical Efficacy Stage: 2., (© 2020 The Authors. Journal of Magnetic Resonance Imaging published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.)

Purpose: The aim of this work is to shed light on the issue of reproducibility in MR image reconstruction in the context of a challenge. Participants had to recreate the results of "Advances in sensitivity encoding with arbitrary k-space trajectories" by Pruessmann et al. METHODS: The task of the challenge was to reconstruct radially acquired multicoil k-space data (brain/heart) following the method in the original paper, reproducing its key figures. Results were compared to consolidated reference implementations created after the challenge, accounting for the two most common programming languages used in the submissions (Matlab/Python)., Results: Visually, differences between submissions were small. Pixel-wise differences originated from image orientation, assumed field-of-view, or resolution. The reference implementations were in good agreement, both visually and in terms of image similarity metrics., Discussion and Conclusion: While the description level of the published algorithm enabled participants to reproduce CG-SENSE in general, details of the implementation varied, for example, density compensation or Tikhonov regularization. Implicit assumptions about the data lead to further differences, emphasizing the importance of sufficient metadata accompanying open datasets. Defining reproducibility quantitatively turned out to be nontrivial for this image reconstruction challenge, in the absence of ground-truth results. Typical similarity measures like NMSE of SSIM were misled by image intensity scaling and outlier pixels. Thus, to facilitate reproducibility, researchers are encouraged to publish code and data alongside the original paper. Future methodological papers on MR image reconstruction might benefit from the consolidated reference implementations of CG-SENSE presented here, as a benchmark for methods comparison., (© 2020 International Society for Magnetic Resonance in Medicine.)

The large number of available MRI sequences means patients cannot realistically undergo them all, so the range of sequences to be acquired during a scan are protocolled based on clinical details. Adapting this to unexpected findings identified early on in the scan requires experience and vigilance. We investigated whether deep learning of the images acquired in the first few minutes of a scan could provide an automated early alert of abnormal features. Anatomy sequences from 375 CMR scans were used as a training set. From these, we annotated 1500 individual slices and used these to train a convolutional neural network to perform automatic segmentation of the cardiac chambers, great vessels and any pleural effusions. 200 scans were used as a testing set. The system then assembled a 3D model of the thorax from which it made clinical measurements to identify important abnormalities. The system was successful in segmenting the anatomy slices (Dice 0.910) and identified multiple features which may guide further image acquisition. Diagnostic accuracy was 90.5% and 85.5% for left and right ventricular dilatation, 85% for left ventricular hypertrophy and 94.4% for ascending aorta dilatation. The area under ROC curve for diagnosing pleural effusions was 0.91. We present proof-of-concept that a neural network can segment and derive accurate clinical measurements from a 3D model of the thorax made from transaxial anatomy images acquired in the first few minutes of a scan. This early information could lead to dynamic adaptive scanning protocols, and by focusing scanner time appropriately and prioritizing cases for supervision and early reporting, improve patient experience and efficiency.

Importance: Persistent symptoms after mild traumatic brain injury (mTBI) represent a major public health problem., Objective: To identify neuroanatomical substrates of mTBI and the optimal timing for magnetic resonance imaging (MRI)., Design, Setting, and Participants: This prospective multicenter cohort study encompassed all eligible patients from the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study (December 19, 2014, to December 17, 2017) and a local cohort (November 20, 2012, to December 19, 2013). Patients presented to the hospital within 24 hours of an mTBI (Glasgow Coma Score, 13-15), satisfied local criteria for computed tomographic scanning, and underwent MRI scanning less than 72 hours (MR1) and 2 to 3 weeks (MR2) after injury. In addition, 104 control participants were enrolled across all sites. Data were analyzed from January 1, 2019, to December 31, 2020., Exposure: Mild TBI., Main Outcomes and Measures: Volumes and diffusion parameters were extracted via automated bespoke pipelines. Symptoms were measured using the Rivermead Post Concussion Symptoms Questionnaire in the short term and the extended Glasgow Outcome Scale at 3 months., Results: Among the 81 patients included in the analysis (73 CENTER-TBI and 8 local), the median age was 45 (interquartile range [IQR], 24-59; range, 14-85) years, and 57 (70.4%) were male. Structural sequences were available for all scans; diffusion data, for 73 MR1 and 79 MR2 scans. After adjustment for multiple comparisons between scans, visible lesions did not differ significantly, but cerebral white matter volume decreased (MR2:MR1 ratio, 0.98; 95% CI, 0.96-0.99) and ventricular volume increased (MR2:MR1 ratio, 1.06; 95% CI, 1.02-1.10). White matter volume was within reference limits on MR1 scans (patient to control ratio, 0.99; 95% CI, 0.97-1.01) and reduced on MR2 scans (patient to control ratio, 0.97; 95% CI, 0.95-0.99). Diffusion parameters changed significantly between scans in 13 tracts, following 1 of 3 trajectories. Symptoms measured by Rivermead Post Concussion Symptoms Questionnaire scores worsened in the progressive injury phenotype (median, +5.00; IQR, +2.00 to +5.00]), improved in the minimal change phenotype (median, -4.50; IQR, -9.25 to +1.75), and were variable in the pseudonormalization phenotype (median, 0.00; IQR, -6.25 to +9.00) (P = .02). Recovery was favorable for 33 of 65 patients (51%) and was more closely associated with MR1 than MR2 (area under the curve, 0.87 [95% CI, 0.78-0.96] vs 0.75 [95% CI, 0.62-0.87]; P = .009)., Conclusions and Relevance: These findings suggest that advanced MRI reveals potential neuroanatomical substrates of mTBI in white matter and is most strongly associated with odds of recovery if performed within 72 hours, although future validation is required.

The in vivo assessment of tissue metabolism represents a novel strategy for the evaluation of oncologic disease. Hepatocellular carcinoma (HCC) is a high-prevalence, high-mortality tumor entity often discovered at a late stage. Recent evidence indicates that survival differences depend on metabolic alterations in tumor tissue, with particular focus on glucose metabolism and lactate production. Here, we present an in vivo imaging technique for metabolic tumor phenotyping in rat models of HCC. Endogenous HCC was induced in Wistar rats by oral diethyl-nitrosamine administration. Peak lactate-to-alanine signal ratios (L/A) were assessed with hyperpolarized magnetic resonance spectroscopic imaging (HPMRSI) after [1- 13 C]pyruvate injection. Cell lines were derived from a subset of primary tumors, re-implanted in nude rats, and assessed in vivo with dynamic hyperpolarized magnetic resonance spectroscopy (HPMRS) after [1- 13 C]pyruvate injection and kinetic modelling of pyruvate metabolism, taking into account systemic lactate production and recirculation. For ex vivo validation, enzyme activity and metabolite concentrations were spectroscopically quantified in cell and tumor tissue extracts. Mean peak L/A was higher in endogenous HCC compared to non-tumorous tissue. Dynamic HPMRS revealed higher pyruvate-to-lactate conversion rates (k pl ) and lactate signal in subcutaneous tumors derived from high L/A tumor cells, consistent with ex vivo measurements of higher lactate dehydrogenase (LDH) levels in these cells. In conclusion, HPMRS and HPMRSI reveal distinct tumor phenotypes corresponding to differences in glycolytic metabolism in HCC tumor tissue.

Functional connectivity analysis of resting-state fMRI data has recently become one of the most common approaches to characterizing individual brain function. It has been widely suggested that the functional connectivity matrix is a useful approximate representation of the brain's connectivity, potentially providing behaviorally or clinically relevant markers. However, functional connectivity estimates are known to be detrimentally affected by various artifacts, including those due to in-scanner head motion. Moreover, as individual functional connections generally covary only very weakly with head motion estimates, motion influence is difficult to quantify robustly, and prone to be neglected in practice. Although the use of individual estimates of head motion, or group-level correlation of motion and functional connectivity has been suggested, a sufficiently sensitive measure of individual functional connectivity quality has not yet been established. We propose a new intuitive summary index, Typicality of Functional Connectivity, to capture deviations from standard brain functional connectivity patterns. In a resting-state fMRI dataset of 245 healthy subjects, this measure was significantly correlated with individual head motion metrics. The results were further robustly reproduced across atlas granularity, preprocessing options, and other datasets, including 1,081 subjects from the Human Connectome Project. In principle, Typicality of Functional Connectivity should be sensitive also to other types of artifacts, processing errors, and possibly also brain pathology, allowing extensive use in data quality screening and quantification in functional connectivity studies as well as methodological investigations., (© 2020 The Authors. Human Brain Mapping published by Wiley Periodicals LLC.)

The developing Human Connectome Project (dHCP) aims to create a detailed 4-dimensional connectome of early life spanning 20-45 weeks post-menstrual age. This is being achieved through the acquisition of multi-modal MRI data from over 1000 in- and ex-utero subjects combined with the development of optimised pre-processing pipelines. In this paper we present an automated and robust pipeline to minimally pre-process highly confounded neonatal resting-state fMRI data, robustly, with low failure rates and high quality-assurance. The pipeline has been designed to specifically address the challenges that neonatal data presents including low and variable contrast and high levels of head motion. We provide a detailed description and evaluation of the pipeline which includes integrated slice-to-volume motion correction and dynamic susceptibility distortion correction, a robust multimodal registration approach, bespoke ICA-based denoising, and an automated QC framework. We assess these components on a large cohort of dHCP subjects and demonstrate that processing refinements integrated into the pipeline provide substantial reduction in movement related distortions, resulting in significant improvements in SNR, and detection of high quality RSNs from neonates., Competing Interests: Declaration of Competing Interest MJ, SS, and JA receive royalties from the commercial licensing of FSL (it is free for non-commercial use). The authors report no other conflicts of interest., (Copyright © 2020. Published by Elsevier Inc.)

Purpose: To develop a method that can reduce and estimate uncertainty in quantitative MR parameter maps without the need for hand-tuning of any hyperparameters., Methods: We present an estimation method where uncertainties are reduced by incorporating information on spatial correlations between neighbouring voxels. The method is based on a Bayesian hierarchical non-linear regression model, where the parameters of interest are sampled, using Markov chain Monte Carlo (MCMC), from a high-dimensional posterior distribution with a spatial prior. The degree to which the prior affects the model is determined by an automatic hyperparameter search using an information criterion and is, therefore, free from manual user-dependent tuning. The samples obtained further provide a convenient means to obtain uncertainties in both voxels and regions. The developed method was evaluated on T 1 estimations based on the variable flip angle method., Results: The proposed method delivers noise-reduced T 1 parameter maps with associated error estimates by combining MCMC sampling, the widely applicable information criterion, and total variation-based denoising. The proposed method results in an overall decrease in estimation error when compared to conventional voxel-wise maximum likelihood estimation. However, this comes with an increased bias in some regions, predominately at tissue interfaces, as well as an increase in computational time., Conclusions: This study provides a method that generates more precise estimates compared to the conventional method, without incorporating user subjectivity, and with the added benefit of uncertainty estimation.

Brain structure in later life reflects both influences of intrinsic aging and those of lifestyle, environment and disease. We developed a deep neural network model trained on brain MRI scans of healthy people to predict "healthy" brain age. Brain regions most informative for the prediction included the cerebellum, hippocampus, amygdala and insular cortex. We then applied this model to data from an independent group of people not stratified for health. A phenome-wide association analysis of over 1,410 traits in the UK Biobank with differences between the predicted and chronological ages for the second group identified significant associations with over 40 traits including diseases (e.g., type I and type II diabetes), disease risk factors (e.g., increased diastolic blood pressure and body mass index), and poorer cognitive function. These observations highlight relationships between brain and systemic health and have implications for understanding contributions of the latter to late life dementia risk.

In this study we use undersampled MRI acquisition methods to obtain accelerated 3D mono and biexponential spin-lattice relaxation time in the rotating frame (T 1ρ ) mapping of knee cartilage, reducing the usual long scan time. We compare the accelerated T 1ρ maps obtained by deep learning-based variational network (VN) and compressed sensing (CS). Both methods were compared with spatial (S) and spatio-temporal (ST) filters. Complex-valued fitting was used for T 1ρ parameters estimation. We tested with seven in vivo and six synthetic datasets, with acceleration factors (AF) from 2 to 10. Median normalized absolute deviation (MNAD), analysis of variance (ANOVA), and coefficient of variation (CV) were used for analysis. The methods CS-ST, VN-S, and VN-ST performed well for accelerating monoexponential T 1ρ mapping, with MNAD around 5% for AF = 2, which increases almost linearly with the AF to an MNAD of 13% for AF = 8, with all methods. For biexponential mapping, the VN-ST was the best method starting with MNAD of 7.4% for AF = 2 and reaching MNAD of 13.1% for AF = 8. The VN was able to produce 3D-T 1ρ mapping of knee cartilage with lower error than CS. The best results were obtained by VN-ST, improving CS-ST method by nearly 7.5%.

Twelve to 66% of patients with clinically non-functioning pituitary adenoma (NFPA) experience tumor recurrence 1-5 years after the first surgery. Nevertheless, there is still no recurrence prediction factor concisely established and reproduced in the literature for NFPA management. The present study evaluates the prognostic value of MRI Radiomics features combined with machine learning models to assess recurrence after the first surgery in patients with clinically non-functioning pituitary adenomas (NFPA). We carried out a retrospective study on 27 patients with NFPA, 10 patients having experienced tumor recurrence after the first surgery and 17 who did not. Preoperative 3D T 1 contrast-enhanced MR images of patients were used to extract up to 255 Radiomics features from two and three-dimensional segmented regions. Additionally, gender, age at first surgery, and the presence of remnant tumor tissue were investigated to find the correlation with NFPA recurrence. Conventional statistics tests were used to evaluate whether the outcome patient groups (stable and recurrent) were different considering each feature individually. Additionally, five well-known machine-learning algorithms were used in combination with Radiomic features to classify recurrent and stable lesions. We found statistical evidence (p < 0.02) for 6 two-dimensional and 13 three-dimensional radiomic features. We achieved accuracies of up to 96.3% for 3D-feature based models and up to 92.6% accuracies for 2D-feature based models. 3D-feature based models achieved better performances using considerably fewer features when compared to 2D-feature based models. We concluded that Radiomics have the potential of NFPA recurrence prediction after the first surgery. Three-dimensional Radiomics have superior discrimination power to predict NFPA recurrence than two-dimensional radiomic features. Finally, the combination of Radiomics with machine-learning algorithms can offer computational models capable of non-invasive, unbiased, and quick assessment that might improve the prediction of NFPA recurrence., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Background: Tissue characterisation with cardiovascular magnetic resonance (CMR) parametric mapping has the potential to detect and quantify both focal and diffuse alterations in myocardial structure not assessable by late gadolinium enhancement. Native T 1 mapping in particular has shown promise as a useful biomarker to support diagnostic, therapeutic and prognostic decision-making in ischaemic and non-ischaemic cardiomyopathies., Methods: Convolutional neural networks (CNNs) with Bayesian inference are a category of artificial neural networks which model the uncertainty of the network output. This study presents an automated framework for tissue characterisation from native shortened modified Look-Locker inversion recovery ShMOLLI T 1 mapping at 1.5 T using a Probabilistic Hierarchical Segmentation (PHiSeg) network (PHCUMIS 119-127, 2019). In addition, we use the uncertainty information provided by the PHiSeg network in a novel automated quality control (QC) step to identify uncertain T 1 values. The PHiSeg network and QC were validated against manual analysis on a cohort of the UK Biobank containing healthy subjects and chronic cardiomyopathy patients (N=100 for the PHiSeg network and N=700 for the QC). We used the proposed method to obtain reference T 1 ranges for the left ventricular (LV) myocardium in healthy subjects as well as common clinical cardiac conditions., Results: T 1 values computed from automatic and manual segmentations were highly correlated (r=0.97). Bland-Altman analysis showed good agreement between the automated and manual measurements. The average Dice metric was 0.84 for the LV myocardium. The sensitivity of detection of erroneous outputs was 91%. Finally, T 1 values were automatically derived from 11,882 CMR exams from the UK Biobank. For the healthy cohort, the mean (SD) corrected T 1 values were 926.61 (45.26), 934.39 (43.25) and 927.56 (50.36) for global, interventricular septum and free-wall respectively., Conclusions: The proposed pipeline allows for automatic analysis of myocardial native T 1 mapping and includes a QC process to detect potentially erroneous results. T 1 reference values were presented for healthy subjects and common clinical cardiac conditions from the largest cohort to date using T 1 -mapping images.

Background: Texture analysis (TA) is an image-analysis technique that detects complex intervoxel statistical patterns. 3D TA has shown potential in detecting cerebral degeneration not perceptible to the human eye in many neurological disorders. The reliability of this method's application in a multicenter study is unknown., Purpose: To assess the intrasite and intersite reliability of a novel 3D TA method from data acquired systematically from the Canadian ALS Neuroimaging Consortium (CALSNIC)., Study Type: Prospective multicenter data with harmonized MR sequence parameters acquired from five sites., Population: Six healthy subjects., Field Strength: 3T 3D-MPRAGE and 3D-SPGR T 1 -weighted MRI of the brain., Assessment: Voxel-based 3D TA was performed on the whole brain to produce texture maps., Statistical Tests: Intra- and intersite reliability of texture features was assessed using a two-way mixed-effects model for intraclass correlation coefficients (ICC). ICCs were calculated in a region-of-interest (ROI) analysis of predetermined anatomically relevant areas. A voxelwise approach was used to assess the whole brain., Results: In the ROI analyses, intrasite reliability was excellent (ICC > 0.75) across most regions and texture features (autocorrelation [autoc], contrast [contr], energy [energ]). Intersite reliability was excellent for most regions with autoc, ranging from fair to excellent for contr, and ICCs ranging from poor to good (<0.40-0.75) for energ. Voxelwise analyses revealed a large range in ICC across the brain for both intrasite and intersite ICCs (0.0-0.90), with higher reliability in the cortical gray matter compared with deeper subcortical structures., Data Conclusion: Overall, the reliability of 3D TA was highly dependent on texture feature, region studied, and method of analysis (ROI or voxelwise). Intrasite reproducibility was good to excellent, and better than intersite. ROI-based analyses present higher reliability in comparison with voxelwise analyses. Autoc has overall excellent reliability. These factors might be considered when designing future 3D TA studies., Level of Evidence: 2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2020;51:1200-1209., (© 2019 International Society for Magnetic Resonance in Medicine.)

Background: The relationship between microvasculopathy, autonomic denervation, and myocardial fibrosis, in Chagas cardiomyopathy is incompletely understood. The aim of this study was to explore the relative extent and anatomic distribution of myocardial hypoperfusion, autonomic denervation, and myocardial scarring using Single-Photon Emission Computerized Tomography (SPECT) imaging and Magnetic Resonance Imaging (MRI)., Methods: Thirteen patients with Chagas disease all had Iodine-123-metaiodobenzylguanidine (MIBG) SPECT, 99m Tc-Sestamibi (MIBI) rest-stress SPECT, and gadolinium late enhancement MRI imaging within a 2-month interval. The anatomic location and extent of denervation, of stress-induced hypoperfusion and fibrosis, were assessed through image co-registration and quantification of abnormal tissue areas as a percent of total myocardium., Results: The results showed a strong general anatomic concordance between areas of hypoperfusion, denervation, and fibrosis, suggesting that the three abnormal features may be correlated. Myocardial denervation was anatomically and quantitatively closely associated areas of stress hypoperfusion., Conclusion: Combined myocardial analysis of the extent and location of autonomic denervation, hypoperfusion, and scarring may allow for better understanding of the pathophysiology of Chagas cardiomyopathy. Autonomic myocardial denervation may be a more sensitive marker of cardiac involvement in Chagas Disease than finding by other imaging modalities.

Purpose: Three-dimensional (3D) late gadolinium enhancement magnetic resonance (LGE-MR) imaging enables the quantification of myocardial scar at high resolution with unprecedented volumetric visualization. Automated segmentation of myocardial scar is critical for the potential clinical translation of this technique given the number of tomographic images acquired., Methods: In this paper, we describe the development of cascaded multi-planar U-Net (CMPU-Net) to efficiently segment the boundary of the left ventricle (LV) myocardium and scar from 3D LGE-MR images. In this approach, two subnets, each containing three U-Nets, were cascaded to first segment the LV myocardium and then segment the scar within the presegmented LV myocardium. The U-Nets were trained separately using two-dimensional (2D) slices extracted from axial, sagittal, and coronal slices of 3D LGE-MR images. We used 3D LGE-MR images from 34 subjects with chronic ischemic cardiomyopathy. The U-Nets were trained using 8430 slices, extracted in three orthogonal directions from 18 images. In the testing phase, the outputs of U-Nets of each subnet were combined using the majority voting system for final label prediction of each voxel in the image. The developed method was tested for accuracy by comparing its results to manual segmentations of LV myocardium and LV scar from 7250 slices extracted from 16 3D LGE-MR images. Our method was also compared to numerous alternative methods based on machine learning, energy minimization, and intensity-thresholds., Results: Our algorithm reported a mean dice similarity coefficient (DSC), absolute volume difference (AVD), and Hausdorff distance (HD) of 85.14% ± 3.36%, 43.72 ± 27.18 cm 3 , and 19.21 ± 4.74 mm for determining the boundaries of LV myocardium from LGE-MR images. Our method also yielded a mean DSC, AVD, and HD of 88.61% ± 2.54%, 9.33 ± 7.24 cm 3 , and 17.04 ± 9.93 mm for LV scar segmentation on the unobserved test dataset. Our method significantly outperformed the alternative techniques in segmentation accuracy (P < 0.05)., Conclusions: The CMPU-Net method provided fully automated segmentation of LV scar from 3D LGE-MR images and outperformed the alternative techniques., (© 2020 American Association of Physicists in Medicine.)

Gradient-based texture analysis methods have become popular in computer vision and image processing and has many applications including medical image analysis. This motivates us to develop a texture feature extraction method to discriminate Amyotrophic Lateral Sclerosis (ALS) patients from controls. But, the lack of data in ALS research is a major constraint and can be mitigated by using data from multiple centers. However, multi-center data gives some other challenges such as differing scanner parameters and variation in intensity of the medical images, which motivate the development of the proposed method. To investigate these challenges, we propose a gradient-based texture feature extraction method called Modified Co-occurrence Histograms of Oriented Gradients (M-CoHOG) to extract texture features from 2D Magnetic Resonance Images (MRI). We also propose a new feature-normalization technique before feeding the normalized M-CoHOG features into an ensemble of classifiers, which can accommodate for variation of data from different centers. ALS datasets from four different centers are used in the experiments. We analyze the classification accuracy of single center data as well as that arising from multiple centers. It is observed that the extracted texture features from downsampled images are more significant in distinguishing between patients and controls. Moreover, using an ensemble of classifiers shows improvement in classification accuracy over a single classifier in multi-center data. The proposed method outperforms the state-of-the-art methods by a significant margin., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

We present the application of limited one-time sampling irregularity map (LOTS-IM): a fully automatic unsupervised approach to extract brain tissue irregularities in magnetic resonance images (MRI), for quantitatively assessing white matter hyperintensities (WMH) of presumed vascular origin, and multiple sclerosis (MS) lesions and their progression. LOTS-IM generates an irregularity map (IM) that represents all voxels as irregularity values with respect to the ones considered "normal". Unlike probability values, IM represents both regular and irregular regions in the brain based on the original MRI's texture information. We evaluated and compared the use of IM for WMH and MS lesions segmentation on T2-FLAIR MRI with the state-of-the-art unsupervised lesions' segmentation method, Lesion Growth Algorithm from the public toolbox Lesion Segmentation Toolbox (LST-LGA), with several well established conventional supervised machine learning schemes and with state-of-the-art supervised deep learning methods for WMH segmentation. In our experiments, LOTS-IM outperformed unsupervised method LST-LGA on WMH segmentation, both in performance and processing speed, thanks to the limited one-time sampling scheme and its implementation on GPU. Our method also outperformed supervised conventional machine learning algorithms (i.e., support vector machine (SVM) and random forest (RF)) and deep learning algorithms (i.e., deep Boltzmann machine (DBM) and convolutional encoder network (CEN)), while yielding comparable results to the convolutional neural network schemes that rank top of the algorithms developed up to date for this purpose (i.e., UResNet and UNet). LOTS-IM also performed well on MS lesions segmentation, performing similar to LST-LGA. On the other hand, the high sensitivity of IM on depicting signal change deems suitable for assessing MS progression, although care must be taken with signal changes not reflective of a true pathology., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Quantifying the intracranial tissue volume changes in magnetic resonance imaging (MRI) assists specialists to analyze the effects of natural or pathological changes. Since these changes can be subtle, the accuracy of the automatic compartmentalization method is always criticized by specialists. We propose and then evaluate an automatic segmentation method based on modified q-entropy (Mqe) through a modified Markov Random Field (MMRF) enhanced by Alzheimer anatomic reference (AAR) to provide a high accuracy brain tissues parcellation approach (Mqe-MMRF). We underwent two strategies to evaluate Mqe-MMRF; a simulation of different levels of noise and non-uniformity effect on MRI data (7 subjects) and a set of twenty MRI data available from MRBrainS13 as patient brain tissue segmentation challenge. We accessed eleven quality metrics compared to reference tissues delineations to evaluate Mqe-MMRF. MRI segmentation scores decreased by only 4.6% on quality metrics after noise and non-uniformity simulations of 40% and 9%, respectively. We found significant mean improvements in the metrics of the five training subjects, for whole-brain 0.86%, White Matter 3.20%, Gray Matter 3.99%, and Cerebrospinal Fluid 4.16% (p-values < 0.02) when Mqe-MMRF compared to the other reference methods. We also processed the Mqe-MMRF on 15 evaluation subjects group from MRBrainS13 online challenge, and the results held a higher rank than the reference tools; FreeSurfer, SPM, and FSL. Since the proposed method improved the precision of brain segmentation, specifically, for GM, and thus one can use it in quantitative and morphological brain studies., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Background and Purpose- Cerebral small vessel disease is characterized by a wide range of focal and global brain changes. We used a magnetic resonance imaging segmentation tool to quantify multiple types of small vessel disease-related brain changes and examined their individual and combined predictive value on cognitive and functional abilities. Methods- Magnetic resonance imaging scans of 560 older individuals from LADIS (Leukoaraiosis and Disability Study) were analyzed using automated atlas- and convolutional neural network-based segmentation methods yielding volumetric measures of white matter hyperintensities, lacunes, enlarged perivascular spaces, chronic cortical infarcts, and global and regional brain atrophy. The subjects were followed up with annual neuropsychological examinations for 3 years and evaluation of instrumental activities of daily living for 7 years. Results- The strongest predictors of cognitive performance and functional outcome over time were the total volumes of white matter hyperintensities, gray matter, and hippocampi ( P <0.001 for global cognitive function, processing speed, executive functions, and memory and P <0.001 for poor functional outcome). Volumes of lacunes, enlarged perivascular spaces, and cortical infarcts were significantly associated with part of the outcome measures, but their contribution was weaker. In a multivariable linear mixed model, volumes of white matter hyperintensities, lacunes, gray matter, and hippocampi remained as independent predictors of cognitive impairment. A combined measure of these markers based on Z scores strongly predicted cognitive and functional outcomes ( P <0.001) even above the contribution of the individual brain changes. Conclusions- Global burden of small vessel disease-related brain changes as quantified by an image segmentation tool is a powerful predictor of long-term cognitive decline and functional disability. A combined measure of white matter hyperintensities, lacunar, gray matter, and hippocampal volumes could be used as an imaging marker associated with vascular cognitive impairment.