To extract biologically interpretable information, a common approach is to fit a microstructural tissue model to a set of signals acquired with different dMRI acquisition settings (Alexander et al., 2019; Lampinen et al., 2023; Jelescu et al., 2020). In the absence of diffusion time dependence, these typically include different combinations of gradient strengths (commonly quantified by the b-value), directions (b-vector), and B-tensor shape (Westin et al., 2014). Microstructural parameters estimated by these models - including compartmental signal fractions and diffusivities - have shown to be sensitive to changes in brain structure due to diseases like multiple sclerosis (Alotaibi et al., 2021), Alzheimer's disease (Parker et al., 2018) and Parkinson's disease (Kim et al., 2016), and can provide a more fundamental understanding of tissue microstructure in both healthy and pathological tissues (Zhang et al., 2012). The Standard Model of white matter (SM) (Novikov et al., 2019) describes the signal arising from white matter by a kernel consisting of three compartments (intra-axonal, extra-axonal, and free water (occasionally omitted)) convolved with a fiber orientation distribution (FOD) (Tournier et al., 2007b). Compartmental signal fractions and diffusivities can be estimated, alongside the parameters that describe the FOD (usually in the form of a spherical harmonics (SH) series). Nevertheless, the high-dimensional parameter space of the SM complicates the estimation of its parameters, potentially leading to low accuracy, precision, and degeneracy of estimates (Jelescu et al., 2016).

--Early and accurate assessment of brain microstruc-ture using diffusion Magnetic Resonance Imaging (dMRI) is crucial for identifying neurodevelopmental disorders in neonates, but remains challenging due to low signal-to-noise ratio (SNR), motion artifacts, and ongoing myelination. In this study, we propose a rotationally equivariant Spherical Convolutional Neural Network (sCNN) framework tailored for neonatal dMRI. We predict the Fiber Orientation Distribution (FOD) from multi-shell dMRI signals acquired with a reduced set of gradient directions (30% of the full protocol), enabling faster and more cost-effective acquisitions. We train and evaluate the performance of our sCNN using real data from 43 neonatal dMRI datasets provided by the Developing Human Connectome Project (dHCP). Our results demonstrate that the sCNN achieves significantly lower mean squared error (MSE) and higher angular correlation coefficient (ACC) compared to a Multi-Layer Perceptron (MLP) baseline, indicating improved accuracy in FOD estimation. Furthermore, tractography results based on the sCNN-predicted FODs show improved anatomical plausibility, coverage, and coherence compared to those from the MLP . These findings highlight that sCNNs, with their inherent rotational equivariance, offer a promising approach for accurate and clinically efficient dMRI analysis, paving the way for improved diagnostic capabilities and characterization of early brain development. Medical diagnostics is undergoing a transformative shift, fueled by the rapid advancements in artificial intelligence (AI) and deep learning.

White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.

This research introduces an innovative method for the early screening of cardiorespiratory diseases based on an acquisition protocol, which leverages commodity smartphone's Inertial Measurement Units (IMUs) and deep learning techniques. We collected, in a clinical setting, a dataset featuring recordings of breathing kinematics obtained by accelerometer and gyroscope readings from five distinct body regions. We propose an end-to-end deep learning pipeline for early cardiorespiratory disease screening, incorporating a preprocessing step segmenting the data into individual breathing cycles, and a recurrent bidirectional module capturing features from diverse body regions. We employed Leave-one-out-cross-validation with Bayesian optimization for hyperparameter tuning and model selection. The experimental results consistently demonstrated the superior performance of a bidirectional Long-Short Term Memory (Bi-LSTM) as a feature encoder architecture, yielding an average sensitivity of $0.81 \pm 0.02$, specificity of $0.82 \pm 0.05$, F1 score of $0.81 \pm 0.02$, and accuracy of $80.2\% \pm 3.9$ across diverse seed variations. We also assessed generalization capabilities on a skewed distribution, comprising exclusively healthy patients not used in training, revealing a true negative rate of $74.8 \% \pm 4.5$. The sustained accuracy of predictions over time during breathing cycles within a single patient underscores the efficacy of the preprocessing strategy, highlighting the model's ability to discern significant patterns throughout distinct phases of the respiratory cycle. This investigation underscores the potential usefulness of widely available smartphones as devices for timely cardiorespiratory disease screening in the general population, in at-home settings, offering crucial assistance to public health efforts (especially during a pandemic outbreaks, such as the recent COVID-19).

Estimating $T_2$ relaxation time distributions from multi-echo $T_2$-weighted MRI ($T_2W$) data can provide valuable biomarkers for assessing inflammation, demyelination, edema, and cartilage composition in various pathologies, including neurodegenerative disorders, osteoarthritis, and tumors. Deep neural network (DNN) based methods have been proposed to address the complex inverse problem of estimating $T_2$ distributions from MRI data, but they are not yet robust enough for clinical data with low Signal-to-Noise ratio (SNR) and are highly sensitive to distribution shifts such as variations in echo-times (TE) used during acquisition. Consequently, their application is hindered in clinical practice and large-scale multi-institutional trials with heterogeneous acquisition protocols. We propose a physically-primed DNN approach, called $P_2T_2$, that incorporates the signal decay forward model in addition to the MRI signal into the DNN architecture to improve the accuracy and robustness of $T_2$ distribution estimation. We evaluated our $P_2T_2$ model in comparison to both DNN-based methods and classical methods for $T_2$ distribution estimation using 1D and 2D numerical simulations along with clinical data. Our model improved the baseline model's accuracy for low SNR levels ($SNR<80$) which are common in the clinical setting. Further, our model achieved a $\sim$35\% improvement in robustness against distribution shifts in the acquisition process compared to previously proposed DNN models. Finally, Our $P_2T_2$ model produces the most detailed Myelin-Water fraction maps compared to baseline approaches when applied to real human MRI data. Our $P_2T_2$ model offers a reliable and precise means of estimating $T_2$ distributions from MRI data and shows promise for use in large-scale multi-institutional trials with heterogeneous acquisition protocols.

Breast density estimation is one of the key tasks in recognizing individuals predisposed to breast cancer. It is often challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Most of the time, the breast density is estimated manually where a radiologist assigns one of the four density categories decided by the Breast Imaging and Reporting Data Systems (BI-RADS). There have been efforts in the direction of automating a breast density classification pipeline. Breast density estimation is one of the key tasks performed during a screening exam. Dense breasts are more susceptible to breast cancer. The density estimation is challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Traditional mammograms are being replaced by tomosynthesis and its other low radiation dose variants (for example Hologic' Intelligent 2D and C-View). Because of the low-dose requirement, increasingly more screening centers are favoring the Intelligent 2D view and C-View. Deep-learning studies for breast density estimation use only a single modality for training a neural network. However, doing so restricts the number of images in the dataset. In this paper, we show that a neural network trained on all the modalities at once performs better than a neural network trained on any single modality. We discuss these results using the area under the receiver operator characteristics curves.

Biophysical modelling of the diffusion MRI signal provides estimates of specific microstructural tissue properties. Model parameters estimates can be obtained by fitting the model to the measured signal. Although nonlinear optimization such as non-linear least squares (NLLS) is the most widespread method for model estimation, it suffers from local minima, high computational cost and uncertain accuracy. Deep Learning approaches are steadily replacing NL fitting, but come with the limitation that the model needs to be retrained for each acquisition protocol and noise level. The White Matter Tract Integrity (WMTI)- Watson model was proposed as an implementation of the Standard Model of diffusion in white matter that estimates model parameters from the diffusion and kurtosis tensors (DKI), thereby overcoming fitting the model signal equation. Here we proposed a deep learning approach based on the encoder-decoder recurrent neural network (RNN) to increase the robustness and accelerate the parameter estimation of WMTI-Watson. We use an embedding approach to render the model insensitive to potential differences in distributions between training data and experimental data. This RNN-based solver thus has the advantage of being highly efficient in computation and more readily translatable to other datasets, irrespective of acquisition protocol and underlying parameter distributions as long as diffusion and kurtosis tensors (or their typical derived scalars) were pre-computed from the data. In this study, we evaluated the performance of NLLS, the RNN-based method and a baseline DL architecture based on multilayer perceptron (MLP) on synthetic and in vivo datasets of rat and human brain. We showed that the proposed RNN-based fitting approach had the advantage of highly reduced computation time over NLLS (from hours to seconds), with similar accuracy and precision but improved robustness, and superior translatability to new datasets over MLP, irrespective of acquisition protocol or species being rat or human. Keywords Diffusion MRI, white matter, WMTI-Watson, model fitting, deep learning 1. Introduction Diffusion magnetic resonance imaging (dMRI) which encodes information about brain white matter (WM) microstructure in diffusion-weighted signal has emerged in recent years as a highly promising technique to provide specific information about microstructure features.

Removing the bias and variance of multicentre data has always been a challenge in large scale digital healthcare studies, which requires the ability to integrate clinical features extracted from data acquired by different scanners and protocols to improve stability and robustness. Previous studies have described various computational approaches to fuse single modality multicentre datasets. However, these surveys rarely focused on evaluation metrics and lacked a checklist for computational data harmonisation studies. In this systematic review, we summarise the computational data harmonisation approaches for multi-modality data in the digital healthcare field, including harmonisation strategies and evaluation metrics based on different theories. In addition, a comprehensive checklist that summarises common practices for data harmonisation studies is proposed to guide researchers to report their research findings more effectively. Last but not least, flowcharts presenting possible ways for methodology and metric selection are proposed and the limitations of different methods have been surveyed for future research.

Standardized body region labelling of individual images provides data that can improve human and computer use of medical images. A CNN-based classifier was developed to identify body regions in CT and MRI. 17 CT (18 MRI) body regions covering the entire human body were defined for the classification task. Three retrospective databases were built for the AI model training, validation, and testing, with a balanced distribution of studies per body region. The test databases originated from a different healthcare network. Accuracy, recall and precision of the classifier was evaluated for patient age, patient gender, institution, scanner manufacturer, contrast, slice thickness, MRI sequence, and CT kernel. The data included a retrospective cohort of 2,934 anonymized CT cases (training: 1,804 studies, validation: 602 studies, test: 528 studies) and 3,185 anonymized MRI cases (training: 1,911 studies, validation: 636 studies, test: 638 studies). 27 institutions from primary care hospitals, community hospitals and imaging centers contributed to the test datasets. The data included cases of all genders in equal proportions and subjects aged from a few months old to +90 years old. An image-level prediction accuracy of 91.9% (90.2 - 92.1) for CT, and 94.2% (92.0 - 95.6) for MRI was achieved. The classification results were robust across all body regions and confounding factors. Due to limited data, performance results for subjects under 10 years-old could not be reliably evaluated. We show that deep learning models can classify CT and MRI images by body region including lower and upper extremities with high accuracy.

We present a method for estimating intravoxel parameters from a DW-MRI based on deep learning techniques. We show that neural networks (DNNs) have the potential to extract information from diffusion-weighted signals to reconstruct cerebral tracts. We present two DNN models: one that estimates the axonal structure in the form of a voxel and the other to calculate the structure of the central voxel using the voxel neighborhood. Our methods are based on a proposed parameter representation suitable for the problem. Since it is practically impossible to have real tagged data for any acquisition protocol, we used a self-supervised strategy. Experiments with synthetic data and real data show that our approach is competitive, and the computational times show that our approach is faster than the SOTA methods, even if training times are considered. This computational advantage increases if we consider the prediction of multiple images with the same acquisition protocol.