This study proposes Scout-Dose-TCM for direct, prospective estimation of organ-level doses under tube current modulation (TCM) and compares its performance to two established methods. We analyzed contrast-enhanced chest-abdomen-pelvis CT scans from 130 adults (120 kVp, TCM). Reference doses for six organs (lungs, kidneys, liver, pancreas, bladder, spleen) were calculated using MC-GPU and TotalSegmentator. Based on these, we trained Scout-Dose-TCM, a deep learning model that predicts organ doses corresponding to discrete cosine transform (DCT) basis functions, enabling real-time estimates for any TCM profile. The model combines a feature learning module that extracts contextual information from lateral and frontal scouts and scan range with a dose learning module that output DCT-based dose estimates. A customized loss function incorporated the DCT formulation during training. For comparison, we implemented size-specific dose estimation per AAPM TG 204 (Global CTDIvol) and its organ-level TCM-adapted version (Organ CTDIvol). A 5-fold cross-validation assessed generalizability by comparing mean absolute percentage dose errors and r-squared correlations with benchmark doses. Average absolute percentage errors were 13% (Global CTDIvol), 9% (Organ CTDIvol), and 7% (Scout-Dose-TCM), with bladder showing the largest discrepancies (15%, 13%, and 9%). Statistical tests confirmed Scout-Dose-TCM significantly reduced errors vs. Global CTDIvol across most organs and improved over Organ CTDIvol for the liver, bladder, and pancreas. It also achieved higher r-squared values, indicating stronger agreement with Monte Carlo benchmarks. Scout-Dose-TCM outperformed Global CTDIvol and was comparable to or better than Organ CTDIvol, without requiring organ segmentations at inference, demonstrating its promise as a tool for prospective organ-level dose estimation in CT.

Fast and accurate organ-at-risk (OAR) and gross tumor volume (GTV) contour propagation methods are needed to improve the efficiency of magnetic resonance (MR) imaging-guided radiotherapy. We trained deformable image registration networks to accurately propagate contours from planning to fraction MR images.
Approach: Data from 140 stage 1-2 lung cancer patients treated at a 0.35T MR-Linac were split into 102/17/21 for training/validation/testing. Additionally, 18 central lung tumor patients, treated at a 0.35T MR-Linac externally, and 14 stage 3 lung cancer patients from a phase 1 clinical trial, treated at 0.35T or 1.5T MR-Linacs at three institutions, were used for external testing. Planning and fraction images were paired (490 pairs) for training. Two hybrid transformer-convolutional neural network TransMorph models with mean squared error (MSE), Dice similarity coefficient (DSC), and regularization losses (TM_{MSE+Dice}) or MSE and regularization losses (TM_{MSE}) were trained to deformably register planning to fraction images. The TransMorph models predicted diffeomorphic dense displacement fields. Multi-label images including seven thoracic OARs and the GTV were propagated to generate fraction segmentations. Model predictions were compared with contours obtained through B-spline, vendor registration and the auto-segmentation method nnUNet. Evaluation metrics included the DSC and Hausdorff distance percentiles (50th and 95th) against clinical contours.
Main results: TM_{MSE+Dice} and TM_{MSE} achieved mean OARs/GTV DSCs of 0.90/0.82 and 0.90/0.79 for the internal and 0.84/0.77 and 0.85/0.76 for the central lung tumor external test data. On stage 3 data, TM_{MSE+Dice} achieved mean OARs/GTV DSCs of 0.87/0.79 and 0.83/0.78 for the 0.35 T MR-Linac datasets, and 0.87/0.75 for the 1.5 T MR-Linac dataset. TM_{MSE+Dice} and TM_{MSE} had significantly higher geometric accuracy than other methods on external data. No significant difference between TM_{MSE+Dice} and TM_{MSE} was found.
Significance: TransMorph models achieved time-efficient segmentation of fraction MRIs with high geometrical accuracy and accurately segmented images obtained at different field strengths.

The peripheral immune system is essential for maintaining central nervous system homeostasis. This study investigates the effects of peripheral immune markers on accelerated brain aging and dementia using brain-predicted age difference based on neuroimaging. By leveraging data from the UK Biobank, Cox regression was used to explore the relationship between peripheral immune markers and dementia, and multivariate linear regression to assess associations between peripheral immune biomarkers and brain structure. Additionally, we established a brain age prediction model using Simple Fully Convolutional Network (SFCN) deep learning architecture. Analysis of the resulting brain-Predicted Age Difference (PAD) revealed relationships between accelerated brain aging, peripheral immune markers, and dementia. During the median follow-up period of 14.3 years, 4, 277 dementia cases were observed among 322, 761 participants. Both innate and adaptive immune markers correlated with dementia risk. NLR showed the strongest association with dementia risk (HR = 1.14; 95% CI: 1.11-1.18, P<0.001). Multivariate linear regression revealed significant associations between peripheral immune markers and brain regional structural indices. Utilizing the deep learning-based SFCN model, the estimated brain age of dementia subjects (MAE = 5.63, r2 = - 0.46, R = 0.22) was determined. PAD showed significant correlation with dementia risk and certain peripheral immune markers, particularly in individuals with positive brain age increment. This study employs brain age as a quantitative marker of accelerated brain aging to investigate its potential associations with peripheral immunity and dementia, highlighting the importance of early intervention targeting peripheral immune markers to delay brain aging and prevent dementia.

Accurate gestational age (GA) estimation, ideally through fetal ultrasound measurement, is a crucial aspect of providing excellent antenatal care. However, deriving GA from manual fetal biometric measurements depends on the operator and is time-consuming. Hence, automatic computer-assisted methods are demanded in clinical practice. In this paper, we present a novel feature fusion framework to estimate GA using fetal ultrasound images without any measurement information. We adopt a deep learning model to extract deep representations from ultrasound images. We extract radiomic features to reveal patterns and characteristics of fetal brain growth. To harness the interpretability of radiomics in medical imaging analysis, we estimate GA by fusing radiomic features and deep representations. Our framework estimates GA with a mean absolute error of 8.0 days across three trimesters, outperforming current machine learning-based methods at these gestational ages. Experimental results demonstrate the robustness of our framework across different populations in diverse geographical regions. Our code is publicly available on \href{https://github.com/13204942/RadiomicsImageFusion_FetalUS}.

Recent developments in neural networks have improved deformable image registration (DIR) by amortizing iterative optimization, enabling fast and accurate DIR results. However, learning-based methods often face challenges with limited training data, large deformations, and tend to underperform compared to iterative approaches when label supervision is unavailable. While iterative methods can achieve higher accuracy in such scenarios, they are considerably slower than learning-based methods. To address these limitations, we propose VoxelOpt, a discrete optimization-based DIR framework that combines the strengths of learning-based and iterative methods to achieve a better balance between registration accuracy and runtime. VoxelOpt uses displacement entropy from local cost volumes to measure displacement signal strength at each voxel, which differs from earlier approaches in three key aspects. First, it introduces voxel-wise adaptive message passing, where voxels with lower entropy receives less influence from their neighbors. Second, it employs a multi-level image pyramid with 27-neighbor cost volumes at each level, avoiding exponential complexity growth. Third, it replaces hand-crafted features or contrastive learning with a pretrained foundational segmentation model for feature extraction. In abdominal CT registration, these changes allow VoxelOpt to outperform leading iterative in both efficiency and accuracy, while matching state-of-the-art learning-based methods trained with label supervision. The source code will be available at https://github.com/tinymilky/VoxelOpt

Regular mammography screening is essential for early breast cancer detection. Deep learning-based risk prediction methods have sparked interest to adjust screening intervals for high-risk groups. While early methods focused only on current mammograms, recent approaches leverage the temporal aspect of screenings to track breast tissue changes over time, requiring spatial alignment across different time points. Two main strategies for this have emerged: explicit feature alignment through deformable registration and implicit learned alignment using techniques like transformers, with the former providing more control. However, the optimal approach for explicit alignment in mammography remains underexplored. In this study, we provide insights into where explicit alignment should occur (input space vs. representation space) and if alignment and risk prediction should be jointly optimized. We demonstrate that jointly learning explicit alignment in representation space while optimizing risk estimation performance, as done in the current state-of-the-art approach, results in a trade-off between alignment quality and predictive performance and show that image-level alignment is superior to representation-level alignment, leading to better deformation field quality and enhanced risk prediction accuracy. The code is available at https://github.com/sot176/Longitudinal_Mammogram_Alignment.git.

Measuring enamel depth distribution (EDD) is of great importance for preoperative design of tooth preparations, restorative aesthetic preview and monitoring enamel wear. But, currently there are no non-invasive methods available to efficiently obtain EDD. This study aimed to develop a machine learning (ML) framework to achieve noninvasive and radiation-free EDD predictions with intraoral scanning (IOS) images. Cone-beam computed tomography (CBCT) and IOS images of right maxillary central incisors, canines, and first premolars from 200 volunteers were included and preprocessed with surface parameterization. During the training stage, the EDD ground truths were obtained from CBCT. Five-dimensional features (incisal-gingival position, mesial-distal position, local surface curvature, incisal-gingival stretch, mesial-distal stretch) were extracted on labial enamel surfaces and served as inputs to the ML models. An eXtreme gradient boosting (XGB) model was trained to establish the mapping of features to the enamel depth values. R² and mean absolute error (MAE) were utilized to evaluate the training accuracy of XGB model. In prediction stage, the predicted EDDs were compared with the ground truths, and the EDD discrepancies were analyzed using a paired t-test and Frobenius norm. The XGB model achieved superior performance in training with average R² and MAE values of 0.926 and 0.080, respectively. Independent validation confirmed its robust EDD prediction ability, showing no significant deviation from ground truths in paired t-test and low prediction errors (Frobenius norm: 12.566-18.312), despite minor noise in IOS-based predictions. This study performed preliminary validation of an IOS-based ML model for high-quality EDD prediction.

Image registration is used in many medical image analysis applications, such as tracking the motion of tissue in cardiac images, where cardiac kinematics can be an indicator of tissue health. Registration is a challenging problem for deep learning algorithms because ground truth transformations are not feasible to create, and because there are potentially multiple transformations that can produce images that appear correlated with the goal. Unsupervised methods have been proposed to learn to predict effective transformations, but these methods take significantly longer to predict than established baseline methods. For a deep learning method to see adoption in wider research and clinical settings, it should be designed to run in a reasonable time on common, mid-level hardware. Fast methods have been proposed for the task of image registration but often use patch-based methods which can affect registration accuracy for a highly dynamic organ such as the heart. In this thesis, a fast, volumetric registration model is proposed for the use of quantifying cardiac strain. The proposed Deep Learning Neural Network (DLNN) is designed to utilize an architecture that can compute convolutions incredibly efficiently, allowing the model to achieve registration fidelity similar to other state-of-the-art models while taking a fraction of the time to perform inference. The proposed fast and lightweight registration (FLIR) model is used to predict tissue motion which is then used to quantify the non-uniform strain experienced by the tissue. For acquisitions taken from the same patient at approximately the same time, it would be expected that strain values measured between the acquisitions would have very small differences. Using this metric, strain values computed using the FLIR method are shown to be very consistent.

Purpose: To develop an age prediction model which is interpretable and robust to demographic and technological variances in brain MRI scans. Materials and Methods: We propose a transformer-based architecture that leverages self-supervised pre-training on large-scale datasets. Our model processes pseudo-3D T1-weighted MRI scans from three anatomical views and incorporates brain volumetric information. By introducing a stem architecture, we reduce the conventional quadratic complexity of transformer models to linear complexity, enabling scalability for high-dimensional MRI data. We trained our model on ADNI2 $\&$ 3 (N=1348) and OASIS3 (N=716) datasets (age range: 42 - 95) from the North America, with an 8:1:1 split for train, validation and test. Then, we validated it on the AIBL dataset (N=768, age range: 60 - 92) from Australia. Results: We achieved an MAE of 3.65 years on ADNI2 $\&$ 3 and OASIS3 test set and a high generalizability of MAE of 3.54 years on AIBL. There was a notable increase in brain age gap (BAG) across cognitive groups, with mean of 0.15 years (95% CI: [-0.22, 0.51]) in CN, 2.55 years ([2.40, 2.70]) in MCI, 6.12 years ([5.82, 6.43]) in AD. Additionally, significant negative correlation between BAG and cognitive scores was observed, with correlation coefficient of -0.185 (p < 0.001) for MoCA and -0.231 (p < 0.001) for MMSE. Gradient-based feature attribution highlighted ventricles and white matter structures as key regions influenced by brain aging. Conclusion: Our model effectively fused information from different views and volumetric information to achieve state-of-the-art brain age prediction accuracy, improved generalizability and interpretability with association to neurodegenerative disorders.

In brain gliomas, non-invasive biomarkers reflecting tumor cellularity would be useful to guide supramarginal resections and to plan stereotactic biopsies. We aim to validate a previously-trained machine learning algorithm that generates cellularity prediction maps (CPM) from multiparametric MRI data to an independent, retrospective external cohort of gliomas undergoing image-guided biopsies, and to compare the performance of CPM and diffusion MRI apparent diffusion coefficient (ADC) in predicting cellularity. A cohort of patients with treatment-naïve or recurrent gliomas were prospectively studied. All patients underwent pre-surgical MRI according to the standardized brain tumor imaging protocol. The surgical sampling site was planned based on image-guided biopsy targets and tissue was stained with hematoxylin-eosin for cell density count. The correlation between MRI-derived CPM values and histological cellularity, and between ADC and histological cellularity, was evaluated both assuming independent observations and accounting for non-independent observations. Sixty-six samples from twenty-seven patients were collected. Thirteen patients had treatment-naïve tumors and fourteen had recurrent lesions. CPM value accurately predicted histological cellularity in treatment-naïve patients (b = 1.4, R² = 0.2, p = 0.009, rho = 0.41, p = 0.016, RMSE = 1503 cell/mm²), but not in the recurrent sub-cohort. Similarly, ADC values showed a significant association with histological cellularity only in treatment-naive patients (b = 1.3, R² = 0.22, p = 0.007; rho = -0.37, p = 0.03), not statistically different from the CPM correlation. These findings were confirmed with statistical tests accounting for non-independent observations. MRI-derived machine learning generated cellularity prediction maps (CPM) enabled a non-invasive evaluation of tumor cellularity in treatment-naïve glioma patients, although CPM did not clearly outperform ADC alone in this cohort.