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Background: Multiparametric breast MRI data might improve tumor diagnostics, characterization, and treatment planning. Accurate alignment and delineation of images acquired at different field strengths such as 3T and 7T, remain challenging research tasks. Purpose: To address alignment challenges and enable consistent tumor segmentation across different MRI field strengths. Study type: Retrospective. Subjects: Nine female subjects with breast tumors were involved: six histologically proven invasive ductal carcinomas (IDC) and three fibroadenomas. Field strength/sequence: Imaging was performed at 3T and 7T scanners using post-contrast T1-weighted three-dimensional time-resolved angiography with stochastic trajectories (TWIST) sequence. Assessments: The method's performance for joint image registration and tumor segmentation was evaluated using several quantitative metrics, including signal-to-noise ratio (PSNR), structural similarity index (SSIM), normalized cross-correlation (NCC), Dice coefficient, F1 score, and relative sum of squared differences (rel SSD). Statistical tests: The Pearson correlation coefficient was used to test the relationship between the registration and segmentation metrics. Results: When calculated for each subject individually, the PSNR was in a range from 27.5 to 34.5 dB, and the SSIM was from 82.6 to 92.8%. The model achieved an NCC from 96.4 to 99.3% and a Dice coefficient of 62.9 to 95.3%. The F1 score was between 55.4 and 93.2% and the rel SSD was in the range of 2.0 and 7.5%. The segmentation metrics Dice and F1 Score are highly correlated (0.995), while a moderate correlation between NCC and SSIM (0.681) was found for registration. Data conclusion: Initial results demonstrate that the proposed method may be feasible in providing joint tumor segmentation and registration of MRI data acquired at different field strengths.

This study presents an open-source toolkit to address critical challenges in preprocessing data for self-supervised learning (SSL) for 3D medical imaging, focusing on data privacy and computational efficiency. The toolkit comprises two main components: a segmentation network that delineates foreground regions to optimize data sampling and thus reduce training time, and a segmentation network that identifies anonymized regions, preventing erroneous supervision in reconstruction-based SSL methods. Experimental results demonstrate high robustness, with mean Dice scores exceeding 98.5 across all anonymization methods and surpassing 99.5 for foreground segmentation tasks, highlighting the efficacy of the toolkit in supporting SSL applications in 3D medical imaging for both CT and MRI images. The weights and code is available at https://github.com/MIC-DKFZ/Foreground-and-Anonymization-Area-Segmentation., Comment: 6 pages

Acoustic articulatory inversion is a major processing challenge, with a wide range of applications from speech synthesis to feedback systems for language learning and rehabilitation. In recent years, deep learning methods have been applied to the inversion of less than a dozen geometrical positions corresponding to sensors glued to easily accessible articulators. It is therefore impossible to know the shape of the whole tongue from root to tip. In this work, we use high-quality real-time MRI data to track the contour of the tongue. The data used to drive the inversion are therefore the unstructured speech signal and the tongue contours. Several architectures relying on a Bi-MSTM including or not an autoencoder to reduce the dimensionality of the latent space, using or not the phonetic segmentation have been explored. The results show that the tongue contour can be recovered with a median accuracy of 2.21 mm (or 1.37 pixel) taking a context of 1 MFCC frame (static, delta and double-delta cepstral features).

Deep learning models in medical contexts face challenges like data scarcity, inhomogeneity, and privacy concerns. This study focuses on improving ventricular segmentation in brain MRI images using synthetic data. We employed two latent diffusion models (LDMs): a mask generator trained using 10,000 masks, and a corresponding SPADE image generator optimized using 6,881 scans to create an MRI conditioned on a 3D brain mask. Conditioning the mask generator on ventricular volume in combination with classifier-free guidance enabled the control of the ventricular volume distribution of the generated synthetic images. Next, the performance of the synthetic data was tested using three nnU-Net segmentation models trained on a real, augmented and entirely synthetic data, respectively. The resulting models were tested on a completely independent hold-out dataset of patients with enlarged ventricles, with manual delineation of the ventricles used as ground truth. The model trained on real data showed a mean absolute error (MAE) of 9.09 \pm 12.18 mL in predicted ventricular volume, while the models trained on synthetic and augmented data showed MAEs of 7.52 \pm 4.81 mL and 6.23 \pm 4.33 mL, respectively. Both the synthetic and augmented model also outperformed the state-of-the-art model SynthSeg, which due to limited performance in cases of large ventricular volumes, showed an MAE of 7.73 \pm 12.12 mL with a factor of 3 higher standard deviation. The model trained on augmented data showed the highest Dice score of 0.892 \pm 0.05, slightly outperforming SynthSeg and on par with the model trained on real data. The synthetic model performed similar to SynthSeg. In summary, we provide evidence that guided synthesis of labeled brain MRI data using LDMs improves the segmentation of enlarged ventricles and outperforms existing state-of-the-art segmentation models.

Lumbar disk segmentation is essential for diagnosing and curing spinal disorders by enabling precise detection of disk boundaries in medical imaging. The advent of deep learning has resulted in the development of many segmentation methods, offering differing levels of accuracy and effectiveness. This study assesses the effectiveness of several sophisticated deep learning architectures, including ResUnext, Ef3 Net, UNet, and TransUNet, for lumbar disk segmentation, highlighting key metrics like as Pixel Accuracy, Mean Intersection over Union (Mean IoU), and Dice Coefficient. The findings indicate that ResUnext achieved the highest segmentation accuracy, with a Pixel Accuracy of 0.9492 and a Dice Coefficient of 0.8425, with TransUNet following closely after. Filtering techniques somewhat enhanced the performance of most models, particularly Dense UNet, improving stability and segmentation quality. The findings underscore the efficacy of these models in lumbar disk segmentation and highlight potential areas for improvement., Comment: 8 pages, 2 figures

Major depressive disorder (MDD) is one of the most common mental disorders, with significant impacts on many daily activities and quality of life. It stands as one of the most common mental disorders globally and ranks as the second leading cause of disability. The current diagnostic approach for MDD primarily relies on clinical observations and patient-reported symptoms, overlooking the diverse underlying causes and pathophysiological factors contributing to depression. Therefore, scientific researchers and clinicians must gain a deeper understanding of the pathophysiological mechanisms involved in MDD. There is growing evidence in neuroscience that depression is a brain network disorder, and the use of neuroimaging, such as magnetic resonance imaging (MRI), plays a significant role in identifying and treating MDD. Rest-state functional MRI (rs-fMRI) is among the most popular neuroimaging techniques used to study MDD. Deep learning techniques have been widely applied to neuroimaging data to help with early mental health disorder detection. Recent years have seen a rise in interest in graph neural networks (GNNs), which are deep neural architectures specifically designed to handle graph-structured data like rs-fMRI. This research aimed to develop an ensemble-based GNN model capable of detecting discriminative features from rs-fMRI images for the purpose of diagnosing MDD. Specifically, we constructed an ensemble model by combining features from multiple brain region segmentation atlases to capture brain complexity and detect distinct features more accurately than single atlas-based models. Further, the effectiveness of our model is demonstrated by assessing its performance on a large multi-site MDD dataset. The best performing model among all folds achieved an accuracy of 75.80%, a sensitivity of 88.89%, a specificity of 61.84%, a precision of 71.29%, and an F1-score of 79.12%., Comment: 17 pages, 2 figures, 10 tables

Deep learning (DL) models in medical imaging face challenges in generalizability and robustness due to variations in image acquisition parameters (IAP). In this work, we introduce a novel method using conditional denoising diffusion generative models (cDDGMs) to generate counterfactual magnetic resonance (MR) images that simulate different IAP without altering patient anatomy. We demonstrate that using these counterfactual images for data augmentation can improve segmentation accuracy, particularly in out-of-distribution settings, enhancing the overall generalizability and robustness of DL models across diverse imaging conditions. Our approach shows promise in addressing domain and covariate shifts in medical imaging. The code is publicly available at https: //github.com/pedromorao/Counterfactual-MRI-Data-Augmentation

Deep learning has made significant strides in medical imaging, leveraging the use of large datasets to improve diagnostics and prognostics. However, large datasets often come with inherent errors through subject selection and acquisition. In this paper, we investigate the use of Diffusion Autoencoder (DAE) embeddings for uncovering and understanding data characteristics and biases, including biases for protected variables like sex and data abnormalities indicative of unwanted protocol variations. We use sagittal T2-weighted magnetic resonance (MR) images of the neck, chest, and lumbar region from 11186 German National Cohort (NAKO) participants. We compare DAE embeddings with existing generative models like StyleGAN and Variational Autoencoder. Evaluations on a large-scale dataset consisting of sagittal T2-weighted MR images of three spine regions show that DAE embeddings effectively separate protected variables such as sex and age. Furthermore, we used t-SNE visualization to identify unwanted variations in imaging protocols, revealing differences in head positioning. Our embedding can identify samples where a sex predictor will have issues learning the correct sex. Our findings highlight the potential of using advanced embedding techniques like DAEs to detect data quality issues and biases in medical imaging datasets. Identifying such hidden relations can enhance the reliability and fairness of deep learning models in healthcare applications, ultimately improving patient care and outcomes., Comment: This paper was accepted in the "Workshop on Interpretability of Machine Intelligence in Medical Image Computing" (iMIMIC) at MICCAI 2024

Objective: Brain metastases (BMs) are common in cancer patients and determining the primary tumor site is crucial for effective treatment. This study aims to predict the primary tumor site from BM MRI data using radiomic features and advanced machine learning algorithms. Methods: We utilized a comprehensive dataset from Ocana-Tienda et al. (2023) comprising MRI and clinical data from 75 patients with BMs. Radiomic features were extracted from post-contrast T1-weighted MRI sequences. Feature selection was performed using the GINI index, and data normalization was applied to ensure consistent scaling. We developed and evaluated Random Forest and XGBoost classifiers, both with and without hyperparameter optimization using the FOX (Fox optimizer) algorithm. Model interpretability was enhanced using SHAP (SHapley Additive exPlanations) values. Results: The baseline Random Forest model achieved an accuracy of 0.85, which improved to 0.93 with FOX optimization. The XGBoost model showed an initial accuracy of 0.96, increasing to 0.99 after optimization. SHAP analysis revealed the most influential radiomic features contributing to the models' predictions. The FOX-optimized XGBoost model exhibited the best performance with a precision, recall, and F1-score of 0.99. Conclusion: This study demonstrates the effectiveness of using radiomic features and machine learning to predict primary tumor sites from BM MRI data. The FOX optimization algorithm significantly enhanced model performance, and SHAP provided valuable insights into feature importance. These findings highlight the potential of integrating radiomics and machine learning into clinical practice for improved diagnostic accuracy and personalized treatment planning.

Constrained Spherical Deconvolution (CSD) is crucial for estimating white matter fiber orientations using diffusion MRI data. A relevant parameter in CSD is the maximum order $l_{max}$ used in the spherical harmonics series, influencing the angular resolution of the Fiber Orientation Distributions (FODs). Lower $l_{max}$ values produce smoother and more stable estimates, but result in reduced angular resolution. Conversely, higher $l_{max}$ values, as employed in the Super-Resolved CSD variant, are essential for resolving narrow inter-fiber angles but lead to spurious lobes due to increased noise sensitivity. To address this issue, we propose a novel Spatially Regularized Super-Resolved CSD (SR$^2$-CSD) approach, incorporating spatial priors into the CSD framework. This method leverages spatial information among adjacent voxels, enhancing the stability and noise robustness of FOD estimations. SR$^2$-CSD facilitates the practical use of Super-Resolved CSD by including a J-invariant auto-calibrated total variation FOD denoiser. We evaluated the performance of SR$^2$-CSD against standard CSD and Super-Resolved CSD using phantom numerical data and various real brain datasets, including a test-retest sample of six subjects scanned twice. In phantom data, SR$^2$-CSD outperformed both CSD and Super-Resolved CSD, reducing the angular error (AE) by approximately half and the peak number error (PNE) by a factor of three across all noise levels considered. In real data, SR$^2$-CSD produced more continuous FOD estimates with higher spatial-angular coherency. In the test-retest sample, SR$^2$-CSD consistently yielded more reproducible estimates, with reduced AE, PNE, mean squared error, and increased angular correlation coefficient between the FODs estimated from the two scans for each subject., Comment: 16 pages, 5 figures

This study investigates the impact of self-supervised pretraining of 3D semantic segmentation models on a large-scale, domain-specific dataset. We introduce BRAINS-45K, a dataset of 44,756 brain MRI volumes from public sources, the largest public dataset available, and revisit a number of design choices for pretraining modern segmentation architectures by simplifying and optimizing state-of-the-art methods, and combining them with a novel augmentation strategy. The resulting AMAES framework is based on masked-image-modeling and intensity-based augmentation reversal and balances memory usage, runtime, and finetuning performance. Using the popular U-Net and the recent MedNeXt architecture as backbones, we evaluate the effect of pretraining on three challenging downstream tasks, covering single-sequence, low-resource settings, and out-of-domain generalization. The results highlight that pretraining on the proposed dataset with AMAES significantly improves segmentation performance in the majority of evaluated cases, and that it is beneficial to pretrain the model with augmentations, despite pretraing on a large-scale dataset. Code and model checkpoints for reproducing results, as well as the BRAINS-45K dataset are available at \url{https://github.com/asbjrnmunk/amaes}., Comment: Accepted at ADSMI @ MICCAI 2024

The amount of Magnetic resonance imaging data has grown tremendously recently, creating an urgent need to accelerate data processing, which requires substantial computational resources and time. In this preliminary study, we applied FMRIB Software Library commands on T1-weighted and diffusion-weighted images of a single young adult using the Fugaku supercomputer. The tensor-based measurements and subcortical structure segmentations performed on Fugaku supercomputer were highly consistent with those from conventional systems, demonstrating its reliability and significantly reduced processing time.

Purpose: This study aims to propose and investigate the feasibility of using Kolmogorov-Arnold Network (KAN) for CEST MRI data analysis (CEST-KAN). Methods: CEST MRI data were acquired from twelve healthy volunteers at 3T. Data from ten subjects were used for training, while the remaining two were reserved for testing. The performance of multi-layer perceptron (MLP) and KAN models with the same network settings were evaluated and compared to the conventional multi-pool Lorentzian fitting (MPLF) method in generating water and multiple CEST contrasts, including amide, relayed nuclear Overhauser effect (rNOE), and magnetization transfer (MT). Results: The water and CEST maps generated by both MLP and KAN were visually comparable to the MPLF results. However, the KAN model demonstrated higher accuracy in extrapolating the CEST fitting metrics, as evidenced by the smaller validation loss during training and smaller absolute error during testing. Voxel-wise correlation analysis showed that all four CEST fitting metrics generated by KAN consistently exhibited higher Pearson coefficients than the MLP results, indicating superior performance. Moreover, the KAN models consistently outperformed the MLP models in varying hidden layer numbers despite longer training time. Conclusion: In this study, we demonstrated for the first time the feasibility of utilizing KAN for CEST MRI data analysis, highlighting its superiority over MLP in this task. The findings suggest that CEST-KAN has the potential to be a robust and reliable post-analysis tool for CEST MRI in clinical settings.

Diffusion-weighted MRI (DW-MRI) is used to quantitatively characterize the microscopic structure of soft tissue due to the anisotropic diffusion of water in muscle. Applications such as fiber tractography or modeling of tumor spread in soft tissue require precise detection of muscle fiber orientation, which is derived from the principal eigenvector of the diffusion tensor. For clinical applications, high image quality and high signal-to-noise ratio (SNR) of DW-MRI for fiber orientation must be balanced with an appropriate scan duration. Muscles with known structural heterogeneity, e.g. bipennate muscles such as the thigh rectus femoris, provide a natural quality benchmark to determine fiber orientation at different scan parameters. Here, we analyze DW-MR images of the thigh of a healthy volunteer at different SNRs and use PCA to identify subsets of voxels with different directions of diffusion tensor eigenvectors. We propose to use the mixing index of spatial co-localization of the clustered eigenvectors as a quality metric for fiber orientation detection. Comparing acquisitions at different SNRs, we find that high SNR results in a low mixing index, reflecting a clear separation of the two compartments of the bipennate muscle on either side of the central tendon. Because the mixing index allows joint estimation of spatial and directional noise in DW-MRI as a single parameter, it will allow future quantitative optimization of DW-MRI protocols for soft tissue.

Imaging sites around the world generate growing amounts of medical scan data with ever more versatile and affordable technology. Large-scale studies acquire MRI for tens of thousands of participants, together with metadata ranging from lifestyle questionnaires to biochemical assays, genetic analyses and more. These large datasets encode substantial information about human health and hold considerable potential for machine learning training and analysis. This chapter examines ongoing large-scale studies and the challenge of distribution shifts between them. Transfer learning for overcoming such shifts is discussed, together with federated learning for safe access to distributed training data securely held at multiple institutions. Finally, representation learning is reviewed as a methodology for encoding embeddings that express abstract relationships in multi-modal input formats., Comment: Book chapter pre-print

Systematic in vivo validations of computational models of the aortic valve remain scarce, despite successful validation against in vitro data. Utilizing a combination of computed tomography and 4D flow magnetic resonance imaging data, we developed patient-specific fluid-structure interaction models of the aortic valve immersed in the aorta for five patients in the pre-transcatheter aortic valve replacement configuration. Incorporating also an in vitro setup of the valve, our computational models are subjected to rigorous validation against 4D flow measurements. Our results demonstrate the models' capacity to accurately replicate flow dynamics within established ranges of uncertainties mainly arising from 4D flow noise. In addition, we illustrate how computational models can serve as valuable cross-checks to reduce noise and erratic behaviour of in vivo data. This study represents a significant step towards integrating in silico technologies into real clinical contexts, providing a robust framework for improving aortic stenosis diagnosis and the design of next-generation aortic valve bioprostheses.

Computational fluid dynamics (CFD) can be used for evaluation of hemodynamics. However, its routine use is limited by labor-intensive manual segmentation, CFD mesh creation, and time-consuming simulation. This study aims to train a deep learning model to both generate patient-specific volume-meshes of the pulmonary artery from 3D cardiac MRI data and directly estimate CFD flow fields. This study used 135 3D cardiac MRIs from both a public and private dataset. The pulmonary arteries in the MRIs were manually segmented and converted into volume-meshes. CFD simulations were performed on ground truth meshes and interpolated onto point-point correspondent meshes to create the ground truth dataset. The dataset was split 85/10/15 for training, validation and testing. Image2Flow, a hybrid image and graph convolutional neural network, was trained to transform a pulmonary artery template to patient-specific anatomy and CFD values. Image2Flow was evaluated in terms of segmentation and accuracy of CFD predicted was assessed using node-wise comparisons. Centerline comparisons of Image2Flow and CFD simulations performed using machine learning segmentation were also performed. Image2Flow achieved excellent segmentation accuracy with a median Dice score of 0.9 (IQR: 0.86-0.92). The median node-wise normalized absolute error for pressure and velocity magnitude was 11.98% (IQR: 9.44-17.90%) and 8.06% (IQR: 7.54-10.41), respectively. Centerline analysis showed no significant difference between the Image2Flow and conventional CFD simulated on machine learning-generated volume-meshes. This proof-of-concept study has shown it is possible to simultaneously perform patient specific volume-mesh based segmentation and pressure and flow field estimation. Image2Flow completes segmentation and CFD in ~205ms, which ~7000 times faster than manual methods, making it more feasible in a clinical environment., Comment: 22 pages, 7 figures, 3 tables

Synthetic longitudinal brain MRI simulates brain aging and would enable more efficient research on neurodevelopmental and neurodegenerative conditions. Synthetically generated, age-adjusted brain images could serve as valuable alternatives to costly longitudinal imaging acquisitions, serve as internal controls for studies looking at the effects of environmental or therapeutic modifiers on brain development, and allow data augmentation for diverse populations. In this paper, we present a diffusion-based approach called SynthBrainGrow for synthetic brain aging with a two-year step. To validate the feasibility of using synthetically-generated data on downstream tasks, we compared structural volumetrics of two-year-aged brains against synthetically-aged brain MRI. Results show that SynthBrainGrow can accurately capture substructure volumetrics and simulate structural changes such as ventricle enlargement and cortical thinning. Our approach provides a novel way to generate longitudinal brain datasets from cross-sectional data to enable augmented training and benchmarking of computational tools for analyzing lifespan trajectories. This work signifies an important advance in generative modeling to synthesize realistic longitudinal data with limited lifelong MRI scans. The code is available at XXX., Comment: 8 pages, 4 figures

Quantitative analysis of pseudo-diffusion in diffusion-weighted magnetic resonance imaging (DWI) data shows potential for assessing fetal lung maturation and generating valuable imaging biomarkers. Yet, the clinical utility of DWI data is hindered by unavoidable fetal motion during acquisition. We present IVIM-morph, a self-supervised deep neural network model for motion-corrected quantitative analysis of DWI data using the Intra-voxel Incoherent Motion (IVIM) model. IVIM-morph combines two sub-networks, a registration sub-network, and an IVIM model fitting sub-network, enabling simultaneous estimation of IVIM model parameters and motion. To promote physically plausible image registration, we introduce a biophysically informed loss function that effectively balances registration and model-fitting quality. We validated the efficacy of IVIM-morph by establishing a correlation between the predicted IVIM model parameters of the lung and gestational age (GA) using fetal DWI data of 39 subjects. IVIM-morph exhibited a notably improved correlation with gestational age (GA) when performing in-vivo quantitative analysis of fetal lung DWI data during the canalicular phase. IVIM-morph shows potential in developing valuable biomarkers for non-invasive assessment of fetal lung maturity with DWI data. Moreover, its adaptability opens the door to potential applications in other clinical contexts where motion compensation is essential for quantitative DWI analysis. The IVIM-morph code is readily available at: https://github.com/TechnionComputationalMRILab/qDWI-Morph., Comment: Accepted for publication in the journal: "Medical Image Analysis"

Automated segmentation of distinct tumor regions is critical for accurate diagnosis and treatment planning in pediatric brain tumors. This study evaluates the efficacy of the Multi-Planner U-Net (MPUnet) approach in segmenting different tumor subregions across three challenging datasets: Pediatrics Tumor Challenge (PED), Brain Metastasis Challenge (MET), and Sub-Sahara-Africa Adult Glioma (SSA). These datasets represent diverse scenarios and anatomical variations, making them suitable for assessing the robustness and generalization capabilities of the MPUnet model. By utilizing multi-planar information, the MPUnet architecture aims to enhance segmentation accuracy. Our results show varying performance levels across the evaluated challenges, with the tumor core (TC) class demonstrating relatively higher segmentation accuracy. However, variability is observed in the segmentation of other classes, such as the edema and enhancing tumor (ET) regions. These findings emphasize the complexity of brain tumor segmentation and highlight the potential for further refinement of the MPUnet approach and inclusion of MRI more data and preprocessing.

Purpose: To derive kinetic equations for multi-compartmental contrast agent distribution from first principles and apply it to two and three compartments for Gd-EOB-DTPA using low time resolution human liver DCE-MRI data. Methods: The continuity and diffusion equation were combined and used to derive a general form for differential equations governing multi-compartmental particle exchange. They were applied to two (equivalent to the Tofts model) and three compartments. Both models were fit to human DCE-MRI data with low temporal resolution and three compartment model's parameters' implications are discussed. Results: The model derived for two compartments is shown to be equivalent with the Tofts model. Using reasonable biological and physical assumptions an analytical solution for the three compartment model is obtained. The three compartment model was able to fit all Gd-EOB-DTPA DCE-MRI data whereas the Tofts model did not. Differences were increased for cases with large as well as rapid uptake of contrast. Conclusion: We demonstrated the ability to fit sparse Gd-EOB-DTPA DCE-MRI data using a three compartment model derived from first principles whose parameters can be used to help quantify overall and regional liver function.

The integration of different imaging modalities, such as structural, diffusion tensor, and functional magnetic resonance imaging, with deep learning models has yielded promising outcomes in discerning phenotypic characteristics and enhancing disease diagnosis. The development of such a technique hinges on the efficient fusion of heterogeneous multimodal features, which initially reside within distinct representation spaces. Naively fusing the multimodal features does not adequately capture the complementary information and could even produce redundancy. In this work, we present a novel joint self-supervised and supervised contrastive learning method to learn the robust latent feature representation from multimodal MRI data, allowing the projection of heterogeneous features into a shared common space, and thereby amalgamating both complementary and analogous information across various modalities and among similar subjects. We performed a comparative analysis between our proposed method and alternative deep multimodal learning approaches. Through extensive experiments on two independent datasets, the results demonstrated that our method is significantly superior to several other deep multimodal learning methods in predicting abnormal neurodevelopment. Our method has the capability to facilitate computer-aided diagnosis within clinical practice, harnessing the power of multimodal data., Comment: 35 pages. Submitted to journal

There has been much recent interest in adapting undersampled trajectories in MRI based on training data. In this work, we propose a novel patient-adaptive MRI sampling algorithm based on grouping scans within a training set. Scan-adaptive sampling patterns are optimized together with an image reconstruction network for the training scans. The training optimization alternates between determining the best sampling pattern for each scan (based on a greedy search or iterative coordinate descent (ICD)) and training a reconstructor across the dataset. The eventual scan-adaptive sampling patterns on the training set are used as labels to predict sampling design using nearest neighbor search at test time. The proposed algorithm is applied to the fastMRI knee multicoil dataset and demonstrates improved performance over several baselines.

Image segmentation, real-value prediction, and cross-modal translation are critical challenges in medical imaging. In this study, we propose a versatile multi-task neural network framework, based on an enhanced Transformer U-Net architecture, capable of simultaneously, selectively, and adaptively addressing these medical image tasks. Validation is performed on a public repository of human brain MR and CT images. We decompose the traditional problem of synthesizing CT images into distinct subtasks, which include skull segmentation, Hounsfield unit (HU) value prediction, and image sequential reconstruction. To enhance the framework's versatility in handling multi-modal data, we expand the model with multiple image channels. Comparisons between synthesized CT images derived from T1-weighted and T2-Flair images were conducted, evaluating the model's capability to integrate multi-modal information from both morphological and pixel value perspectives., Comment: 4 pages, 3 figures, 2 tables

Identifying and utilising various biomarkers for tracking Alzheimer's disease (AD) progression have received many recent attentions and enable helping clinicians make the prompt decisions. Traditional progression models focus on extracting morphological biomarkers in regions of interest (ROIs) from MRI/PET images, such as regional average cortical thickness and regional volume. They are effective but ignore the relationships between brain ROIs over time, which would lead to synergistic deterioration. For exploring the synergistic deteriorating relationship between these biomarkers, in this paper, we propose a novel spatio-temporal similarity measure based multi-task learning approach for effectively predicting AD progression and sensitively capturing the critical relationships between biomarkers. Specifically, we firstly define a temporal measure for estimating the magnitude and velocity of biomarker change over time, which indicate a changing trend(temporal). Converting this trend into the vector, we then compare this variability between biomarkers in a unified vector space(spatial). The experimental results show that compared with directly ROI based learning, our proposed method is more effective in predicting disease progression. Our method also enables performing longitudinal stability selection to identify the changing relationships between biomarkers, which play a key role in disease progression. We prove that the synergistic deteriorating biomarkers between cortical volumes or surface areas have a significant effect on the cognitive prediction.

Objectives:To develop a framework for obtaining dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) derived relative cerebral blood volume (rCBV) maps without gadolinium-based contrast agent (GBCA) injection. Methods:This retrospective study included 146 patients (124 IDH wildtype; 22 IDH mutation) diagnosed with glioma. The DSC-MRI-derived rCBV maps were synthesized from intravoxel incoherent motion (IVIM) MRI data by the deep neural network trained only with IDH wildtype data due to thedata imbalance. Linear regression analysis, Pearson correlation coefficient, and Bland-Altman analysis, were done to evaluate the consistency between real and synthetic rCBV maps. The generalizability of the proposed framework was evaluated with IDH mutation data. IDH mutation status identification ability of real and synthetic rCBV maps was analyzed and compared using ROC analysis and the DeLong test. Results:Linear regression analysis shows a linear relationship between real and synthetic rCBV maps with a relatively high Pearson correlation coefficient (IDH wildtype: Pearson P = 0.7536; IDH mutation: Pearson P = 0.8933). Bland-Altman analysis between real and synthetic rCBV maps shows that almost all the data distribute within the 95% limits of agreement (IDH wildtype: 19 of 20 [95%]; IDH mutation: 19 of 20 [95%]). ROC analysis and the DeLong test show that the IDH mutation status identification abilities of real (AUC = 0.8375) and synthetic rCBV (AUC = 0.8325) are comparable and show no significant difference (P = 0.9075). Conclusions:It is feasible to obtain DSC-MRI-derived rCBV maps without the injection of GBCA. The synthetic rCBV map shows high consistency with real one.