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Femoroacetabular impingement (FAI) cam morphology is routinely assessed using manual measurements of two-dimensional (2D) alpha angles which are prone to high rater variability and do not provide direct three-dimensional (3D) data on these osseous formations. We present CamMorph, a fully automated 3D pipeline for segmentation, statistical shape assessment and measurement of cam volume, surface area and height from clinical magnetic resonance (MR) images of the hip in FAI patients.The novel CamMorph pipeline involves two components: (I) accurate proximal femur segmentation generated by combining the 3D U-net to identify both global (region) and local (edge) features in clinical MR images and focused shape modelling to generate a 3D anatomical model for creating patient-specific proximal femur models; (II) patient-specific anatomical information from 3D focused shape modelling to simulate 'healthy' femoral bone models with cam-affected region constraints applied to the anterosuperior femoral head-neck region to quantify cam morphology in FAI patients. The CamMorph pipeline, which generates patient-specific data within 5 min, was used to analyse multi-site clinical MR images of the hip to measure and assess cam morphology in male (n=56) and female (n=41) FAI patients.There was excellent agreement between manual and CamMorph segmentations of the proximal femur as demonstrated by the mean Dice similarity index (DSI; 0.964±0.006), 95% Hausdorff distance (HD; 2.123±0.876 mm) and average surface distance (ASD; 0.539±0.189 mm) values. Compared to female FAI patients, male patients had a significantly larger median cam volume (969.22The fully automated 3D CamMorph pipeline developed in the present study successfully segmented and measured cam morphology from clinical MR images of the hip in male and female patients with differing FAI severity and pathoanatomical characteristics.

Only 10% of CT scans unveil positive findings in mild traumatic brain injury, raising concerns of its overuse in this population. A number of clinical rules have been developed to address this issue, but they still suffer limitations in their specificity. Machine learning models have been applied in limited studies to mimic clinical rules; however, further improvement in terms of balanced sensitivity and specificity is still needed. In this work, the authors applied a deep artificial neural networks (DANN) model and an instance hardness threshold algorithm to reproduce the Pediatric Emergency Care Applied Research Network (PECARN) clinical rule in a pediatric population collected as a part of the PECARN study between 2004 and 2006.The DANN model was applied using 14,983 patients younger than 18 years with Glasgow Coma Scale scores ≥ 14 who had head CT reports. The clinical features of the PECARN rules, PECARN-A (group A, age2 years) and PECARN-B (group B, age ≤ 2 years), were used to directly evaluate the model. The average accuracy, sensitivity, precision, and specificity were calculated by comparing the model's prediction outcome to that reported by the PECARN investigators. The instance hardness threshold and DANN model were applied to predict the need for CT in pediatric patients using 5-fold cross-validation.In the first phase, the DANN model resulted in 98.6% sensitivity and 99.7% specificity for predicting the need for CT using the predictors of the two PECARN clinical rules combined to train the model. In the second phase, the DANN model was superior to both the PECARN-A and PECARN-B rules using the predictors for each age group separately to train the model. Compared with the clinical rule, for group A, the model achieved an average sensitivity (93.7% versus 100%) and specificity (97.5% versus 53.6%); for group B, the average sensitivity of the model was 99.2% versus 98.6%, and the specificity was 98.8% versus 58.2%.In this study, a DANN model achieved comparable sensitivity and outstanding specificity for replicating the PECARN clinical rule and predicting the need for CT in pediatric patients after mild traumatic brain injury compared with the original statistically derived clinical rule.

Convolutional neural networks (CNN) have demonstrated outstanding Compressed Sensing (CS) performance compared to traditional, hand-crafted methods. However, they are broadly limited in terms of generalisability, inductive bias and difficulty to model long distance relationships. Transformer neural networks (TNN) overcome such issues by implementing an attention mechanism designed to capture dependencies between inputs. However, high-resolution tasks typically require vision Transformers (ViT) to decompose an image into patch-based tokens, limiting inputs to inherently local contexts. We propose a novel image decomposition that naturally embeds images into low-resolution inputs. These Kaleidoscope tokens (KD) provide a mechanism for global attention, at the same computational cost as a patch-based approach. To showcase this development, we replace CNN components in a well-known CS-MRI neural network with TNN blocks and demonstrate the improvements afforded by KD. We also propose an ensemble of image tokens, which enhance overall image quality and reduces model size. Supplementary material is available: https://github.com/uqmarlonbran/TCS.git, 4 Pages, 4 Figures, 2 Tables

Magnetic resonance (MR) imaging visualises soft tissue contrast in exquisite detail without harmful ionising radiation. In this work, we provide a state-of-the-art review on the use of deep learning in MR image reconstruction from different image acquisition types involving compressed sensing techniques, parallel image acquisition and multi-contrast imaging. Publications with deep learning-based image reconstruction for MR imaging were identified from the literature (PubMed and Google Scholar), and a comprehensive description of each of the works was provided. A detailed comparison that highlights the differences, the data used and the performance of each of these works were also made. A discussion of the potential use cases for each of these methods is provided. The sparse image reconstruction methods were found to be most popular in using deep learning for improved performance, accelerating acquisitions by around 4-8 times. Multi-contrast image reconstruction methods rely on at least one pre-acquired image, but can achieve 16-fold, and even up to 32- to 50-fold acceleration depending on the set-up. Parallel imaging provides frameworks to be integrated in many of these methods for additional speed-up potential. The successful use of compressed sensing techniques and multi-contrast imaging with deep learning and parallel acquisition methods could yield significant MR acquisition speed-ups within clinical routines in the near future.

IntroductionTraumatic brain injury (TBI) is a heterogeneous condition with a broad spectrum of injury severity, pathophysiological processes and variable outcomes. For moderate-to-severe TBI survivors, recovery is often protracted and outcomes can range from total dependence to full recovery. Despite advances in medical treatment options, prognosis remains largely unchanged. The objective of this study is to develop a machine learning predictive model for neurological outcomes at 6 months in patients with a moderate-to-severe TBI, incorporating longitudinal clinical, multimodal neuroimaging and blood biomarker predictor variables.Methods and analysisA prospective, observational, cohort study will enrol 300 patients with moderate-to-severe TBI from seven Australian hospitals over 3 years. Candidate predictors including demographic and general health variables, and longitudinal clinical, neuroimaging (CT and MRI), blood biomarker and patient-reported outcome measures will be collected at multiple time points within the acute phase of injury. The predictor variables will populate novel machine learning models to predict the Glasgow Outcome Scale Extended 6 months after injury. The study will also expand on current prognostic models by including novel blood biomarkers (circulating cell-free DNA), and the results of quantitative neuroimaging such as Quantitative Susceptibility Mapping and Dynamic Contrast Enhanced MRI as predictor variables.Ethics and disseminationEthical approval has been obtained by the Royal Brisbane and Women’s Hospital Human Research Ethics Committee, Queensland. Participants or their substitute decision-maker/s will receive oral and written information about the study before providing written informed consent. Study findings will be disseminated by peer-review publications and presented at national and international conferences and clinical networks.Trial registration numberACTRN12620001360909.

To obtain automated measurements of cam volume, surface area, and height from baseline (preintervention) and 12-month magnetic resonance (MR) images acquired from male and female patients allocated to physiotherapy (PT) or arthroscopic surgery (AS) management for femoroacetabular impingement (FAI) in the Australian FASHIoN trial.An automated segmentation pipeline (CamMorph) was used to obtain cam morphology data from three-dimensional (3D) MR hip examinations in FAI patients classified with mild, moderate, or major cam volumes. Pairwise comparisons between baseline and 12-month cam volume, surface area, and height data were performed within the PT and AS patient groups using pairedA total of 43 patients were included with 15 PT patients (9 males, 6 females) and 28 AS patients (18 males, 10 females) for premanagement and postmanagement cam morphology assessments. Within the PT male and female patient groups, there were no significant differences between baseline and 12-month mean cam volume (male: 1269 vs 1288 mmAutomated measurement of cam morphology from baseline (preintervention) and 12-month MR images demonstrated that the cam volume, surface area, maximum-height, and average height were significantly smaller in AS patients following ostectomy, whereas there were no significant differences in these cam measures in PT patients from the Australian FASHIoN study.Level II, cohort study.

Sampling strategies are important for sparse imaging methodologies, especially those employing the discrete Fourier transform (DFT). Chaotic sensing is one such methodology that employs deterministic, fractal sampling in conjunction with finite, iterative reconstruction schemes to form an image from limited samples. Using a sampling pattern constructed entirely from periodic lines in DFT space, chaotic sensing was found to outperform traditional compressed sensing for magnetic resonance imaging; however, only one such sampling pattern was presented and the reason for its fractal nature was not proven. Through the introduction of a novel image transform known as the kaleidoscope transform, which formalises and extends upon the concept of downsampling and concatenating an image with itself, this paper: (1) demonstrates a fundamental relationship between multiplication in modular arithmetic and downsampling; (2) provides a rigorous mathematical explanation for the fractal nature of the sampling pattern in the DFT; and (3) leverages this understanding to develop a collection of novel fractal sampling patterns for the 2D DFT with customisable properties. The ability to design tailor-made fractal sampling patterns expands the utility of the DFT in chaotic imaging and may form the basis for a bespoke chaotic sensing methodology, in which the fractal sampling matches the imaging task for improved reconstruction., 6 pages, 7 figures

Automated segmentation using deep learning approaches have shown significant promise for medical images. However, existing methods generally suffer from high computational complexity when utilised in 3D due to their large memory requirements, thus restricting training to high-performing computing hardware only. We present an extremely compact convolutional neural network with a shallow memory footprint to address this problem and train the model with a novel loss function to segment imbalanced classes with extra shape constrain in 3D MR images. The proposed approaches can directly process large full-size 3D input volumes (no patches) and allow inference times within just seconds using the CPU. The proposed network efficiently retains model parameters required to outperform other methods for 3D segmentation (U-Net3D, improved U-Net3D and V-Net) under severe memory limitations, while achieving several times faster inference times. It can also achieve favourable performance compared to a complex pipeline for knee cartilage segmentation with hundred times faster inference.

Head computed tomography (CT) is the gold standard in emergency departments (EDs) to evaluate mild traumatic brain injury (mTBI) patients, especially for paediatrics. Data-driven models for successfully classifying head CT scans that have mTBI will be valuable in terms of timeliness and cost-effectiveness for TBI diagnosis. This study applied two different machine learning (ML) models to diagnose mTBI in a paediatric population collected as part of the paediatric emergency care applied research network (PECARN) study between 2004 and 2006. The models were conducted using 15,271 patients under the age of 18 years with mTBI and had a head CT report. In the conventional model, random forest (RF) ranked the features to reduce data dimensionality and the top ranked features were used to train a shallow artificial neural network (ANN) model. In the second model, a deep ANN applied to classify positive and negative mTBI patients using the entirety of the features available. The dataset was divided into two subsets: 80% for training and 20% for testing using five-fold cross-validation. Accuracy, sensitivity, precision, and specificity were calculated by comparing the model's prediction outcome to the actual diagnosis for each patient. RF ranked ten clinical demographic features and twelve CT-findings; the hybrid RF-ANN model achieved an average specificity of 99.96%, sensitivity of 95.98%, precision of 99.25%, and accuracy of 99.74% in identifying positive mTBI from negative mTBI subjects. The deep ANN proved its ability to carry out the task efficiently with an average specificity of 99.9%, sensitivity of 99.2%, precision of 99.9%, and accuracy of 99.9%. The performance of the two proposed models demonstrated the feasibility of using ANN to diagnose mTBI in a paediatric population. This is the first study to investigate deep ANN in a paediatric cohort with mTBI using clinical and non-imaging data and diagnose mTBI with balanced sensitivity and specificity using shallow and deep ML models. This method, if validated, would have the potential to reduce the burden of TBI evaluation in EDs and aide clinicians in the decision-making process.

Direct automatic segmentation of objects from 3D medical imaging, such as magnetic resonance (MR) imaging, is challenging as it often involves accurately identifying a number of individual objects with complex geometries within a large volume under investigation. To address these challenges, most deep learning approaches typically enhance their learning capability by substantially increasing the complexity or the number of trainable parameters within their models. Consequently, these models generally require long inference time on standard workstations operating clinical MR systems and are restricted to high-performance computing hardware due to their large memory requirement. Further, to fit 3D dataset through these large models using limited computer memory, trade-off techniques such as patch-wise training are often used which sacrifice the fine-scale geometric information from input images which could be clinically significant for diagnostic purposes. To address these challenges, we present a compact convolutional neural network with a shallow memory footprint to efficiently reduce the number of model parameters required for state-of-art performance. This is critical for practical employment as most clinical environments only have low-end hardware with limited computing power and memory. The proposed network can maintain data integrity by directly processing large full-size 3D input volumes with no patches required and significantly reduces the computational time required for both training and inference. We also propose a novel loss function with extra shape constraint to improve the accuracy for imbalanced classes in 3D MR images., Comment: 21 pages, 7 figures

Background Magnetic resonance (MR) T2 and T2* mapping sequences allow in vivo quantification of biochemical characteristics within joint cartilage of relevance to clinical assessment of conditions such as hip osteoarthritis (OA). Purpose To evaluate an automated immediate reliability analysis of T2 and T2* mapping from MR examinations of hip joint cartilage using a bone and cartilage segmentation pipeline based around focused shape modelling. Study type Technical validation. Subjects 17 asymptomatic volunteers (M: F 7:10, aged 22–47 years, mass 50–90 kg, height 163-189 cm) underwent unilateral hip joint MR examinations. Automated analysis of cartilage T2 and T2* data immediate reliability was evaluated in 9 subjects (M: F 4: 5) for each sequence. Field strength/sequence A 3 T MR system with a body matrix flex-coil was used to acquire images with the following sequences: T2 weighted 3D-trueFast Imaging with Steady-State Precession (water excitation; 10.18 ms repetition time (TR); 4.3 ms echo time (TE); Voxel Size (VS): 0.625 × 0.625 × 0.65 mm; 160 mm field of view (FOV); Flip Angle (FA): 30 degrees; Pixel Bandwidth (PB): 140 Hz/pixel); a multi-echo spin echo (MESE) T2 mapping sequence (TR/TE: 2080/18–90 ms (5 echoes); VS: 4 × 0.78 × 0.78 mm; FOV: 200 mm; FA: 180 degrees; PB: 230 Hz/pixel) and a MESE T2* mapping sequence (TR/TE: 873/3.82–19.1 ms (5 echoes); VS: 3 × 0.625 × 0.625 mm; FOV: 160 mm; FA: 25 degrees; PB: 250 Hz/pixel). Assessment Automated cartilage segmentation and quantitative analysis provided T2 and T2* data from test-retest MR examinations to assess immediate reliability. Statistical tests Coefficient of variation (CV) and intraclass correlations (ICC2, 1) to analyse automated T2 and T2* mapping reliability focusing on the clinically important superior cartilage regions of the hip joint. Results Comparisons between test-retest T2 and (T2*) data revealed mean CV's of 3.385% (1.25%), mean ICC2, 1′s of 0.871 (0.984) and median mean differences of −1.139ms (+0.195ms). Conclusion The T2 and T2* times from automated analyses of hip cartilage from test-retest MR examinations had high (T2) and excellent (T2*) immediate reliability.

Multi-contrast (MC) Magnetic Resonance Imaging (MRI) of the same patient usually requires long scanning times, despite the images sharing redundant information. In this work, we propose a new iterative network that utilizes the sharable information among MC images for MRI acceleration. The proposed network has reinforced data fidelity control and anatomy guidance through an iterative optimization procedure of Gradient Descent, leading to reduced uncertainties and improved reconstruction results. Through a convolutional network, the new method incorporates a learnable regularization unit that is capable of extracting, fusing, and mapping shareable information among different contrasts. Specifically, a dilated inception block is proposed to promote multi-scale feature extractions and increase the receptive field diversity for contextual information incorporation. Lastly, an optimal MC information feeding protocol is built through the design of a complementary feature extractor block. Comprehensive experiments demonstrated the superiority of the proposed network, both qualitatively and quantitatively.

Finite element analysis (FEA) provides a powerful approach for estimating the in-vivo loading characteristics of the hip joint during various locomotory and functional activities. However, time-consuming procedures, such as the generation of high-quality FE meshes and setup of FE simulation, typically make the method impractical for rapid applications which could be used in clinical routine. Alternatively, discrete element analysis (DEA) has been developed to quantify mechanical conditions of the hip joint in a fraction of time compared to FEA. Although DEA has proven effective in the estimation of contact stresses and areas in various complex applications, it has not yet been well characterised by its ability to evaluate contact mechanics for the hip joint during gait cycle loading using data from several individuals. The objective of this work was to compare DEA modelling against well-established FEA for analysing contact mechanics of the hip joint during walking gait. Subject-specific models were generated from magnetic resonance images of the hip joints in five asymptomatic subjects. The DEA and FEA models were then simulated for 13 loading time-points extracted from a full gait cycle. Computationally, DEA was substantially more efficient compared to FEA (simulation times of seconds vs. hours). The DEA and FEA methods had similar predictions for contact pressure distribution for the hip joint during normal walking. In all 13 simulated loading time-points across five subjects, the maximum difference in average contact pressures between DEA and FEA was within ±0.06 MPa. Furthermore, the difference in contact area ratio computed using DEA and FEA was less than ±6%.

High resolution three-dimensional (3D) magnetic resonance (MR) images are well suited for automated cartilage segmentation in the human knee joint. However, volumetric scans such as 3D Double-Echo Steady-State (DESS) images are not routinely acquired in clinical practice which limits opportunities for reliable cartilage segmentation using (fully) automated algorithms. In this work, a method for generating synthetic 3D MR (syn3D-DESS) images with better contrast and higher spatial resolution from routine, low resolution, two-dimensional (2D) Turbo-Spin Echo (TSE) clinical knee scans is proposed.A UNet convolutional neural network is employed for synthesizing enhanced artificial MR images suitable for automated knee cartilage segmentation. Training of the model was performed on a large, publically available dataset from the OAI, consisting of 578 MR examinations of knee joints from 102 healthy individuals and patients with knee osteoarthritis.The generated synthetic images have higher spatial resolution and better tissue contrast than the original 2D TSE, which allow high quality automated 3D segmentations of the cartilage. The proposed approach was evaluated on a separate set of MR images from 88 subjects with manual cartilage segmentations. It provided a significant improvement in automated segmentation of knee cartilages when using the syn3D-DESS images compared to the original 2D TSE images.The proposed method can successfully synthesize 3D DESS images from 2D TSE images to provide images suitable for automated cartilage segmentation.

Combining high-resolution magnetic resonance imaging (MRI) with a linear accelerator (Linac) as a single MRI-Linac system provides the capability to monitor intra-fractional motion and anatomical changes during radiotherapy, which facilitates more accurate delivery of radiation dose to the tumour and less exposure to healthy tissue. The gradient non-linearity (GNL) induced distortions in MRI; however, hinder the implementation of MRI-Linac system in image-guided radiotherapy where highly accurate geometry and anatomy of the target tumour is indispensable. To correct the geometric distortions in MR images, in particular, for the 1 Tesla (T) MRI-Linac system, a deep fully-connected neural network was proposed to automatically learn the intricate relationship between the undistorted (theoretical) and distorted (real) space. A data set, consisting of spatial samples acquired by phantom measurement that covers both inside and outside the working diameter of spherical volume (DSV), was utilised for training the neural network; which offers the ability to describe subtle deviations of the GNL field within the entire region of interest (ROI). The performance of the proposed method was evaluated on MR images of a three-dimensional (3D) phantom and the pelvic region of an adult volunteer scanned in the 1T MRI-Linac system. The experimental results showed that the severe geometric distortions within the entire ROI had been successfully corrected with an error less than the pixel size. Also, the presented network is highly efficient, which achieved significant improvement in terms of computational efficiency compared to existing methods. The feasibility of the presented deep neural network for characterising the GNL field deviations in the 1T MRI-Linac system was demonstrated in this study, which shows promise in facilitating the MRI-Linac system to be routinely implemented in real-time MRI-guided radiotherapy.

Mammographic mass detection and segmentation are usually performed as serial and separate tasks, with segmentation often only performed on manually confirmed true positive detections in previous studies. We propose a fully-integrated computer-aided detection (CAD) system for simultaneous mammographic mass detection and segmentation without user intervention. The proposed CAD only consists of a pseudo-color image generation and a mass detection-segmentation stage based on Mask R-CNN. Grayscale mammograms are transformed into pseudo-color images based on multi-scale morphological sifting where mass-like patterns are enhanced to improve the performance of Mask R-CNN. Transfer learning with the Mask R-CNN is then adopted to simultaneously detect and segment masses on the pseudo-color images. Evaluated on the public dataset INbreast, the method outperforms the state-of-the-art methods by achieving an average true positive rate of 0.90 at 0.9 false positive per image and an average Dice similarity index of 0.88 for mass segmentation.

HDR-MRI is a sophisticated non-linear image fusion technique for MRI which enhances image quality by fusing multiple contrast types into a single composite image. It offers improved outcomes in automatic segmentation and potentially in diagnostic power, but the existing technique is slow and requires accurate image co-registration in order to function reliably. In this work, a lightweight fully convolutional neural network architecture is developed with the goal of approximating HDR-MRI images in real-time. The resulting Contrast Enhancement Network (CEN) is capable of performing near-perfect ( $\text{SSIM} =0.98$ ) 2D approximations of HDR-MRI in 10ms and full 3D approximations in 1s, running two orders of magnitude faster than the original implementation. It is also able to perform the approximation ( $\text{SSIM} =0.93$ ) with only two of the three contrasts required to generate the original HDR-MRI image, while requiring no image co-registration.

Biomedical imaging analysis typically comprises a variety of complex tasks requiring sophisticated algorithms and visualising high dimensional data. The successful integration and deployment of the enabling software to clinical (research) partners, for rigorous evaluation and testing, is a crucial step to facilitate adoption of research innovations within medical settings. In this paper, we introduce the Simple Medical Imaging Library Interface (SMILI), an object oriented open-source framework with a compact suite of objects geared for rapid biomedical imaging (cross-platform) application development and deployment. SMILI supports the development of both command-line (shell and Python scripting) and graphical applications utilising the same set of processing algorithms. It provides a substantial subset of features when compared to more complex packages, yet it is small enough to ship with clinical applications with limited overhead and has a license suitable for commercial use. After describing where SMILI fits within the existing biomedical imaging software ecosystem, by comparing it to other state-of-the-art offerings, we demonstrate its capabilities in creating a clinical application for manual measurement of cam-type lesions of the femoral head-neck region for the investigation of femoro-acetabular impingement (FAI) from three dimensional (3D) magnetic resonance (MR) images of the hip. This application for the investigation of FAI proved to be convenient for radiological analyses and resulted in high intra (ICC=0.97) and inter-observer (ICC=0.95) reliabilities for measurement of α-angles of the femoral head-neck region. We believe that SMILI is particularly well suited for prototyping biomedical imaging applications requiring user interaction and/or visualisation of 3D mesh, scalar, vector or tensor data.

To develop a local contrast-enhancing and feature-preserving high dynamic range (HDR) image processing algorithm for multichannel and multisequence MR images of multiple body regions and tissues, and to evaluate its performance for structure visualization, bias field (correction) mitigation, and automated tissue segmentation. A multiscale-shape and detail-enhancement HDR-MRI algorithm is applied to data sets of multichannel and multisequence MR images of the brain, knee, breast, and hip. In multisequence 3T hip images, agreement between automatic cartilage segmentations and corresponding synthesized HDR-MRI series were computed for mean voxel overlap established from manual segmentations for a series of cases. Qualitative comparisons between the developed HDR-MRI and standard synthesis methods were performed on multichannel 7T brain and knee data, and multisequence 3T breast and knee data. The synthesized HDR-MRI series provided excellent enhancement of fine-scale structure from multiple scales and contrasts, while substantially reducing bias field effects in 7T brain gradient echo, T1 and T2 breast images and 7T knee multichannel images. Evaluation of the HDR-MRI approach on 3T hip multisequence images showed superior outcomes for automatic cartilage segmentations with respect to manual segmentation, particularly around regions with hyperintense synovial fluid, across a set of 3D sequences. The successful combination of multichannel/sequence MR images into a single-fused HDR-MR image format provided consolidated visualization of tissues within 1 omnibus image, enhanced definition of thin, complex anatomical structures in the presence of variable or hyperintense signals, and improved tissue (cartilage) segmentation outcomes.

Active shape models (ASMs) have proved successful in automatic segmentation by using shape and appearance priors in a number of areas such as prostate segmentation, where accurate contouring is important in treatment planning for prostate cancer. The ASM approach however, is heavily reliant on a good initialisation for achieving high segmentation quality. This initialisation often requires algorithms with high computational complexity, such as three dimensional (3D) image registration. In this work, we present a fast, self-initialised ASM approach that simultaneously fits multiple objects hierarchically controlled by spatially weighted shape learning. Prominent objects are targeted initially and spatial weights are progressively adjusted so that the next (more difficult, less visible) object is simultaneously initialised using a series of weighted shape models. The scheme was validated and compared to a multi-atlas approach on 3D magnetic resonance (MR) images of 38 cancer patients and had the same (mean, median, inter-rater) Dice's similarity coefficients of (0.79, 0.81, 0.85), while having no registration error and a computational time of 12-15 min, nearly an order of magnitude faster than the multi-atlas approach.

Even with the advance in medical imaging techniques such as CT/MRI, it is still challenging and time-consuming to reconstruct anatomically accurate lung geometries. It is even more challenging to study variability in inhalation dosimetry or pulmonary drug delivery, which requires a large cohort of lung models to ensure statistically significant results. This study used the statistical shape modeling (SSM) that bases on a limited number of lung models (40) to generate infinitely large numbers of parameterized models, which can span all major features inherent in the database of lung geometries. We demonstrated this model in lung models with more than 400 outlets (G9), which first identified the principal components (PCs) of base models, and then regenerated new models by systematically varying the mode (eigenvector) and its eigenvalues. The new models included airway remodeling at varying locations (left upper lobe and right lower lobe) and with varying levels of airway distensibility (compliance) and constriction (resistance). Airflow and aerosol dynamics within these lung geometries were numerically computed and compared. Results showed that even though the airway remodeling can be local, its influences on flow partition and deposition distribution can be global. Asthma-induced bronchiolar constriction, when severe, can strikingly alter the airflow and particle deposition mapping throughout the lungs. The highest deposition variability due to airway remodeling was found to come from particles of 4–10 μm in the upper lobes, and of 10–20 μm in the lower lobe. Statistical shape modeling is an imaging processing method that has often been used in computer sciences. This is the first study, to the author's knowledge, that SSM was applied in lung models with high complexity to quantify the resultant variances from these geometry remodeling. This method was also applied to lung models with 3000 outlets (G11) to generate diseased lung models at varying locations.

Medical imaging visualization technology takes a significant role in the medical community. With the assistance of medical imaging visualization applications, huge convenience has been brought into clinical diagnosis, monitoring, and treatment. It allows doctors and researchers to see inside the human body, to identify medical problems, and to diagnose diseases. This article presents a lightweight, fast and user-friendly image viewer for medical imaging called SPIFFY. Some developing methodologies with the integration of VTK, ITK, and Qt will be presented in this article. Besides, the minimalist user interface(UI) design of SPIFFY with an application of Human-Computer Interaction(HCI) psychology principles will also be introduced. Moreover, this article will identify the benefits provided by SPIFFY and present a benchmark against some existing medical visualization applications. Experiments using cognitive walkthrough evaluation shows that SPIFFY provides both high effectiveness and efficiency.

We propose a sparse imaging methodology called Chaotic Sensing (ChaoS) that enables the use of limited yet deterministic linear measurements through fractal sampling. A novel fractal in the discrete Fourier transform is introduced that always results in the artefacts being turbulent in nature. These chaotic artefacts have characteristics that are image independent, facilitating their removal through dampening (via image denoising) and obtaining the maximum likelihood solution. In contrast with existing methods, such as compressed sensing, the fractal sampling is based on digital periodic lines that form the basis of discrete projected views of the image without requiring additional transform domains. This allows the creation of finite iterative reconstruction schemes in recovering an image from its fractal sampling that is also new to discrete tomography. As a result, ChaoS supports linear measurement and optimisation strategies, while remaining capable of recovering a theoretically exact representation of the image. We apply the method to simulated and experimental limited magnetic resonance (MR) imaging data, where restrictions imposed by MR physics typically favour linear measurements for reducing acquisition time.

To develop an automated approach for 3D quantitative assessment and measurement of alpha angles from the femoral head-neck (FHN) junction using bone models derived from magnetic resonance (MR) images of the hip joint.Bilateral MR images of the hip joints were acquired from 30 male volunteers (healthy active individuals and high-performance athletes, aged 18–49 years) using a water-excited 3D dual echo steady state (DESS) sequence. In a subset of these subjects (18 water-polo players), additional True Fast Imaging with Steady-state Precession (TrueFISP) images were acquired from the right hip joint. For both MR image sets, an active shape model based algorithm was used to generate automated 3D bone reconstructions of the proximal femur. Subsequently, a local coordinate system of the femur was constructed to compute a 2D shape map to project femoral head sphericity for calculation of alpha angles around the FHN junction. To evaluate automated alpha angle measures, manual analyses were performed on anterosuperior and anterior radial MR slices from the FHN junction that were automatically reformatted using the constructed coordinate system.High intra- and inter-rater reliability (intra-class correlation coefficients > 0.95) was found for manual alpha angle measurements from the auto-extracted anterosuperior and anterior radial slices. Strong correlations were observed between manual and automatic measures of alpha angles for anterosuperior (r = 0.84) and anterior (r = 0.92) FHN positions. For matched DESS and TrueFISP images, there were no significant differences between automated alpha angle measures obtained from the upper anterior quadrant of the FHN junction (two-way repeated measures ANOVA, F

To validate a fully automated scheme to extract biochemical information from the hip joint cartilages using MR T2 mapping images incorporating segmentation of co-registered three-dimensional Fast-Spin-Echo (3D-SPACE) images.Manual analyses of unilateral hip (3 Tesla) MR images of 24 asymptomatic volunteers were used to validate a 3D deformable model method for automated cartilage segmentation of SPACE scans, partitioning of the individual femoral and acetabular cartilage plates into clinically defined sub-regions and propagating these results to T2 maps to calculate region-wise T2 value statistics. Analyses were completed on a desktop computer (∼ 10 min per case).The mean voxel overlap between automated A and manual M segmentations of the cartilage volumes in the (clinically based) SPACE images was 73% (100 × 2|A∩M|/[|A|+|M|]). The automated and manual analyses demonstrated a relative difference error10% in the median "T2 average signal" for each cartilage plate. The automated and manual analyses showed consistent patterns between significant differences in T2 data across the hip cartilage sub-regions.The good agreement between the manual and automatic analyses of T2 values indicates the use of structural 3D-SPACE MR images with the proposed method provides a promising approach for automated quantitative T2 assessment of hip joint cartilages.

Breast mass detection and segmentation are difficult tasks due to the variation in size and shape of breast masses. Constructing classifiers for this problem is also challenging due to the fact that normal tissue regions overwhelmingly outnumber abnormal regions. In this paper, we propose a novel approach for detecting and segmenting breast masses in mammography based on multi-scale morphological filtering and a self-adaptive cascade of random forests (CasRFs). CasRFs can cope with severe class imbalance by adding layers to the cascade until a minimum number of false-positives (FPs) is reached. The approach achieves an average sensitivity of 0.94 with 1.99 FPs/image on INbreast and a sensitivity of 0.77 with 3.93 FPs/image on DDSM BCRP.

Summary Objective To validate an automatic scheme for the segmentation and quantitative analysis of the medial meniscus (MM) and lateral meniscus (LM) in magnetic resonance (MR) images of the knee. Method We analysed sagittal water-excited double-echo steady-state MR images of the knee from a subset of the Osteoarthritis Initiative (OAI) cohort. The MM and LM were automatically segmented in the MR images based on a deformable model approach. Quantitative parameters including volume, subluxation and tibial-coverage were automatically calculated for comparison (Wilcoxon tests) between knees with variable radiographic osteoarthritis (rOA), medial and lateral joint space narrowing (mJSN, lJSN) and pain. Automatic segmentations and estimated parameters were evaluated for accuracy using manual delineations of the menisci in 88 pathological knee MR examinations at baseline and 12 months time-points. Results The median (95% confidence-interval (CI)) Dice similarity index (DSI) ( 2 ∗ | Auto ∩ Manual | / ( | Auto | + | Manual | ) ∗ 100 ) between manual and automated segmentations for the MM and LM volumes were 78.3% (75.0–78.7), 83.9% (82.1–83.9) at baseline and 75.3% (72.8–76.9), 83.0% (81.6–83.5) at 12 months. Pearson coefficients between automatic and manual segmentation parameters ranged from r = 0.70 to r = 0.92. MM in rOA/mJSN knees had significantly greater subluxation and smaller tibial-coverage than no-rOA/no-mJSN knees. LM in rOA knees had significantly greater volumes and tibial-coverage than no-rOA knees. Conclusion Our automated method successfully segmented the menisci in normal and osteoarthritic knee MR images and detected meaningful morphological differences with respect to rOA and joint space narrowing (JSN). Our approach will facilitate analyses of the menisci in prospective MR cohorts such as the OAI for investigations into pathophysiological changes occurring in early osteoarthritis (OA) development.

This study presents an integer-only algorithm to exactly recover an image from its discrete projected views that can be computed with the same computational complexity as the fast Fourier transform (FFT). Most discrete transforms for image reconstruction rely on the FFT, via the Fourier slice theorem (FST), in order to compute reconstructions with lowcomputational complexity. Consequently, complex arithmetic and floating point representations are needed, the latter of which is susceptible to round-off errors. This study shows that the slice theorem is valid within integer fields, via modulo arithmetic, using a circulant theory of the Radon transform (RT). The resulting number-theoretic RT (NRT) provides a representation of images as discrete projections that is always exact and real-valued. The NRT is ideally suited as part of a discrete tomographic algorithm, an encryption scheme or for when numerical overflow is likely, such as when computing a large number of convolutions on the projections. The low-computational complexity of the NRT algorithm also provides an efficient method to generate discrete projected views of image data.

Magnetic resonance (MR) imaging is an important imaging modality for diagnostic medicine due to its ability to visualize the soft tissue of the human body in three dimensions (3D) without ionizing radiation. MR imaging however, typically relies on measurement techniques that do not exploit the geometry of discrete Fourier space, so called k-space, where the measurements are made. In this work, we firstly present a novel k-space tiling scheme that utilizes the finite geometry of discrete Fourier space via the discrete Fourier slice theorem. This produces a sampling of k-space that is pseudo-radial, to be more noise and patient-movement tolerant, and pseudo-random, further improving robustness to noise, whilst sampling with sufficient density near the central k-space region, where the majority of power of anatomical images lies. Secondly, we introduce a stable and iterative discrete reconstruction scheme for recovering images from their limited k-space measurements (in the form discrete slices) based on the maximum likelihood expectation maximization approach. We study the performance of the proposed approach using simulated MR measurements in k-space.

Purpose Magnetic resonance (MR) imaging plays a key role in investigating early degenerative disorders and traumatic injuries of the glenohumeral cartilages. Subtle morphometric and biochemical changes of potential relevance to clinical diagnosis, treatment planning, and evaluation can be assessed from measurements derived from in vivo MR segmentation of the cartilages. However, segmentation of the glenohumeral cartilages, using approaches spanning manual to automated methods, is technically challenging, due to their thin, curved structure and overlapping intensities of surrounding tissues. Automatic segmentation of the glenohumeral cartilages from MR imaging is not at the same level compared to the weight-bearing knee and hip joint cartilages despite the potential applications with respect to clinical investigation of shoulder disorders. In this work, the authors present a fully automated segmentation method for the glenohumeral cartilages using MR images of healthy shoulders. Methods The method involves automated segmentation of the humerus and scapula bones using 3D active shape models, the extraction of the expected bone–cartilage interface, and cartilage segmentation using a graph-based method. The cartilage segmentation uses localization, patient specific tissue estimation, and a model of the cartilage thickness variation. The accuracy of this method was experimentally validated using a leave-one-out scheme on a database of MR images acquired from 44 asymptomatic subjects with a true fast imaging with steady state precession sequence on a 3 T scanner (Siemens Trio) using a dedicated shoulder coil. The automated results were compared to manual segmentations from two experts (an experienced radiographer and an experienced musculoskeletal anatomist) using the Dice similarity coefficient (DSC) and mean absolute surface distance (MASD) metrics. Results Accurate and precise bone segmentations were achieved with mean DSC of 0.98 and 0.93 for the humeral head and glenoid fossa, respectively. Mean DSC scores of 0.74 and 0.72 were obtained for the humeral and glenoid cartilage volumes, respectively. The manual interobserver reliability evaluated by DSC was 0.80 ± 0.03 and 0.76 ± 0.04 for the two cartilages, implying that the automated results were within an acceptable 10% difference. The MASD between the automatic and the corresponding manual cartilage segmentations was less than 0.4 mm (previous studies reported mean cartilage thickness of 1.3 mm). Conclusions This work shows the feasibility of volumetric segmentation and separation of the glenohumeral cartilages from MR images. To their knowledge, this is the first fully automated algorithm for volumetric segmentation of the individual glenohumeral cartilages from MR images. The approach was validated against manual segmentations from experienced analysts. In future work, the approach will be validated on imaging datasets acquired with various MR contrasts in patients.

Traditional shape learning of medical image data has been implemented via Principal Component Analysis (PCA). These PCA based statistical shape models batch process all shapes at once to generate a fixed model of shape variation as principal components, which may require significant computation resources for large number of shapes. This paper applies incremental PCA (IPCA) on a dataset of 728 surfaces (derived from magnetic resonance imaging examinations displaying the articulating bones of the knee joint) that can efficiently adapt to changes in training sets. After comparing the compactness and the accuracy of shape reconstruction of both batch PCA and IPCA models, our results show that IPCA produces a model comparable to batch PCA in terms of compactness and applicability to shape reconstruction, while requiring considerably shorter processing time and computer memory for computation.

The Discrete Fourier Transform (DFT) underpins the solution to many inverse problems commonly possessing missing or un-measured frequency information. This incomplete coverage of Fourier space always produces systematic artefacts called Ghosts. In this paper, a fast and exact method for de-convolving cyclic artefacts caused by missing slices of the DFT is presented. The slices discussed here originate from the exact partitioning of DFT space, under the projective Discrete Radon Transform, called the Discrete Fourier Slice Theorem. The method has a computational complexity of O(n log2 n) (where n = N^2) and is constructed from a new Finite Ghost theory. This theory is also shown to unify several aspects of work done on Ghosts over the past three decades. The paper concludes with a significant application to fast, exact, non-iterative image reconstruction from sets of discrete slices obtained for a limited range of projection angles., 10 pages, 18 figures (submitted to IEEE Image Proc.)

Accurate localization of the prostate and its surrounding tissue is essential in the treatment of prostate cancer. This paper presents a novel approach to fully automatically segment the prostate, including its seminal vesicles, within a few minutes of a magnetic resonance (MR) scan acquired without an endorectal coil. Such MR images are important in external beam radiation therapy, where using an endorectal coil is highly undesirable. The segmentation is obtained using a deformable model that is trained on-the-fly so that it is specific to the patient's scan. This case specific deformable model consists of a patient specific initialized triangulated surface and image feature model that are trained during its initialization. The image feature model is used to deform the initialized surface by template matching image features (via normalized cross-correlation) to the features of the scan. The resulting deformations are regularized over the surface via well established simple surface smoothing algorithms, which is then made anatomically valid via an optimized shape model. Mean and median Dice's similarity coefficients (DSCs) of 0.85 and 0.87 were achieved when segmenting 3T MR clinical scans of 50 patients. The median DSC result was equal to the inter-rater DSC and had a mean absolute surface error of 1.85 mm. The approach is showed to perform well near the apex and seminal vesicles of the prostate. © 1982-2012 IEEE.

Breast mass detection and segmentation are challenging tasks due to the fact that breast masses vary in size and appearance. In this work, we present a simultaneous detection and segmentation scheme for mammographic lesions that is constructed in a sifting architecture. It utilizes a novel region candidate selection approach and cascaded learning techniques to achieve state-of-the-art results while handling a high class imbalance. The region candidates are generated by a novel multi-scale morphological sifting (MMS) approach, where oriented linear structuring elements are used to sieve out the mass-like objects in mammograms including stellate patterns. This method can accurately segment masses of various shapes and sizes from the background tissue. To tackle the class imbalance problem, two different ensemble learning methods are utilized: a novel self-grown cascaded random forests (CasRFs) and the random under-sampling boost (RUSBoost). The CasRFs is designed to handle class imbalance adaptively using a probability-ranking based under-sampling approach, while RUSBoost uses a random under-sampling technique. This work is evaluated on two publicly available datasets: INbreast and DDSM BCRP. On INbreast, the proposed method achieves an average sensitivity of 0.90 with 0.9 false positives per image (FPI) using CasRFs and with 1.2 FPI using RUSBoost. On DDSM BCRP, the method yields a sensitivity of 0.81 with 3.1 FPI using CasRFs and with 2.9 FPI using RUSboost. The performance of the proposed method compares favorably to the state-of-the-art methods on both datasets, especially on highly spiculated lesions.

Automated segmentation of intervertebral discs (IVDs) from magnetic resonance imaging has the potential to enhance the efficiencies of radiological investigations of large clinical and research imaging datasets. This work presents an automated method for localization and 3D segmentation of IVDs that is applied to magnetic resonance imaging of the thoraco-lumbar spine as part of the segmentation challenge at the 3rd MICCAI Workshop & Challenge on Computational Methods and Clinical Applications for Spine Imaging - MICCAI–CSI2015. Our initialization method involves multi-atlas registration and a hierarchical conditional shape regression for localization of all imaged lumbar and thoracic discs, and active shape model based 3D segmentation. Comparisons between manual (ground truth) and automated segmentation of 105 disc volumes (T11/T12 - L5/S1) revealed a mean Dice score of \(0.896\,{\pm }\,0.024\) and mean absolute square distance of \(0.642\,{\pm }\,0.169\) mm. Our automated segmentation approach provided accurate segmentation of IVDs from turbo spine echo images which are highly competitive with leading state-of-the-art 3D segmentation techniques.

Purpose To validate automatic substitute computed tomography CT (sCT) scans generated from standard T2-weighted (T2w) magnetic resonance (MR) pelvic scans for MR-Sim prostate treatment planning. Patients and Methods A Siemens Skyra 3T MR imaging (MRI) scanner with laser bridge, flat couch, and pelvic coil mounts was used to scan 39 patients scheduled for external beam radiation therapy for localized prostate cancer. For sCT generation a whole-pelvis MRI scan (1.6 mm 3-dimensional isotropic T2w SPACE [Sampling Perfection with Application optimized Contrasts using different flip angle Evolution] sequence) was acquired. Three additional small field of view scans were acquired: T2w, T2*w, and T1w flip angle 80° for gold fiducials. Patients received a routine planning CT scan. Manual contouring of the prostate, rectum, bladder, and bones was performed independently on the CT and MR scans. Three experienced observers contoured each organ on MRI, allowing interobserver quantification. To generate a training database, each patient CT scan was coregistered to their whole-pelvis T2w using symmetric rigid registration and structure-guided deformable registration. A new multi-atlas local weighted voting method was used to generate automatic contours and sCT results. Results The mean error in Hounsfield units between the sCT and corresponding patient CT (within the body contour) was 0.6 ± 14.7 (mean ± 1 SD), with a mean absolute error of 40.5 ± 8.2 Hounsfield units. Automatic contouring results were very close to the expert interobserver level (Dice similarity coefficient): prostate 0.80 ± 0.08, bladder 0.86 ± 0.12, rectum 0.84 ± 0.06, bones 0.91 ± 0.03, and body 1.00 ± 0.003. The change in monitor units between the sCT-based plans relative to the gold standard CT plan for the same dose prescription was found to be 0.3% ± 0.8%. The 3-dimensional γ pass rate was 1.00 ± 0.00 (2 mm/2%). Conclusions The MR-Sim setup and automatic sCT generation methods using standard MR sequences generates realistic contours and electron densities for prostate cancer radiation therapy dose planning and digitally reconstructed radiograph generation.

We present a statistical shape model approach for automated segmentation of the proximal humerus and scapula with subsequent bone-cartilage interface (BCI) extraction from 3D magnetic resonance (MR) images of the shoulder region. Manual and automated bone segmentations from shoulder MR examinations from 25 healthy subjects acquired using steady-state free precession sequences were compared with the Dice similarity coefficient (DSC). The mean DSC scores between the manual and automated segmentations of the humerus and scapula bone volumes surrounding the BCI region were 0.926 ± 0.050 and 0.837 ± 0.059, respectively. The mean DSC values obtained for BCI extraction were 0.806 ± 0.133 for the humerus and 0.795 ± 0.117 for the scapula. The current model-based approach successfully provided automated bone segmentation and BCI extraction from MR images of the shoulder. In future work, this framework appears to provide a promising avenue for automated segmentation and quantitative analysis of cartilage in the glenohumeral joint.

Accurate segmentation of hip joint cartilage from magnetic resonance (MR) images offers opportunities for quantitative investigations of pathoanatomical conditions such as osteoarthritis. In this paper, we present a fully automatic scheme for the segmentation of the individual femoral and acetabular cartilage plates in the human hip joint from high-resolution 3D MR images. The developed scheme uses an improved optimal multi-object multi-surface graph search framework with an arc-weighted graph representation that incorporates prior morphological knowledge as a basis for segmentation of the individual femoral and acetabular cartilage plates despite weak or incomplete boundary interfaces. This automated scheme was validated against manual segmentations from 3D true fast imaging with steady-state precession (TrueFISP) MR examinations of the right hip joints in 52 asymptomatic volunteers. Compared with expert manual segmentations of the combined, femoral and acetabular cartilage volumes, the automatic scheme obtained mean (± standard deviation) Dice's similarity coefficients of 0.81 (± 0.03), 0.79 (± 0.03) and 0.72 (± 0.05). The corresponding mean absolute volume difference errors were 8.44% (± 6.36), 9.44% (± 7.19) and 9.05% (± 8.02). The mean absolute differences between manual and automated measures of cartilage thickness for femoral and acetabular cartilage plates were 0.13 mm (± 0.12) and 0.11 mm (± 0.11), respectively.

International audience; The discrete Fourier slice theorem is an important tool for signal processing, especially in the context of the exact reconstruction of an image from its projected views. This paper presents a digital reconstruction algorithm to recover a two dimensional (2-D) image from sets of discrete one dimensional (1-D) projected views. The proposed algorithm has the same computational complexity as the 2-D fast Fourier transform and remains robust to the addition of significant levels of noise. A mapping of discrete projections is constructed to allow aperiodic projections to be converted to projections that assume periodic image boundary conditions. Each remapped projection forms a 1-D slice of the 2-D Discrete Fourier Transform (DFT) that requires no interpolation. The discrete projection angles are selected so that the set of remapped 1-D slices exactly tile the 2-D DFT space. This permits direct and mathematically exact reconstruction of the image via the inverse DFT. The reconstructions are artefact free, except for projection inconsistencies that arise from any additive and remapped noise. We also present methods to generate compact sets of rational projection angles that exactly tile the 2-D DFT space. The improvement in noise suppression that comes with the reconstruction of larger sized images needs to be balanced against the corresponding increase in computation time.

Accurate bone segmentation in the hip joint region from magnetic resonance (MR) images can provide quantitative data for examining pathoanatomical conditions such as femoroacetabular impingement through to varying stages of osteoarthritis to monitor bone and associated cartilage morphometry. We evaluate two state-of-the-art methods (multi-atlas and active shape model (ASM) approaches) on bilateral MR images for automatic 3D bone segmentation in the hip region (proximal femur and innominate bone). Bilateral MR images of the hip joints were acquired at 3T from 30 volunteers. Image sequences included water-excitation dual echo stead state (FOV 38.6 × 24.1 cm, matrix 576 × 360, thickness 0.61 mm) in all subjects and multi-echo data image combination (FOV 37.6 × 23.5 cm, matrix 576 × 360, thickness 0.70 mm) for a subset of eight subjects. Following manual segmentation of femoral (head–neck, proximal-shaft) and innominate (ilium+ischium+pubis) bone, automated bone segmentation proceeded via two approaches: (1) multi-atlas segmentation incorporating non-rigid registration and (2) an advanced ASM-based scheme. Mean inter- and intra-rater reliability Dice's similarity coefficients (DSC) for manual segmentation of femoral and innominate bone were (0.970, 0.963) and (0.971, 0.965). Compared with manual data, mean DSC values for femoral and innominate bone volumes using automated multi-atlas and ASM-based methods were (0.950, 0.922) and (0.946, 0.917), respectively. Both approaches delivered accurate (high DSC values) segmentation results; notably, ASM data were generated in substantially less computational time (12 min versus 10 h). Both automated algorithms provided accurate 3D bone volumetric descriptions for MR-based measures in the hip region. The highly computational efficient ASM-based approach is more likely suitable for future clinical applications such as extracting bone–cartilage interfaces for potential cartilage segmentation.

International audience; We present algorithms to reconstruct images from minimal sets of discrete Mojette projections using direct back-projection (DBP) with various forms of correction. This paper extends previous work on discrete projection inversion by Servières et al [1, 2, 3]. The number of Mojette projections needed for exact inversion by DBP (EI-DBP) scales as O(N²). A new form of discrete interpolation is developed to expand the point spread function (PSF) of a minimal (Katz-sufficient) set of discrete projections to encompass new directions and thus augment the size of the reconstruction region to which EI-DBP applies. Additionally, we propose a Fourier domain filter for Mojette back-projection that is built from the discrete PSF of the given Mojette angle set and the autocorrelation function of the image domain. These discrete reconstruction methods are targeted for use with noisy sets of real projection data.

Deformable models incorporating shape priors have proved to be a successful approach in segmenting anatomical regions and specific structures in medical images. This paper introduces weighted shape priors for deformable models in the context of 3D magnetic resonance (MR) image segmentation of the bony elements of the human hip joint. The fully automated approach allows the focusing of the shape model energy to a priori selected anatomical structures or regions of clinical interest by preferentially ordering the shape representation (or eigen-modes) within this type of model to the highly weighted areas. This focused shape model improves accuracy of the shape constraints in those regions compared to standard approaches. The proposed method achieved femoral head and acetabular bone segmentation mean absolute surface distance errors of 0.55±0.18mm and 0.75±0.20mm respectively in 35 3D unilateral MR datasets from 25 subjects acquired at 3T with different limited field of views for individual bony components of the hip joint.

This paper presents a validation study on the application of a novel interslice interpolation technique for musculoskeletal structure segmentation of articulated joints and muscles on human magnetic resonance imaging data. The interpolation technique is based on morphological shape-based interpolation combined with intensity based voxel classification. Shape-based interpolation in the absence of the original intensity image has been investigated intensively. However, in some applications of medical image analysis, the intensity image of the slice to be interpolated is available. For example, when manual segmentation is conducted on selected slices, the segmentation on those unselected slices can be obtained by interpolation. We proposed a two- step interpolation method to utilize both the shape information in the manual segmentation and local intensity information in the image. The method was tested on segmentations of knee, hip and shoulder joint bones and hamstring muscles. The results were compared with two existing interpolation methods. Based on the calculated Dice similarity coefficient and normalized error rate, the proposed method outperformed the other two methods.

The accurate segmentation of the bone from Magnetic Resonance (MR) images of the hip is important for clinical studies and drug trials into conditions like Osteoarthritis. This paper presents an automatic segmentation scheme that utilises a deformable model robust to different field of views by training shape priors from partial and full bone surfaces. The deformable model with these priors were used to segment the hip joint within 16 unilateral 3T MR images having different field of views, so that parts of the model outside the image could be ignored fully without affecting the accuracy of the segmentation within the image. Mean and median Dice's Similarity Coefficients of 0.91 & 0.92 for the femur and 0.86 & 0.88 for one half of the pelvis were obtained using a leave-one-out approach.