scholarly journals Meningioma Segmentation in T1-Weighted MRI Leveraging Global Context and Attention Mechanisms

2021 ◽  
Vol 1 ◽  
Author(s):  
David Bouget ◽  
André Pedersen ◽  
Sayied Abdol Mohieb Hosainey ◽  
Ole Solheim ◽  
Ingerid Reinertsen
Keyword(s):  
Three Dimensional ◽  
Specific Treatment ◽  
Primary Brain Tumor ◽  
University Hospital ◽  
Patient Specific ◽  
Entire Volume ◽  
Global Context ◽  
Multi Scale ◽  
Magnetic Resonance Imaging Mri ◽  
The Impact

Purpose: Meningiomas are the most common type of primary brain tumor, accounting for ~30% of all brain tumors. A substantial number of these tumors are never surgically removed but rather monitored over time. Automatic and precise meningioma segmentation is, therefore, beneficial to enable reliable growth estimation and patient-specific treatment planning.Methods: In this study, we propose the inclusion of attention mechanisms on top of a U-Net architecture used as backbone: (i) Attention-gated U-Net (AGUNet) and (ii) Dual Attention U-Net (DAUNet), using a three-dimensional (3D) magnetic resonance imaging (MRI) volume as input. Attention has the potential to leverage the global context and identify features' relationships across the entire volume. To limit spatial resolution degradation and loss of detail inherent to encoder–decoder architectures, we studied the impact of multi-scale input and deep supervision components. The proposed architectures are trainable end-to-end and each concept can be seamlessly disabled for ablation studies.Results: The validation studies were performed using a five-fold cross-validation over 600 T1-weighted MRI volumes from St. Olavs Hospital, Trondheim University Hospital, Norway. Models were evaluated based on segmentation, detection, and speed performances, and results are reported patient-wise after averaging across all folds. For the best-performing architecture, an average Dice score of 81.6% was reached for an F1-score of 95.6%. With an almost perfect precision of 98%, meningiomas smaller than 3 ml were occasionally missed hence reaching an overall recall of 93%.Conclusion: Leveraging global context from a 3D MRI volume provided the best performances, even if the native volume resolution could not be processed directly due to current GPU memory limitations. Overall, near-perfect detection was achieved for meningiomas larger than 3 ml, which is relevant for clinical use. In the future, the use of multi-scale designs and refinement networks should be further investigated. A larger number of cases with meningiomas below 3 ml might also be needed to improve the performance for the smallest tumors.

scholarly journals Age- and sex-related changes of the volume of maxillary sinuses quantified via cone beam computed tomography

2021 ◽  
Vol 10 (14) ◽  
pp. e312101422220
Author(s):  
Lucas Eigi Borges Tanaka ◽  
Ademir Franco ◽  
Rafael Ferreira Abib ◽  
Luiz Roberto Coutinho Manhães-Junior ◽  
Sergio Lucio Pereira de Castro Lopes
Keyword(s):  
Computed Tomography ◽  
Cone Beam Computed Tomography ◽  
Three Dimensional ◽  
Specific Treatment ◽  
Cone Beam ◽  
Patient Specific ◽  
Sample Collection ◽  
Left And Right ◽  
Age And Sex ◽  
Maxillary Sinuses

Anatomical studies found in cone beam computed tomography (CBCT) an optimal resource for the three-dimensional (3D) assessment of the head and neck. When it comes to the maxillary sinuses, CBCT enables a life-size reliable volumetric analysis. This study aimed to assess the age and sex-related changes of the maxillary sinuses using volumetric CBCT analysis. The sample consisted of CBCT scans of 112 male (n = 57) and female (n = 55) individuals (224 maxillary sinuses) distributed in 5 age categories: 20 |— 30, 31 |— 40, 41 |— 50, 51 |— 60 and > 60 years. Image acquisition was accomplished with the i-CAT Next Generation device set with voxel size of 0.25 mm and field of view that included the maxillary sinuses (retrospective sample collection from an existing database). Image segmentation was performed in itk-SNAP (www.itksnap.org) software. The volume (mm3) of the segmented sinuses was quantified and compared pairwise based on side (left and right), sex (male and female) and age (five groups). Differences between left and right sides volume were not statistically significant (p > 0.05). The mean volume of maxillary sinuses in males was 22% higher than females (p = 0.0001). Volumetric differences were not statistically significant between age categories for males and females (p > 0.05). The discriminant power of sinuses’ volume may support customized and patient-specific treatment planning based on sex.

scholarly journals Impact of Inflow Boundary Conditions on the Calculation of CT-Based FFR

Fluids ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. 60 ◽  
Author(s):  
Ernest Lo ◽  
Leon Menezes ◽  
Ryo Torii
Keyword(s):  
Boundary Conditions ◽  
Coronary Arteries ◽  
Three Dimensional ◽  
Patient Specific ◽  
Fractional Flow ◽  
Anatomical Models ◽  
Diastolic Phase ◽  
Flow Reserve ◽  
Population Average ◽  
The Impact

Background: Calculation of fractional flow reserve (FFR) using computed tomography (CT)-based 3D anatomical models and computational fluid dynamics (CFD) has become a common method to non-invasively assess the functional severity of atherosclerotic narrowing in coronary arteries. We examined the impact of various inflow boundary conditions on computation of FFR to shed light on the requirements for inflow boundary conditions to ensure model representation. Methods: Three-dimensional anatomical models of coronary arteries for four patients with mild to severe stenosis were reconstructed from CT images. FFR and its commonly-used alternatives were derived using the models and CFD. A combination of four types of inflow boundary conditions (BC) was employed: pulsatile, steady, patient-specific and population average. Results: The maximum difference of FFR between pulsatile and steady inflow conditions was 0.02 (2.4%), approximately at a level similar to a reported uncertainty level of clinical FFR measurement (3–4%). The flow with steady BC appeared to represent well the diastolic phase of pulsatile flow, where FFR is measured. Though the difference between patient-specific and population average BCs affected the flow more, the maximum discrepancy of FFR was 0.07 (8.3%), despite the patient-specific inflow of one patient being nearly twice as the population average. Conclusions: In the patients investigated, the type of inflow boundary condition, especially flow pulsatility, does not have a significant impact on computed FFRs in narrowed coronary arteries.

The impact of metal transport processes on bioavailability of free and complex metal ions in methanogenic granular sludge

2012 ◽  
Vol 65 (10) ◽  
pp. 1875-1881 ◽  
Author(s):  
Jan Bartacek ◽  
Fernando G. Fermoso ◽  
Frank Vergeldt ◽  
Edo Gerkema ◽  
Josef Maca ◽  
...  
Keyword(s):  
Granular Sludge ◽  
Major Effect ◽  
Transport Processes ◽  
Metal Species ◽  
Anaerobic Sludge ◽  
Entire Volume ◽  
Methanogenic Activity ◽  
Magnetic Resonance Imaging Mri ◽  
Anaerobic Sludge Blanket ◽  
The Impact

Bioavailability of metals in anaerobic granular sludge has been extensively studied, because it can have a major effect on metal limitation and metal toxicity to microorganisms present in the sludge. Bioavailability of metals can be manipulated by bonding to complexing molecules such as ethylenediaminetetraacetate (EDTA) or diethylenetriaminepentaacetate (DTPA). It has been shown that although the stimulating effect of the complexed metal species (e.g. [CoEDTA]2−) is very fast, it is not sustainable when applied to metal-limited continuously operated reactors. The present paper describes transport phenomena taking place inside single methanogenic granules when the granules are exposed to various metal species. This was done using magnetic resonance imaging (MRI). The MRI results were subsequently related to technological observations such as changes in methanogenic activity upon cobalt injection into cobalt-limited up-flow anaerobic sludge blanket (UASB) reactors. It was shown that transport of complexed metal species is fast (minutes to tens of minutes) and complexed metal can therefore quickly reach the entire volume of the granule. Free metal species tend to interact with the granular matrix resulting in slower transport (tens of minutes to hours) but higher final metal concentrations.

scholarly journals Patient-Specific Aortic Phantom With Tunable Compliance

2019 ◽  
Vol 2 (4) ◽  
Author(s):  
Antonio Gallarello ◽  
Andrea Palombi ◽  
Giacomo Annio ◽  
Shervanthi Homer-Vanniasinkam ◽  
Elena De Momi ◽  
...  
Keyword(s):  
Aortic Arch ◽  
Computational Models ◽  
Three Dimensional ◽  
Complex Interventions ◽  
Patient Specific ◽  
Arch Model ◽  
Magnetic Resonance Imaging Mri ◽  
Variable Wall ◽  
Silicone Model

Abstract Validation of computational models using in vitro phantoms is a nontrivial task, especially in the replication of the mechanical properties of the vessel walls, which varies with age and pathophysiological state. In this paper, we present a novel aortic phantom reconstructed from patient-specific data with variable wall compliance that can be tuned without recreating the phantom. The three-dimensional (3D) geometry of an aortic arch was retrieved from a computed tomography angiography scan. A rubber-like silicone phantom was manufactured and connected to a compliance chamber in order to tune its compliance. A lumped resistance was also coupled with the system. The compliance of the aortic arch model was validated using the Young's modulus and characterized further with respect to clinically relevant indicators. The silicone model demonstrates that compliance can be finely tuned with this system under pulsatile flow conditions. The phantom replicated values of compliance in the physiological range. Both, the pressure curves and the asymmetrical behavior of the expansion, are in agreement with the literature. This novel design approach allows obtaining for the first time a phantom with tunable compliance. Vascular phantoms designed and developed with the methodology proposed in this paper have high potential to be used in diverse conditions. Applications include training of physicians, pre-operative trials for complex interventions, testing of medical devices for cardiovascular diseases (CVDs), and comparative Magnetic-resonance-imaging (MRI)-based computational studies.

Simulation of personalised haemodynamics by various mounting positions of a prosthetic valve using computational fluid dynamics

2019 ◽  
Vol 64 (2) ◽  
pp. 147-156 ◽  
Author(s):  
Markus Bongert ◽  
Marius Geller ◽  
Werner Pennekamp ◽  
Volkmar Nicolas
Keyword(s):  
Blood Flow ◽  
Aortic Valve ◽  
Three Dimensional ◽  
Maximum Velocity ◽  
Heart Valve Disease ◽  
Patient Specific ◽  
Opening Angle ◽  
The European Union ◽  
Prosthetic Valves ◽  
Magnetic Resonance Imaging Mri

Abstract Diseases of the cardiovascular system account for nearly 42% of all deaths in the European Union. In Germany, approximately 12,000 patients receive surgical replacement of the aortic valve due to heart valve disease alone each year. A three-dimensional (3D) numerical model based on patient-specific anatomy derived from four-dimensional (4D) magnetic resonance imaging (MRI) data was developed to investigate preoperatively the flow-induced impact of mounting positions of aortic prosthetic valves to select the best orientation for individual patients. Systematic steady-state analysis of blood flow for different rotational mounting positions of the valve is only possible using a virtual patient model. A maximum velocity of 1 m/s was used as an inlet boundary condition, because the opening angle of the valve is at its largest at this velocity. For a comparative serial examination, it is important to define the standardised general requirements to avoid impacts other than the rotated implantation of the prosthetic aortic valve. In this study, a uniform velocity profile at the inlet for the inflow of the aortic valve and the real aortic anatomy were chosen for all simulations. An iterative process, with the weighted parameters flow resistance (1), shear stress (2) and velocity (3), was necessary to determine the best rotated orientation. Blood flow was optimal at a 45° rotation from the standard implantation orientation, which will offer a supply to the coronary arteries.

scholarly journals Virtual surgeries in patients with congenital heart disease: a multi-scale modelling test case

2011 ◽  
Vol 369 (1954) ◽  
pp. 4316-4330 ◽  
Author(s):  
A. Baretta ◽  
C. Corsini ◽  
W. Yang ◽  
I. E. Vignon-Clementel ◽  
A. L. Marsden ◽  
...  
Keyword(s):  
Boundary Conditions ◽  
Congenital Heart ◽  
Closed Loop ◽  
Three Dimensional ◽  
Scale Model ◽  
Patient Specific ◽  
Loop Model ◽  
Multi Scale ◽  
Venae Cavae ◽  
Lumped Parameter

The objective of this work is to perform a virtual planning of surgical repairs in patients with congenital heart diseases—to test the predictive capability of a closed-loop multi-scale model. As a first step, we reproduced the pre-operative state of a specific patient with a univentricular circulation and a bidirectional cavopulmonary anastomosis (BCPA), starting from the patient's clinical data. Namely, by adopting a closed-loop multi-scale approach, the boundary conditions at the inlet and outlet sections of the three-dimensional model were automatically calculated by a lumped parameter network. Successively, we simulated three alternative surgical designs of the total cavopulmonary connection (TCPC). In particular, a T-junction of the venae cavae to the pulmonary arteries (T-TCPC), a design with an offset between the venae cavae (O-TCPC) and a Y-graft design (Y-TCPC) were compared. A multi-scale closed-loop model consisting of a lumped parameter network representing the whole circulation and a patient-specific three-dimensional finite volume model of the BCPA with detailed pulmonary anatomy was built. The three TCPC alternatives were investigated in terms of energetics and haemodynamics. Effects of exercise were also investigated. Results showed that the pre-operative caval flows should not be used as boundary conditions in post-operative simulations owing to changes in the flow waveforms post-operatively. The multi-scale approach is a possible solution to overcome this incongruence. Power losses of the Y-TCPC were lower than all other TCPC models both at rest and under exercise conditions and it distributed the inferior vena cava flow evenly to both lungs. Further work is needed to correlate results from these simulations with clinical outcomes.

scholarly journals Random and systematic set-up errors in three-dimensional conformal radiotherapy – impact on planning target volume margins: the experience of the Radiation Oncology Centre of Sassari

2013 ◽  
Vol 13 (2) ◽  
pp. 166-179
Author(s):  
Matteo Tamponi ◽  
Angela Poggiu ◽  
Maria F. Dedola ◽  
Rossella Madeddu ◽  
Antonella Carnevale ◽  
...  
Keyword(s):  
Planning Target Volume ◽  
Three Dimensional ◽  
Conformal Radiotherapy ◽  
Target Volume ◽  
Patient Specific ◽  
Geometric Uncertainties ◽  
Three Dimensional Conformal Radiotherapy ◽  
Set Up ◽  
Oncology Centre ◽  
The Impact

AbstractPurposeGeometric uncertainties limit the accuracy of three-dimensional conformal radiotherapy treatments. This study aims to evaluate typical random and systematic set-up errors and analyse the impact of no action level (NAL) correction protocol on systematic set-up errors and clinical target volume (CTV)–planning target volume (PTV) margins.Materials and methodsA total 668 pairs of orthogonal electronic portal images were compared with digitally reconstructed radiographs from computed tomography planning scans for 100 patients consecutively treated during 2011. Patients were divided into groups depending on the treated anatomical region. Patient-specific and population random and systematic set-up errors were calculated. Impact of application of NAL correction protocol on systematic set-up errors and CTV–PTV expansions were evaluated.ResultsPopulation set-up errors resulted from about 1 mm in head and neck to 2–3 mm in prostate, rectum, lung, breast and gynaecological districts. Patient-specific systematic set-up errors were higher for breast and gynaecological districts and application of NAL correction protocol gave significant reductions, even higher than 30%. Calculated CTV–PTV margins ranged from 10 mm on left–right direction for prostate to 20 mm on superior–inferior direction for lung.ConclusionsSet-up errors resulted reasonably controlled and application of NAL correction protocol could further improve the level of accuracy. However, the NAL application alone did not seem to add any substantial benefit on CTV–PTV total margins without the adoption of corrective strategies to reduce other important uncertainties limiting accuracy of three-dimensional conformal radiotherapy.

Fabrication of 3D Models for Microtia Reconstruction Using Smartphone-Based Technology

2021 ◽  
pp. 000348942110240
Author(s):  
Peng You ◽  
Yi-Chun Carol Liu ◽  
Rodrigo C. Silva
Keyword(s):  
3D Model ◽  
Low Cost ◽  
Tertiary Care ◽  
Three Dimensional ◽  
Basic Research ◽  
3D Models ◽  
University Hospital ◽  
Patient Specific ◽  
Surface Scanning ◽  
Barrier To Entry

Objective: Microtia reconstruction is technically challenging due to the intricate contours of the ear. It is common practice to use a two-dimensional tracing of the patient’s normal ear as a template for the reconstruction of the affected side. Recent advances in three-dimensional (3D) surface scanning and printing have expanded the ability to create surgical models preoperatively. This study aims to describe a simple and affordable process to fabricate patient-specific 3D ear models for use in the operating room. Study design: Applied basic research on a novel 3D optical scanning and fabrication pathway for microtia reconstruction. Setting: Tertiary care university hospital. Methods: Optical surface scanning of the patient’s normal ear was completed using a smartphone with facial recognition capability. The Heges application used the phone’s camera to capture the 3D image. The 3D model was digitally isolated and mirrored using the Meshmixer software and printed with a 3D printer (MonopriceTM Select Mini V2) using polylactic acid filaments. Results: The 3D model of the ear served as a helpful intraoperative reference and an adjunct to the traditional 2D template. Collectively, time for imaging acquisition, editing, and fabrication was approximately 3.5 hours. The upfront cost was around $210, and the recurring cost was approximately $0.35 per ear model. Conclusion: A novel, low-cost approach to fabricate customized 3D models of the ear is introduced. It is feasible to create individualized 3D models using currently available consumer technology. The low barrier to entry raises the possibility for clinicians to incorporate 3D printing into various clinical applications.

Impact of Patient-Specific Inflow Velocity Profile on Hemodynamics of the Thoracic Aorta

2017 ◽  
Vol 140 (1) ◽  
Author(s):  
Pouya Youssefi ◽  
Alberto Gomez ◽  
Christopher Arthurs ◽  
Rajan Sharma ◽  
Marjan Jahangiri ◽  
...  
Keyword(s):  
Aortic Valve ◽  
Thoracic Aorta ◽  
Complex Structure ◽  
Three Dimensional ◽  
Velocity Profiles ◽  
Patient Specific ◽  
Inflow Velocity ◽  
Valvular Stenosis ◽  
Computational Fluid Dynamics Cfd ◽  
Magnetic Resonance Imaging Mri

Computational fluid dynamics (CFD) provides a noninvasive method to functionally assess aortic hemodynamics. The thoracic aorta has an anatomically complex inlet comprising of the aortic valve and root, which is highly prone to different morphologies and pathologies. We investigated the effect of using patient-specific (PS) inflow velocity profiles compared to idealized profiles based on the patient's flow waveform. A healthy 31 yo with a normally functioning tricuspid aortic valve (subject A), and a 52 yo with a bicuspid aortic valve (BAV), aortic valvular stenosis, and dilated ascending aorta (subject B) were studied. Subjects underwent MR angiography to image and reconstruct three-dimensional (3D) geometric models of the thoracic aorta. Flow-magnetic resonance imaging (MRI) was acquired above the aortic valve and used to extract the patient-specific velocity profiles. Subject B's eccentric asymmetrical inflow profile led to highly complex velocity patterns, which were not replicated by the idealized velocity profiles. Despite having identical flow rates, the idealized inflow profiles displayed significantly different peak and radial velocities. Subject A's results showed some similarity between PS and parabolic inflow profiles; however, other parameters such as Flowasymmetry were significantly different. Idealized inflow velocity profiles significantly alter velocity patterns and produce inaccurate hemodynamic assessments in the thoracic aorta. The complex structure of the aortic valve and its predisposition to pathological change means the inflow into the thoracic aorta can be highly variable. CFD analysis of the thoracic aorta needs to utilize fully PS inflow boundary conditions in order to produce truly meaningful results.

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