Vascular flow simulations using SimVascular and OpenFOAM (Preprint)

2021 ◽  
Author(s):  
Swetha Yogeswaran ◽  
Fei Liu

UNSTRUCTURED Applications of computational fluid dynamics (CFD) techniques to aid in the diagnosis and treatment of cardiovascular disease have entered the research domain in recent years, due to their ability to provide valuable patient-specific information without risks associated with highly invasive procedures. SimVascular is an open-source software which allows streamlined processing and CFD blood flow analysis of medical imaging data. OpenFOAM is a proven open-source software which allows for versatile modeling of various fluid dynamics phenomena. In this study, both SimVascular and OpenFOAM simulations are set up with identical computational mesh, similar numerical schemes, boundary conditions, and material properties, to model blood flow in the coronary artery of a 10 year old patient with Coarctation of the Aorta (CoA) who underwent end-to-side anastomosis. Difference in the flow fields such as flow rate, pressure, vorticity, and wall shear stress between SimVascular and OpenFOAM are analyzed. Similar results are obtained in both simulations up to a certain model time, before the results become drastically different. Both the similarities and differences are documented and discussed.

2021 ◽  
Author(s):  
Swetha Yogeswaran ◽  
Fei Liu

AbstractApplications of computational fluid dynamics (CFD) techniques to aid in the diagnosis and treatment of cardiovascular disease have entered the research domain in recent years, due to their ability to provide valuable patient-specific information without risks associated with highly invasive procedures. SimVascular [1] [2] is an open-source software which allows streamlined processing and CFD blood flow analysis of medical imaging data. OpenFOAM [3] is a proven open-source software which allows for versatile modeling of various fluid dynamics phenomena. In this study, both SimVascular and OpenFOAM simulations are set up with identical computational mesh, similar numerical schemes, boundary conditions, and material properties, to model blood flow in the coronary artery of a 10 year old patient with Coarctation of the Aorta (CoA) who underwent end-to-side anastomosis. Difference in the flow fields such as flow rate, pressure, vorticity, and wall shear stress between SimVascular and OpenFOAM are analyzed. Similar results are obtained in both simulations up to a certain model time, before the results become drastically different. Both the similarities and differences are documented and discussed.


2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
L Swanson ◽  
B Owen ◽  
A Revell ◽  
M Ngoepe ◽  
A Keshmiri ◽  
...  

Abstract Background Tetralogy of Fallot (ToF) and coarctation of the aorta (CoA) each constitute approximately 7% of congenital heart disease (CHD) births worldwide. Compared to developed countries, developing countries have a disparate level of access to prompt diagnosis and treatment for these diseases. Computational fluid dynamics (CFD) approaches implemented on routinely available non-invasive imaging data may yield low-cost improvements to the management of these patients. Purpose The purpose of this research is to develop a patient-specific computational pipeline that allows the modelling of blood flow in diseased arteries of patients suffering from ToF and CoA. The project aims to prove the feasible use of broadly available imaging techniques - CT angiograms (CTA) and echocardiographs (echo) - for achieving this in low-to-middle income countries. The capability of the pipeline will be demonstrated through a qualitative study of the effects of different systemic to pulmonary shunt configurations used in the palliative treatment of ToF. In addition, the effects of idealised stent configurations on the blood flow through the aorta of a patient with CoA will be studied. Methods A retrospective search through the hospital database was conducted to select suitable CTA data for a CoA and ToF case. Data for patient A, a five-month-old child with typical CoA, and patient B, a twelve-month-old child with typical ToF who had a central shunt in place, was found. Echo data was obtained for patient A through an investigation protocol which focused on CFD application whereas there was no echo data available for patient B. As a result, idealised volume flow rate data was implemented for patient B. Geometries for patient A and patient B were extracted and volume discretisation was implemented for grid independence testing. The Navier-Stokes governing equations for fluid flow were solved using the open source software, OpenFOAM, for the transient case where inlet volume flow rate was defined for four cardiac cycles. Figure 1 shows key features of the flow in the shunt and pulmonary branches (A), the aortic arch (B), the inlet at the ascending aorta (C) and the descending aorta (D) for the geometry extracted from the data set of patient B. Figure 1. Key flow features of patient B Results and discussion We have implemented CFD models which are able to qualitatively assess the favourable or unfavourable impact of different approaches to ToF and CoA repairs on the characteristics of blood flow in the aorta and pulmonary arteries. An echo investigation protocol has been developed and successfully applied. CTA studies have been shown as feasible sources of geometry data in spite of the restriction on quality by the important requirement for low doses of radiation in paediatric patients. This project represents progress towards an advanced tool that may be broadly implemented in both well-resourced and minimally-resourced hospitals. Acknowledgement/Funding National Research Fund, British Heart Foundation, Newton Fund (UK MRC, South African Medical Research Council), University of Cape Town


Author(s):  
Jonathan Shapey ◽  
Thomas Dowrick ◽  
Rémi Delaunay ◽  
Eleanor C. Mackle ◽  
Stephen Thompson ◽  
...  

Abstract Purpose Image-guided surgery (IGS) is an integral part of modern neuro-oncology surgery. Navigated ultrasound provides the surgeon with reconstructed views of ultrasound data, but no commercial system presently permits its integration with other essential non-imaging-based intraoperative monitoring modalities such as intraoperative neuromonitoring. Such a system would be particularly useful in skull base neurosurgery. Methods We established functional and technical requirements of an integrated multi-modality IGS system tailored for skull base surgery with the ability to incorporate: (1) preoperative MRI data and associated 3D volume reconstructions, (2) real-time intraoperative neurophysiological data and (3) live reconstructed 3D ultrasound. We created an open-source software platform to integrate with readily available commercial hardware. We tested the accuracy of the system’s ultrasound navigation and reconstruction using a polyvinyl alcohol phantom model and simulated the use of the complete navigation system in a clinical operating room using a patient-specific phantom model. Results Experimental validation of the system’s navigated ultrasound component demonstrated accuracy of $$<4.5\,\hbox {mm}$$ < 4.5 mm and a frame rate of 25 frames per second. Clinical simulation confirmed that system assembly was straightforward, could be achieved in a clinically acceptable time of $$<15\,\hbox {min}$$ < 15 min and performed with a clinically acceptable level of accuracy. Conclusion We present an integrated open-source research platform for multi-modality IGS. The present prototype system was tailored for neurosurgery and met all minimum design requirements focused on skull base surgery. Future work aims to optimise the system further by addressing the remaining target requirements.


PRILOZI ◽  
2014 ◽  
Vol 35 (3) ◽  
pp. 51-55
Author(s):  
Zoran Zdravkovski

AbstractThe development and availability of personal computers and software as well as printing techniques in the last twenty years have made a profound change in the publication of scientific journals. Additionally, the Internet in the last decade has revolutionized the publication process to the point of changing the basic paradigm of printed journals. The Macedonian Journal of Chemistry and Chemical Engineering in its 40-year history has adopted and adapted to all these transformations. In order to keep up with the inevitable changes, as editor-in-chief I felt my responsibility was to introduce an electronic editorial managing of the journal. The choice was between commercial and open source platforms, and because of the limited funding of the journal we chose the latter. We decided on Open Journal Systems, which provided online submission and management of all content, had flexible configuration - requirements, sections, review process, etc., had options for comprehensive indexing, offered various reading tools, had email notification and commenting ability for readers, had an option for thesis abstracts and was installed locally. However, since there is limited support it requires a moderate computer knowledge/skills and effort in order to set up. Overall, it is an excellent editorial platform and a convenient solution for journals with a low budget or journals that do not want to spend their resources on commercial platforms or simply support the idea of open source software.


Author(s):  
Victor Hugo Hidalgo Diaz ◽  
XianWu Luo ◽  
RenFang Huang ◽  
Edgar Cando

Though commercial CFD codes are widely used in flow analysis, but there are free/open source programs which have been applying for computational fluid dynamics. An open source software makes it possible to customize the solver according to the flow features. In the present paper, cavitating flows over 2D NACA66 hydrofoil were simulated based on open source software, where SALOME is used for mesh generation, OpenFOAM for flow solution under Debian GNU/Linux operating system. The results show the simulated cavitating flow characteristics such as cavity revolution, vortex shedding, cavitation induced pressure vibrations, etc. are validated by experiments and results obtained from proprietary software as Ansys Fluent. Thus, the proposed numerical methods based on open source platform are suitable for flow simulations, even for depicting the complicated physics of cavitation.


2017 ◽  
Vol 10 (3) ◽  
pp. 290-296 ◽  
Author(s):  
P Berg ◽  
S Saalfeld ◽  
S Voß ◽  
T Redel ◽  
B Preim ◽  
...  

BackgroundComputational fluid dynamics (CFD) blood flow predictions in intracranial aneurysms promise great potential to reveal patient-specific flow structures. Since the workflow from image acquisition to the final result includes various processing steps, quantifications of the individual introduced potential error sources are required.MethodsThree-dimensional (3D) reconstruction of the acquired imaging data as input to 3D model generation was evaluated. Six different reconstruction modes for 3D digital subtraction angiography (DSA) acquisitions were applied to eight patient-specific aneurysms. Segmentations were extracted to compare the 3D luminal surfaces. Time-dependent CFD simulations were carried out in all 48 configurations to assess the velocity and wall shear stress (WSS) variability due to the choice of reconstruction kernel.ResultsAll kernels yielded good segmentation agreement in the parent artery; deviations of the luminal surface were present at the aneurysm neck (up to 34.18%) and in distal or perforating arteries. Observations included pseudostenoses as well as noisy surfaces, depending on the selected reconstruction kernel. Consequently, the hemodynamic predictions show a mean SD of 11.09% for the aneurysm neck inflow rate, 5.07% for the centerline-based velocity magnitude, and 17.83%/9.53% for the mean/max aneurysmal WSS, respectively. In particular, vessel sections distal to the aneurysms yielded stronger variations of the CFD values.ConclusionsThe choice of reconstruction kernel for DSA data influences the segmentation result, especially for small arteries. Therefore, if precise morphology measurements or blood flow descriptions are desired, a specific reconstruction setting is required. Furthermore, research groups should be encouraged to denominate the kernel types used in future hemodynamic studies.


2012 ◽  
Vol 2012 ◽  
pp. 1-24 ◽  
Author(s):  
Jürgen Endres ◽  
Markus Kowarschik ◽  
Thomas Redel ◽  
Puneet Sharma ◽  
Viorel Mihalef ◽  
...  

Increasing interest is drawn on hemodynamic parameters for classifying the risk of rupture as well as treatment planning of cerebral aneurysms. A proposed method to obtain quantities such as wall shear stress, pressure, and blood flow velocity is to numerically simulate the blood flow using computational fluid dynamics (CFD) methods. For the validation of those calculated quantities, virtually generated angiograms, based on the CFD results, are increasingly used for a subsequent comparison with real, acquired angiograms. For the generation of virtual angiograms, several patient-specific parameters have to be incorporated to obtain virtual angiograms which match the acquired angiograms as best as possible. For this purpose, a workflow is presented and demonstrated involving multiple phantom and patient cases.


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