Predicting Strokes With HPC

By Nicole Hemsoth

May 12, 2006

A professor at the University of Houston and his research students are working with physicians and scientists at the Methodist Neurological Institute on new technology to help identify which brain aneurysms are at highest risk of rupture and could cause a stroke.

Improving treatment of cerebral aneurysms, which are ballooning weak spots in the wall of a blood vessel in the brain, is at the center of this joint research. The goal of their study is to develop a fully-integrated computational medical tool that will be useful in helping to select patients for treatment whose aneurysms are most likely to rupture.

Ralph Metcalfe, a mechanical engineering professor at UH and deputy director of the UH biomedical engineering program and his graduate student, Aishwarya Mantha, work on this project with a Methodist team consisting of Drs. Charles Strother and Goetz Benndorf, interventional neuroradiologists, and Christof Karmonik, a researcher at the Methodist Hospital Research Institute.

Using computer simulations of blood flow in realistic geometric models of aneurysms, some blood flow characteristics have been identified that may contribute to aneurysm formation. These findings are described in a paper titled “Hemodynamics in a Cerebral Artery Before and After the Formation of an Aneurysm,” appearing in the May issue of the American Journal of Neuroradiology, a scientific journal that publishes original articles dealing with the clinical imaging, endovascular therapy and basic science of the central and peripheral nervous system.

“According to the American Association of Neurological Surgeons, cerebral aneurysms affect up to six percent of the U.S. adult population,” Metcalfe said. “Most aneurysms don't rupture, but if they do, the results are fatal in about 50 percent of the cases. The question is how to predict who is most at risk.”

Since treatment of aneurysms is associated with some risk, Metcalfe's group and his Methodist colleagues are trying to develop a better method of identifying which aneurysms are most vulnerable for rupture. Once these patients are identified, physicians can then determine the best course of medical treatment, using existing technologies and best medical practices.

“One of the key points is that aneurysms don't seem to form randomly,” Metcalfe said. “They do seem to form at locations that are associated with the fluctuations in the flow of blood, leading to the question of what it is about the flow of blood that tends to correlate with the formation of aneurysms.”

The Methodist researchers acquire 3-D images of the intracranial vascular system by injecting dye into the vessels and rotating an X-ray tube around the patient's head, a technique that has become a standard for high-quality vascular imaging in this institution.

By using this geometric and blood flow data taken from a specific patient's clinical profile, Metcalfe's team can perform simulations in their computers of blood flow in that patient's arteries using existing computational fluid dynamics programs in novel applications. This is similar to the way that an aeronautical engineer would study the design of an airplane on a computer or in a wind tunnel. Strother and his colleagues at Methodist anticipate that this process will help researchers better understand how aneurysms form and ultimately discover ways to prevent strokes and death from this common disorder.

“We can't look at a person and tell the likelihood that an aneurysm will rupture,” Strother said. “But we do know that force and stresses created by blood flow produces aneurysms. Our hope is that this study will help us learn enough to predict which ones are at high risk of rupture so that treatment can be offered before they become harmful.”

This work has two potential applications. The first is as a research tool, with Metcalfe's team performing simulations of specific aneurysms. Using a technique employed by Karmonik to simulate removal of an aneurysm on the computer, they analyze how the blood behaves as it flows near the aneurysm site and determine if that can be correlated to a certain type of behavior of the blood at potential sites where aneurysms form. Very accurate simulations are done for a complete description of the flow fields, studying all the fluid dynamic variables in great detail, such as the wall shear stresses, the pressures and the velocity.

“The second application is as a potential clinical tool,” Metcalfe said. “Once we have a reasonable idea of the fluid dynamic variables needed to study and identify a potential problem, we then use a program that provides a detailed, 3-D description of the aneurysms of the real patients.”

Benndorf adds that the potential clinical importance of these computer simulations lies in the future possibility of directly predicting patient-specific blood flow so that patient-specific medical devices can be used in aneurysm treatment. He is studying how stents – small wire mesh tubes that are inserted into the artery to facilitate the occlusion of an aneurysm with small platinum coils – can be tailored to the patient's individual anatomy and blood flow in order to optimize their therapeutic effect and maximize the possibility of a successful outcome.

When Metcalfe's group imports a patient's images into a computer program, they remove some geometric glitches and generate a computational mesh that involves the mapping of hundreds of thousands of tiny elements that represent the area being studied. That mesh is then introduced into a program that actually solves the fluid dynamic equations of motion.

“It takes a lot of computer time to perform these simulations,” Metcalfe said. “There are several hundred thousand elements that are discrete zones within a geometric mesh, and then there are 700 steps representing intervals of time over the cycle of each heart beat.”

Requiring extremely fast computers, the group uses the Beowolf cluster at UH's Texas Learning and Computation Center (TLC2) to significantly improve the visualizations created by the simulations.

“The critical step here is to make these complicated flows much more accessible to people like medical researchers and physicians,” Metcalfe said. “We're developing 3-D visualizations so doctors can go inside the virtual artery and actually see what's happening as the blood cells flow through.”

Halliburton Company supports this joint project by funding the research analysis of the study's findings, which have the potential for substantial impact in neurology and medical science.

—–

Source: University of Houston

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Mira Supercomputer Enables Cancer Research Breakthrough

November 11, 2019

Dynamic partial-wave spectroscopic (PWS) microscopy allows researchers to observe intracellular structures as small as 20 nanometers – smaller than those visible by optical microscopes – in three dimensions at a mill Read more…

By Staff report

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quantum annealing) – ion trap technology is edging into the QC Read more…

By John Russell

Tackling HPC’s Memory and I/O Bottlenecks with On-Node, Non-Volatile RAM

November 8, 2019

On-node, non-volatile memory (NVRAM) is a game-changing technology that can remove many I/O and memory bottlenecks and provide a key enabler for exascale. That’s the conclusion drawn by the scientists and researcher Read more…

By Jan Rowell

What’s New in HPC Research: Cosmic Magnetism, Cryptanalysis, Car Navigation & More

November 8, 2019

In this bimonthly feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

By Oliver Peckham

Machine Learning Fuels a Booming HPC Market

November 7, 2019

Enterprise infrastructure investments for training machine learning models have grown more than 50 percent annually over the past two years, and are expected to shortly surpass $10 billion, according to a new market fore Read more…

By George Leopold

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

IBM Accelerated Insights

Atom by Atom, Supercomputers Shed Light on Alloys

November 7, 2019

Alloys are at the heart of human civilization, but developing alloys in the Information Age is much different than it was in the Bronze Age. Trial-by-error smelting has given way to the use of high-performance computing Read more…

By Oliver Peckham

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quant Read more…

By John Russell

Tackling HPC’s Memory and I/O Bottlenecks with On-Node, Non-Volatile RAM

November 8, 2019

On-node, non-volatile memory (NVRAM) is a game-changing technology that can remove many I/O and memory bottlenecks and provide a key enabler for exascale. Th Read more…

By Jan Rowell

MLPerf Releases First Inference Benchmark Results; Nvidia Touts its Showing

November 6, 2019

MLPerf.org, the young AI-benchmarking consortium, today issued the first round of results for its inference test suite. Among organizations with submissions wer Read more…

By John Russell

Azure Cloud First with AMD Epyc Rome Processors

November 6, 2019

At Ignite 2019 this week, Microsoft's Azure cloud team and AMD announced an expansion of their partnership that began in 2017 when Azure debuted Epyc-backed ins Read more…

By Tiffany Trader

Nvidia Launches Credit Card-Sized 21 TOPS Jetson System for Edge Devices

November 6, 2019

Nvidia has launched a new addition to its Jetson product line: a credit card-sized (70x45mm) form factor delivering up to 21 trillion operations/second (TOPS) o Read more…

By Doug Black

In Memoriam: Steve Tuecke, Globus Co-founder

November 4, 2019

HPCwire is deeply saddened to report that Steve Tuecke, longtime scientist at Argonne National Lab and University of Chicago, has passed away at age 52. Tuecke Read more…

By Tiffany Trader

Spending Spree: Hyperscalers Bought $57B of IT in 2018, $10B+ by Google – But Is Cloud on Horizon?

October 31, 2019

Hyperscalers are the masters of the IT universe, gravitational centers of increasing pull in the emerging age of data-driven compute and AI.  In the high-stake Read more…

By Doug Black

Cray Debuts ClusterStor E1000 Finishing Remake of Portfolio for ‘Exascale Era’

October 30, 2019

Cray, now owned by HPE, today introduced the ClusterStor E1000 storage platform, which leverages Cray software and mixes hard disk drives (HDD) and flash memory Read more…

By John Russell

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a Read more…

By John Russell

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated mo Read more…

By John Russell

Rise of NIH’s Biowulf Mirrors the Rise of Computational Biology

July 29, 2019

The story of NIH’s supercomputer Biowulf is fascinating, important, and in many ways representative of the transformation of life sciences and biomedical res Read more…

By John Russell

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This