Microsoft Customer SolutionHealthcare Industry Case Study

Researchers Reduce Processing Times by Factor of 20 to Improve Colon Cancer Screening

OverviewCountry or Region: United StatesIndustry: Healthcare

Customer ProfileMassachusetts General Hospital (MGH) is the oldest and largest teaching affiliate of Harvard Medical School. It has more than 22,000 employees and is located in Boston, Massachusetts.

Business SituationTo support efficient mass-screening for colon cancer, researchers in the 3-D Imaging Lab at MGH had to reduce the time required to electronically cleanse a 3-D model by more than a factor of 10.

SolutionMGH surpassed its performance goals and streamlined clinical workflow by working with Microsoft, Intel, and Vectorform to optimize its software for parallel processing and develop new solution components for rendering and viewing 3-D images.

Benefits Streamlined clinical workflow Improved patient convenience and

safety Reduced examination costs Improved diagnostic accuracy Fewer colon cancer deaths

“We now have a working, end-to-end solution capable of supporting colon cancer screening for the entire at-risk population.”Dr. Hiro Yoshida, PhD, Director of 3-D Imaging Research at Massachusetts General Hospital

and Associate Professor of Radiology at Harvard Medical School

To make colon cancer screening more broadly accessible, Massachusetts General Hospital (MGH) sought to reduce the processing time required to electronically cleanse and view a three-dimensional (3-D) model of the colon from an hour to five minutes. By working together with Microsoft, Intel, and Vectorform, MGH reduced processing times to about two minutes, achieving the performance required to support mass colon cancer screening. The screening approach pioneered by MGH can also drastically decrease costs and is far more patient-friendly, avoiding the many negatives of an optical colonoscopy. It also improves convenience for radiologists, who can navigate and interpret the 3-D images of a colon by using finger gestures on a touchscreen-enabled PC, and improves diagnostic accuracy through computer-aided identification of potential polyps.

SituationMassachusetts General Hospital (MGH), a founding member of the Partners HealthCare System, offers sophisticated diagnostic and therapeutic care in virtually every specialty and subspecialty of medicine and surgery. MGH has been consistently named one of the best hospitals in the United States by U.S. News & World Report and is the oldest and largest teaching affiliate of Harvard Medical School, where nearly all the hospital’s physicians are faculty members.

Like MGH itself, the hospital’s Radiology Department is world renowned. In 1999, the department established its 3-D Imaging Service. With three-dimensional (3-D) imaging, data from cross-sectional computerized tomography (CT) and magnetic resonance imaging (MRI) studies is run through specialized software to create lifelike 3-D images, which physicians can use to visualize a patient’s anatomy and apply that knowledge to diagnoses, treatment, and surgical planning. Because a single 3-D image can summarize hundreds of individual cross-sectional scans, CT and MRI studies are faster and easier to interpret, which increases clinical productivity. Implications for enhanced patient care are also many: 3-D imaging can help minimize exploratory surgery and facilitate noninvasive surgical planning, reduce operating times, minimize damage to healthy tissues through more accurate targeting of treatment areas, serve as a visual tool for patient education, and ultimately help reduce healthcare costs.

In the 3-D Imaging Research group at MGH, a team of researchers works to apply 3-D imaging and computer-aided diagnosis

to new areas of patient care. One focus is on “virtual colonoscopy,” a noninvasive alternative to a traditional optical colonoscopy. With the traditional procedure, which is performed by a gastroenterologist and an assisting nurse, a flexible tube with a camera on its end is passed through the anus to examine the colon, as a means of visually diagnosing conditions such as colon cancer or the presence of precancerous polyps. As most who have had one can attest, an optical colonoscopy can be highly unpleasant. Patients must prepare the day before by drinking up to a gallon of cathartic (laxative) solution, a nondigestible liquid that flushes the colon of all solid matter, thereby requiring frequent visits to the toilet for several hours. Before the procedure, which takes approximately 20 minutes, the patient is given a drug such as fentanyl or midazolam—intended to sedate the patient, minimize pain during the procedure, and inhibit unpleasant memories by inducing a state of twilight amnesia. However, many people still recall the procedure and complain of significant discomfort. After the procedure, the patient must spend time recovering from the sedation before being driven home.

“More than 50,000 people die from colon cancer in the United States each year, making it the second leading cause of cancer-related death among men and women,” says Dr. Hiro Yoshida, PhD, Director of 3-D Imaging Research at MGH and Associate Professor of Radiology at Harvard Medical School. “However, colon cancer is highly preventable if polyps are detected and removed early, before they turn cancerous—a process that usually

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“The next step is to deploy the solution to MGH and other hospitals for clinical use. If all goes as planned, it may be available for clinical use in the third quarter of 2011.”

Dr. Hiro Yoshida, PhD, Director of 3-D Imaging Research at Massachusetts

General Hospital and Associate Professor of Radiology at Harvard Medical School

takes eight to 10 years. Unfortunately, current optical screening methods are costly and unpleasant, covering only 5 percent of the 80 million people over age fifty for whom screening is recommended. Our goal is to apply 3-D imaging and computer-aided diagnosis to enable screening for polyps in a cost-effective, streamlined, and patient-friendly manner, as a means of extending the process to the entire target population.”

With the approach pioneered at MGH, preparatory laxative cleansing of the colon is not required. Instead, the patient drinks a small amount of a neutral-taste contrast agent with food and water before coming to the hospital so that the contrast agent mixes with the solid matter in the digestive tract. At the hospital, a thin-section CT scan is performed and the hundreds of cross-sectional images captured during the scan are processed by using computer software developed by Yoshida’s team. The software builds a 3-D volume model of the colon, and it uses the presence of the contrast agent to “erase” the solid matter from within the colon—a step in the process called “electronic cleansing.” The software also identifies suspicious shapes that may be polyps within the 3-D volume to aid radiologists in diagnosis. The final 3-D images are then reviewed by using a traditional radiology workstation. “A year ago, we had most of the process figured out, with one major challenge remaining: the processing time required to electronically cleanse the 3-D model of the colon,” says Yoshida. “That computationally intensive process alone took 45 minutes to complete, and it took an additional 15 minutes to load the image for viewing. To

streamline clinical workflow, we had to get the entire one-hour process down to less than five minutes—so that the resulting 3-D image can be reviewed while the patient is still present.”

SolutionBy working with Microsoft, Intel, and Vectorform, MGH was able to get total processing times for constructing and loading an electronically cleansed 3-D image for viewing down to just two minutes—a twenty-fold performance gain made possible by optimizing the code to take full advantage of modern multicore processors and multiprocessor servers, and by taking advantage of dedicated graphics processing units for 3-D rendering. The joint effort also yielded improvements in other parts of the clinical workflow, such as the ability for radiologists to view the 3-D images from any location on the hospital’s network by using one or two finger gestures on a multitouch-enabled computer screen.

“We now have a working, end-to-end solution capable of supporting colon cancer screening for the entire at-risk population—in a manner that’s more patient-friendly and a fraction of the cost of traditional screening techniques,” says Yoshida. Cleansing the 3-D ModelThe creation of the solution began when researchers from the 3-D Imaging Research group at MGH participated in a two-week engagement at the Microsoft Technology Center in Boston, Massachusetts. The original purpose of the engagement was to determine whether the performance of the algorithm for cleansing the 3-D image

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“Each part of the solution is modular…. We can adapt the work we’ve done to support image-based screening such as lung and breast cancer screening, time-critical quantitative imaging such as pneumothoraces volumetry for emergency trauma care, image-guidance for interventional procedures such as radiofrequency ablation and thrombolysis, and so on.”

Dr. Hiro Yoshida, PhD, Director of 3-D Imaging Research at Massachusetts

General Hospital and Associate Professor of Radiology at Harvard Medical School

could be improved by adapting it to run on a 16-node high-performance computing (HPC) cluster. At that time, the algorithm was coded in native C and C++ code and most of it worked on Linux. Although not explicitly designed for HPC, the application was intended to take advantage of parallel processing by creating multiple threads of execution. However, when the application was run on a 16-core server in the lab, it proved unable to fully utilize the available processing power. Figure 1 shows the CPU activity for a test run, with each color representing the activity of a single processor core. While some processors show nearly 100-percent utilization at some point in time, most show little or no activity at any given point—a pattern that indicates lack of efficient parallelization and therefore poor processor utilization.

Further analysis of the code revealed several other problem areas, such as severe I/O (input/output) constraints, leading to the following set of recommendations:

Convert parts of the code to the Microsoft Visual C# programming language, as needed to fully take advantage of the parallel processing support provided in the Microsoft .NET Framework 4.

Refactor the code to improve performance and replace custom-developed functions with functionality provided natively by the .NET Framework 4.

Modify the code to run on the Windows Server 2008 R2 operating system on a 64-bit server, as needed to take advantage of a greater amount of physical memory.

Because it would have been impractical to convert the entire code base to Visual C# within the 150-day proof-of-concept, the team enlisted the aid of Intel, which assisted in applying its Intel® Parallel Studio 2011 tool suite to optimize the code that would need to remain as C++. Developers used the Intel Parallel Advisor threading tool to help identify areas in the application that could benefit the most from parallelism. They also used Intel Parallel Amplifier for performance tuning and the Intel Parallel Inspector to help verify the code and identify potential memory leaks, deadlocks, and race conditions.

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Figure 1. CPU activity for a test run before parallelization.

Through these efforts, MGH was able to reduce processing times from 60 minutes down to five minutes on a single dual-core system. And with the application modified to fully take advantage of parallel processing, that number was reduced to about two minutes on a larger server with several multicore processors.

“By the end of the process, we didn’t even need an HPC cluster,” says Yoshida. “We were able to surpass our original performance goal by simply modifying the application to take advantage of the processing power provided by a single, modern multiprocessor server.”

Rendering and Viewing the Virtual ImageHaving reached its performance goals for cleansing the 3-D model, the team turned its attention to what could be done to improve how radiologists view the model.

At the time, MGH was using software that it had written in OpenGL (Open Graphics Library). Even with that viewing software running on a powerful workstation, it took about 15 minutes to load the image and compute the centerline of the colon, which was required for navigation through the image by using a traditional keyboard and mouse.

The team’s research led to work done by Toby Sharp and others at Microsoft Research, who had developed an innovative 3-D rendering engine. Called the 3-D GPU Volume Rendering Engine, it takes advantage of server-side rendering and uses dedicated graphics processing units (GPUs) instead of the server’s CPUs to support the visualization of 3-D data on-demand and in real time, by multiple simultaneous users, with low latency even on low bandwidth networks and on thin-client devices. The engine can also support client-side rendering on a PC with an appropriate graphics card. Either way, radiologists can begin viewing high definition, diagnostic quality images virtually immediately.“The benefit of rendering on the server is that radiologists no longer need to be in the same place as the data, nor do they need to be tethered to an expensive 3-D workstation,” says Yoshida. After the decision to use the rendering engine from Microsoft Research, one piece of the puzzle remained: how to enable radiologists to interact with the data in the most efficient and productive way possible. The team turned to Vectorform, a Microsoft Registered Partner, which had extensive experience with 3-D visualization—and had

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Figure 2. By using the virtual colonoscopy viewer developed by Vectorform, radiologists can use touchscreen navigation to navigate a 3-D model of a patient’s colon.

recently expanded its business to include a new healthcare business unit. By using the application programming interfaces (APIs) provided for the rendering engine, Vectorform developed a custom-built virtual colonoscopy viewer capable of working on PCs and devices that run the Windows 7 operating system. The engine renders the 3-D volume data as a two-dimensional (2-D) stream in real time, with the 2-D images transmitted frame-by-frame to the Vectorform client in a manner similar to the Microsoft Remote Desktop Protocol. The Vectorform client, which supports touchscreen navigation, is written in Visual C# and is based on Windows Presentation Foundation. A future version for Windows Phone 7 will be based on Microsoft Silverlight.

The Vectorform client works with the GPU Volume Rendering Engine to enable fly-through navigation of the 3-D volume—complete with lifelike color and lighting to help radiologists identify features inside the colon (Figure 2). During the electronic cleansing process, the centerline of the

colon is computed and saved as part of the 3-D volume. The radiologist starts by “entering” the image of the colon through the rectum, using a touch-enabled slider at the bottom of the screen to easily move forward or back along the centerline.When the radiologist sees a point of interest, such as a potential polyp, he or she can double-tap it on the screen. This switches the virtual camera to an orbiting function, upon which the radiologist can pan right, left, up, or down with a finger to view the potential polyp from different angles. Similarly, the radiologist can pinch or stretch with two fingers to zoom in or out.

Timeline for Clinical UseDevelopment of the proof-of-concept began in December 2009 and took approximately 150 days. MGH demonstrated it at Supercomputing 2010 and at the 2010 Radiological Society of North America (RSNA) conference, where it won the Excellence in Design award. “The next step is to deploy the solution to MGH and other hospitals for clinical use. If all goes as planned, it may be available for clinical use in the third quarter of 2011,” says Yoshida.

At the same time, Yoshida’s team plans to explore running the compute-intensive cleansing engine in the cloud, on the Windows Azure platform, as a means of making it readily available to hospitals across the United States. The team also plans to explore running the solution on Windows HPC Server 2008 R2 to further improve performance. Finally, the team is looking at the Microsoft HealthVault healthcare website technology to store cleansed 3-D volume models, as a way to

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“An optical colonoscopy interrupts a patient’s life for two days. Our virtual colonoscopy approach can be completed in as little as 30 minutes, with virtually no inconvenience, risk, or discomfort to the patient before, during, or after the procedure.”

Dr. Hiro Yoshida, PhD, Director of 3-D Imaging Research at Massachusetts

General Hospital and Associate Professor of Radiology at Harvard Medical School

make that data portable for patients—and available to consulting caregivers who do not have access to the hospital’s system in which radiology images are stored.

Yoshida also describes how the individual solution components can be applied to other areas. “Each part of the solution is modular—from the 3-D image construction and cleansing algorithms to the rendering engine to the viewer,” he states. “We can adapt the work we’ve done to support image-based screening such as lung and breast cancer screening, time-critical quantitative imaging such as pneumothoraces volumetry for emergency trauma care, image-guidance for interventional procedures such as radiofrequency ablation and thrombolysis, and so on.”

BenefitsThrough its work with Microsoft, Intel, and Vectorform, MGH overcame the last obstacles it faced in building a solution capable of supporting colon cancer screening for the entire target population. Not only does the lab’s current solution improve the speed with which patients can be screened, but it does so while drastically reducing costs. The approach pioneered by MGH is also more patient-friendly, eliminating the extensive preparation, sedation, and risk of complications associated with an optical colonoscopy. The solution is also more convenient for radiologists, who are no longer bound to an expensive 3-D workstation for viewing the 3-D images. And it provides an opportunity for improved diagnostic accuracy through the application of software designed to detect suspicious shapes and tissue densities within the data.

“The virtual colonoscopy in itself is not new—it’s been around for more than 10 years, but it still required traditional methods of laxative cleansing of the colon prior to a CT scan,” says Yoshida. “The virtual, laxative-free cleansing part is what’s new and, through our work with Microsoft and others, we’ve been able to achieve the image preparation times required to streamline clinical workflow. With the speed issues now addressed, we’re ready to take the next steps toward extending the screening process to the entire population for whom such screening is recommended.”

Streamlined Clinical WorkflowBy working with Microsoft and Intel, MGH was able to optimize its code for parallel processing—leading to a 2,000 percent performance gain on a four-core server with 12 gigabytes of RAM. Improvements to the electronic cleansing step reduced the time required from 45 minutes to about two minutes, and use of the 3-D GPU Volume Rendering Engine from Microsoft Research reduced the 15 minutes to begin rendering the cleansed 3-D image to just a few seconds. Given that a CT scan takes only a few minutes to perform, these performance gains will enable the data capture, image preparation, and review of the 3-D images all to occur within the duration of a standard patient appointment.

“It’s important for clinical workflow that the results can be interpreted while the patient is still present, as needed to give patients immediate peace of mind that everything looks normal—or, if an issue is detected, to schedule an appoint for the removal of polyps or capture another scan for pre-

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“A virtual colonoscopy can be performed for about one-fifth of the cost of a traditional optical procedure.”

Dr. Hiro Yoshida, PhD, Director of 3-D Imaging Research at Massachusetts

General Hospital and Associate Professor of Radiology at Harvard Medical School

surgical evaluation and planning,” says Yoshida.

Improved Patient Convenience and SafetyThrough the approach pioneered by MGH, patient convenience and safety are significantly improved over the traditional optical colonoscopy. Unpleasant advance flushing of the colon with laxatives is eliminated, no sedation is required, no discomfort is involved, post-procedure recovery in the hospital is no longer necessary, and no ride home is needed. The virtual approach also avoids the potential complications of an optical colonoscopy, which can range from a bad drug reaction to perforation of the colon which, although rare, often require immediate surgical treatment.

“An optical colonoscopy interrupts a patient’s life for two days,” says Yoshida. “Our virtual colonoscopy approach can be completed in as little as 30 minutes, with virtually no inconvenience, risk, or discomfort to the patient before, during, or after the procedure.”

Cost Reduced by 80 PercentAccording to Yoshida, a virtual colonoscopy may practically cost only about one-fifth the cost of an optical colonoscopy, which typically costs between U.S.$2,000 and $5,000, including the cost of sedation provided by anesthesiologists. Up until the images are ready for review by a radiologist, the entire process can be managed by a radiology technician.

“A virtual colonoscopy can be performed for about one-fifth of the cost of a traditional optical procedure,” says Yoshida.

“The patient simply comes in, lies on the CT scanner, and the data is captured in 20 seconds. With our latest technology, the results are ready for interpretation a couple of minutes later. Unlike with an optical colonoscopy, there’s no need for sedative drugs, sterile equipment, a gastroenterologist to conduct the exam, a hospital bed for the patient to recover, or a wheelchair ride to the front door of the hospital.”

Greater Convenience for RadiologistsMGH has also improved convenience for radiologists by incorporating the 3-D GPU Volume Rendering Engine and Vectorform virtual colonoscopy viewer into its solution, which eliminates the need for a high-end radiology workstation for image interpretation—and the need to wait 15 minutes for images to load. Instead, images are rendered virtually immediately and, because the processing required to render the 3-D volume as 2-D image frames is done on the server, the images can be viewed on any device running Windows 7.

“The rendering engine and viewer work very similarly to how Terminal Services in Windows Server works—a technology that’s already used in many hospitals,” says Patrick Samona, Director of the new healthcare business unit at Vectorform. “Frames are rendered on the server and sent to the client for display, and the touch inputs for navigation are transmitted in the other direction. The solution performs beautifully over a traditional wired or wireless network.”

Improved Diagnostic AccuracyWith a complete 3-D model of the colon and the flexibility provided by the

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“If we can screen the entire at-risk population for precancerous polyps and remove them before they turn malignant, we can significantly reduce the incidence of colon cancer deaths.”

Dr. Hiro Yoshida, PhD, Director of 3-D Imaging Research at Massachusetts

General Hospital and Associate Professor of Radiology at Harvard Medical School

Vectorform viewer, radiologists can easily view areas that would be difficult to see with a traditional colonoscopy, such as a hidden polyp. In addition, Yoshida is already working to introduce other work being done by the 3-D Imaging Research group into the solution—namely, his ongoing research in computer-aided diagnosis, which would provide a “second set of eyes” for radiologists reviewing the 3-D images through software-based detection and flagging of suspicious shapes and tissue densities.

“With all the data that’s captured in the 3-D image, we can apply computer-aided diagnosis to locate, characterize, and flag potential polyps,” says Yoshida. “For example, polyps are typically cap-shaped, the colon’s haustral folds are ridge-shaped, and the colon wall is typically cup, rut, or saddle-shaped. By identifying these shapes with software, we can flag suspicious areas, with the final diagnostic decision to be made by the radiologists.”

Fewer Colon Cancer DeathsWith its fast and cost-effective approach to colon cancer screening, MGH is making it possible to screen all the at-risk population for colon cancer—or, more accurately, for precancerous polyps. “Colorectal cancers are highly preventable, as the majority

develop slowly from benign adenomas, with an average dwell time—the time it takes to turn cancerous—of eight to ten years,” explains Yoshida. “The objective of screening is to find and remove these polyps when they’re small, because less than one percent of polyps that are less than 5 millimeters in size harbor malignancy. If we can screen the entire at-risk population for such polyps and remove them before they turn malignant, we can significantly reduce the incidence of colon cancer deaths.”

Microsoft Solutions for the Healthcare IndustryHealthcare and life sciences organizations are under tremendous pressure to meet regulatory requirements, improve patient care, and reduce the time it takes to develop drugs and take them to market. To meet this challenge, Microsoft and its partners have developed cost-effective solutions that enable healthcare organizations to streamline and automate daily processes that improve productivity and deliver information whenever and wherever it is needed. The result is enhanced productivity, safety, and quality. 

For more information about Microsoft solutions for the healthcare industry, go to:

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For More InformationFor more information about Microsoft products and services, call the Microsoft Sales Information Center at (800) 426-9400. In Canada, call the Microsoft Canada Information Centre at (877) 568-2495. Customers in the United States and Canada who are deaf or hard-of-hearing can reach Microsoft text telephone (TTY/TDD) services at (800) 892-5234. Outside the 50 United States and Canada, please contact your local Microsoft subsidiary. To access information using the World Wide Web, go to:www.microsoft.com

For more information about Intel Corporation, visit the website at: www.intel.com

For more information about Vectorform, visit the website at: www.vectorform.com

For more information about Massachusetts General Hospital, visit the website at:www.massgeneral.org

This case study is for informational purposes only. MICROSOFT MAKES NO WARRANTIES, EXPRESS OR IMPLIED, IN THIS SUMMARY.

Document published April 2011

Software and Services Microsoft Server Product Portfolio− Windows Server 2008 R2 Enterprise

Windows 7 Technologies− 3-D GPU Volume Rendering Engine

(Microsoft Research)− Microsoft .NET Framework 4− Microsoft Silverlight− Microsoft Visual C#− Windows Presentation Foundation

Third-Party Software Intel Parallel Studio 2011

Partners Intel Vectorform

www.microsoft.com/healthcare

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