SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

Created: 05 September 2001

The SCI Institute has been formally awarded a National Institutes of Health grant from the Biomedical Information Science and Technology Initiative(BISTI). This grant will be used to create a Program of Excellence in Computational Bioimaging and Visualization at the University of Utah. The award totals $2,261,136, distributed over three years, and includes collaborators from the departments of Bioengineering, Radiology, Neurosurgery and the Cardiovascular Research and Training Institute (CVRTI). Through awards such as these, NIH Institutes and Centers seek to establish National Programs of Excellence in Biomedical Computing (NPEBC). Funding for the SCI Institute grant comes from the National Heart, Lung, and Blood Institute within the National Institutes of Health.

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Created: 28 August 2001

On August 28, 2001, Dr. Chris Johnson attended a press conference conducted by Utah Governor Mike Leavitt. The governor launched a new program to generate business activity and investment in Utah's high technology ecosystems. Each ecosystem consists of academic researchers, business leaders, anchor companies, venture capitalists, and professional service providers who collectively promote business activity. Dr. Johnson spoke at this press conference with regard to the multidisciplinary nature of ongoing research at the SCI Institute.

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Created: 14 July 2000

With the rapid advancement of new communication technologies, today's scientists are able to communicate more frequently and easily with collaborators and colleagues throughout the world. Collaborations used to require travelling on sabbaticals and meeting at infrequent conferences. Today, researchers need a way to collaborate remotely beyond the constraints of email and FTP.

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Created: 29 October 2013

The SCI Institute holds a strong belief that providing research opportunities to undergraduate and even high school students will not only encourage them to pursue studies in the sciences, but also give them a head start in their future academic lives. Being allowed to work side by side with PhD-level scientists within a real research institute moves science from something that happens in a text book or highly structured laboratory to the dynamic work environment shared by scientists around the world.

In this year's high school summer intern program, the SCI Institute invited four students, one each from Juan Diego Catholic High School, The Waterford School, and two from West High School. These students were given the opportunity to work with a lead software developer from the National Institutes of Health (NIH) sponsored Center for Integrative Biomedical Computing (CIBC). Their task seemed simple: take Seg3D and ImageVis3D (two advanced software tools developed by the CIBC), find a dataset of interest to the student, load that data, and experiment with the software on both desktop and iPad versions. And then, present your results to your high school peers. In the end, the students learned that research is a full-contact sport, not just a homework assignment. They had to 'dig-in', expand their knowledge, and learn about their subjects of interest, their data, their software, even their computers. In the end, the students translated this process and knowledge to science classes at their school. And, the top question after the presentations? Oddly enough, "how do I get an internship like yours?" Kids excited about a science internship! Mission Accomplished.

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Created: 11 June 2012

by Gregory Scott Jones - NICS

The crater resulting from the Spanish Fork Detonation.

First, the bad news: all across America, trucks and tractor-trailers are transporting industrial explosives on nearly every artery of the country's interstate and highway system. That's right, volatile explosives, including munitions, rocket motors, and dynamite, are moving at a high rate of speed down a roadway not too far from you.

Now, the good news: America's track record in transporting these materials is about as safe as they come. Very rarely, almost never in fact, are the potential dangers of these transports realized, largely due to instituted safeguards that seem to work very well.

However, accidents can happen. Take the August 2005 incident in Spanish Fork Canyon, Utah, for instance. A truck carrying 35,500 pounds of explosives—specifically small boosters used in seismic testing—overturned and exploded, creating a crater in the highway estimated to be between 20 to 35 feet deep and 70 feet wide according to the Utah Department of Transportation. But the damage wasn't solely financial. Four people, including the truck driver and a passenger, were hospitalized.

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Created: 19 December 2013

In collaboration with Dr. Don Tucker and his colleagues at Electrical Geodesics Inc (EGI) and the University of Oregon, this DBP is concerned with improving our ability to reconstruct and visualize neuroelectric sources (source localization) from EEG measurements and also our ability to stimulate specific brain regions using electrodes attached on to the scalp of the subject (transcranial direct current stimulation, tDCS).

For both research and clinical practice, EEG is a cost-effective tool to understand and excite brain activity. EEG advances have significantly improved the spatial resolution of source estimates and offer the promise of precise spatio-temporal monitoring and stimulation of cortical brain activity. By itself, high-resolution EEG would be affordable even for small hospitals in remote locations and could be easily managed by technicians in the field.

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Created: 18 December 2013

Femoroacetabular impingement (FAI) is caused by reduced clearance between the femoral head and acetabulum due to anatomic abnormalities of the femur (cam FAI), acetabulum (pincer FAI), or both (mixed FAI). Cam FAI is characterized by an aspherical femoral head or reduced femoral head-neck offset. During hip flexion, the abnormally shaped femur may cause shearing at the chondrolabral junction, thereby damaging articular cartilage and the acetabular labrum. Currently, diagnosis of cam FAI is largely accomplished using two-dimensional (2D) measurements of femur morphology acquired from radiographic projections or a series of radial planes from computed tomography (CT) or magnetic resonance (MR) images. Two- dimensional measures provide initial diagnosis of cam FAI, but their reliability has been debated. Also, there is no agreement on the range of measurements that should be considered normal. Furthermore, radiographic measures give only a limited description of femur anatomy or shape variation among cam FAI deformities. Together, these limitations of 2D measurements translate into a high misdiagnosis rate. In a series of FAI patients treated with surgery in our clinic, 40% had seen multiple previous musculoskeletal providers and 15% had undergone surgical procedures unrelated to the hip joint (hernia, etc.).

Mean control (left) and cam (right) shapes. Middle images show the mean control shape with color plots depicting how the mean cam shape differed across the femoral head, neck, and proximal shaft. Top and bottom rows show different rotations of the femoral head.	Volumetric CT images from a cam FAI patient. Validated threshold settings were applied to CT images to segment and reconstruct the bony morphology of each femur.

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Created: 17 December 2013

Corview screenshot

Atrial fibrillation (AF) is a cardiac rhythm disturbance in which the atria, the upper chambers of the heart, undergo uncontrolled and uncoordinated electrical activation so that contraction of the atria contributes almost nothing to cardiac output. While not immediately atal (as is ventricular fibrillation) AF dramatically increases the risk of stroke, elevates mortality, and diminishes quality of life. Traditional diagnosis of AF as been limited to ECG-based determination of the time spent in this arrhythmia and there has previously been no other dependable biomarker capable of determining either the progression of the disease or of determining suitable treatment approaches. Therapy for AF consists of either antiarrhythmic drugs that may control the arrhythmia completely or at least reduce the resulting elevated heart rate combined with anticoagulation therapy or ablation. Ablation involves destroying targeted regions of the atria with the goal of either isolated triggers of spurious electrical activity or functionally separating the atrial wall into small enough segments that the putative mechanism of the arrhythmia cannot longer sustain. The latter approach is a form of substrate stabilization, and the management of this disease has suffered from a persistent lack of means to monitor or evaluate the stability of the tissue. It is precisely in this aspect that cardiologist at the University of Utah, with support from the CIBC have made their most significant contributions.

An interdisciplinary team at the Comprehensive Arrhythmia and MAnagement (CARMA) Center have made use of the segmentation, image analysis, and recently mesh generation and simulation capabilities of the CIBC to create a comprehensive program for AF management. The scope of the progress continues to expand each year and this application of CIBC technology has proven very fruitful even as it is very challenging.

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Created: 16 December 2013

For years, a central focus of the Center for Integrative Biomedical Computing has been software dissemination. Over the Center's twelve-year history, the infrastructure of CIBC's software dissemination efforts have undergone a radical evolution, with many lessons learned for both users and developers.

Software Dissemination as a Form of Science and Technology Dissemination

The SCIRun/BioPSE Problem-Solving Environment. This system was designed as a 'computational workbench' and represented a new approach to bringing high-end computational tools to the biomedical researcher.

From the outset, the Center's leadership believed that along with the typical avenues of dissemination, publications, seminars, workshops, conference presentations, etc.‚ software dissemination held a particularly high potential as a means to disseminate the knowledge and advances of the Center and its collaborators. This fundamental belief led to experimentation in a variety of topics, such as software licensing, open source repositories, make systems, operating systems, source code/binary releases, research code versus releasable code, software support, and release schedules.

The origins of our success in developing widely used software tools lie in a set of strategies for algorithm research and software development. One such strategy is the production of software tools with low barriers to entry. This entails the release of documented, tested, complete applications that do not require learning new programming languages or complex, architecture-specific build environments. We also continue to follow an initiative to create a suite of lightweight, stand-alone applications, directed at specific tasks of common interest across a wide set of disciplines. The result is a set of programs, such as Seg3D, with large and growing user bases.

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Created: 16 December 2013

Overview of the DBS system. The DBS electrode is implanted in the brain during stereotactic surgery. The electrode is attached via an extension wire to the IPG, which is implanted in the torso. The entire system is subcutaneous and is designed to deliver continuous stimulation for several years at a time.

In recent years, there has been significant growth in the use of patient-specific models to predict the effects of neuromodulation therapies, such as deep brain stimulation (DBS). However, translating these models from a research environment to the everyday clinical workflow is a challenge, primarily due to the complexity of the models and the expertise required in specialized visualization software. Recently, the CIBC has worked with Dr. Christopher Butson at the University of Wisconsin to deploy the interactive visualization system ImageVis3D Mobile for experimental use in the area of DBS planning. In addition to running on multi-node compute clusters and large desktop systems, ImageVis3D is also designed for mobile computing devices such as the iPhone or iPad. In this case, ImageVis3D was modified for an evaluation environment in order to visualize models of Parkinson's Disease (PD) patients who received DBS therapy¹.

The selection of DBS settings is a significant clinical challenge that requires repeated revisions to achieve optimal therapeutic response, and is often performed without any visual representation of the stimulation system in the patient. We used ImageVis3D Mobile to provide models to movement disorders clinicians and asked them to use the software to determine: 1) which of the four DBS electrode contacts they would select for therapy and 2) what stimulation settings they would choose. We compared the stimulation protocol chosen from the software versus the stimulation protocol that was chosen via clinical practice (independent of the study). Lastly, we compared the amount of time required to reach these settings using the software versus the time required through standard practice. We found that the stimulation settings chosen using ImageVis3D Mobile were similar to those used in standard care, but were selected in drastically less time. We found that our visualization system, available directly at the point of care on a device familiar to the clinician, can be used to guide clinical decision-making for selecting DBS settings. The positive impact of the system could also translate to areas other than DBS.

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