Iowa Neuroimaging Consortium

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  • Facilities

    Overview

    The Iowa Neuroimaging Consortium (INC) is an 8,000 square foot facility at the University of Iowa in the Department of Psychiatry. Approximately 900 square feet is dedicated to the imaging computer lab, 300 square feet is dedicated to a state of the art conference room/training center, and 300 square feet is dedicated to a server room to house the infrastructure of the Iowa Neuroimaging Consortium. The remaining space supports our image analysis technicians, systems programmers, research assistants, and core data management as well as postdoctoral fellows and other trainees working in our program. The imaging computer lab provides several Windows, Apple and Linux workstations that can be used for hands on training sessions or as a general workspace for visiting researchers. The wide range of operating systems gives us the flexibility to meet the needs of researchers and permanent staff. Several systems and laptops are equipped with Adobe Creative Suite giving us the ability to capture and edit images and videos. Ample institutionally funded printing facilities are available to the project that includes multiple copiers and printers.

    Researchers have access to two state of the art conference room and training centers which are outfitted with a high definition video projection system that provides an optimal environment for presentations and training sessions. This system is specially designed for displaying high-end medical images. One room also has a Polycom video conferencing system available for audio and video conferencing to facilitate collaboration with remote sites. A Window/Linux and Mac system are available to provide access to the largest possible number of applications for training and presentations.

    The renovated server room provides space to house five standard 42U racks of computing equipment and contains a dedicated 8-ton cooling system, four high voltage circuits, and dedicated environmental monitoring systems to insure proper environmental control. This facility provides the Iowa Neuroimaging Consortium (INC) with data center space that is very difficult to obtain in most campus environments and will facilitate the growth of the center.

    In conjunction with ITS Research Services, the Department of Psychiatry engages in a tier 3 backup of all imaging computer data. All data is backed up on several different servers located in different areas around the UI campus. One of these sites is the Research Services managed Information Technology Facility (ITF). The ITF is an off-site energy-efficient data center that provides a safe and secure location for the university’s vital IT infrastructure. Construction for this facility was strongly focused on environmental design and was completed in late 2011.

    The Iowa Neuroimaging Consortium (INC) is the major resource for image analysis software development and processing. All image analyses (registration of MR and PET images, segmentation techniques, measurements, 3-D visualization, etc.) are performed in this lab. Locally developed software resources include an image segmentation program, an automated surface generation program, and neural net software for delineating structures in MR images.

    The Iowa Neuroimaging Consortium (INC) employs systems managers and programmers who assist with experiment design, software development and acquisition, hardware set-up, end user support, and training of users. INC is also linked via a Gigabit switched Ethernet network to all the computer resources of the Iowa Institute for Clinical and Translational Science as well as the MR and PET facilities at the University of Iowa.

    Computing and Data Storage

    Major equipment, purchased largely through shared instrumentation grants, other grants, and university contributions from indirect costs, includes the following:

    Compute Nodes

    • 102 64bit Linux Based cores (~10 machines) with a total of 320GB of memory
    • 156 64bit MacOS Based cores (~30 machines) with a total of 270GB of memory

    Data Storage

    Temporary Data Storage for beta testing

    • 1 Network Appliance FAS3020 with 2TB of Online Storage
    • 1 Network Appliance FAS3040c with 26TB of Online Storage

    Tier 1 Data Storage

    • Home directory serviced on ITS managed cluster with roughly 40TB of Online Storage

    Tier 2 Data Storage

    • 3 systems with a total of 102 TB of storage space

    Tier 3 Data Storage

    • Information Technology Facility (ITF) off-site data center

    VMWare Servers – 4 total

    • 4 Dell PowerEdge R710
      • 3@8x2.26GHz 1@12x226GHz Xeon Processing Cores
      • 72GB RAM
       

    Compute Clusters

    • 1 64 Processor 2GHz Computational Cluster using Torq and Maui
    • 1 56 Processor 2GHz+ Computational Cluster using Rocks
    • Access to the University of Iowa Helium cluster, a 3508 processor core HPC system comprised of 359 compute nodes and 3 login nodes

    Other Equipment

    2 Color Printers

    • 2 Black and white printers
    • 1 Color duplex printer/copier/scanner
    • 1 Black and white duplex printer/copier/scanner
    • 1 Teleconferencing-A Polycom Viewstation FX H.323 multi-site videoconference system
     

    Software for Image Analysis

    Slicer

    Slicer is a mult-platform software package for visualization and medical image computing. Slicer is becoming the standard in resampling, viewing, tracing and performing measurements on medical images. Free for use, one of Slicer’s great advantages is the ability to add custom script to focus on the needs of the researcher.

    Brains2

    The core software for our structural image analysis. Provides a highly refined user interface for resampling, viewing, tracing, and performing measurements on images. Performs tissue classification, automated structure identification and surface generation. Statistical methods for PET and fMRI analysis are being incorporated. Development is ongoing, and a current collaboration with the ITK consortium complements and improves our software with many new features.

    FreeSurfer

    A package to generate and manipulate cortical surface representations. We have developed the ability to interface our Brains2 software with FreeSurfer formats to be able to generate spherical or flat maps of the cortical surface. Coregistration of these surfaces to a cortical atlas provides the ability to automate a highly specific parcellation of the cerebral cortex. Surfaces generated with FreeSurfer can also be used in AFNI for the mapping of functional imaging results onto the cortical surface.

    AFNI, SPM

    Software to process, analyze and display functional images. They have advantages over each other under different situations. The following functionalities are available in both AFNI and the SPM:

    Software for Image Analysis

    • 2D and 3D registration (motion correction)
    • Temporal and spatial domain smoothing
    • Linear and non-linear regression of 3D+time series
    • ANOVA tests across a collection of 3D datasets
    • Computation of voxel statistics
    • Computation and color overlay of activation maps

    Oracle and PostgreSQL

    Relational databases. Implemented with web-enabled query system to provide access to structural imaging measurements, subject demographics and results from clinical assessments and cognitive and neuropsychological testing.

    GoToMeeting/Lync

    INC has purchased an account with GoToMeeting, a web conferencing and online meeting program. This enables us to have a meeting with anyone in the world. Meetings can be in large or small groups, or even in a single office. We also have access to Lync which allows video collaboration with people in and outside the University of Iowa.

    XCode

    Xcode is an integrated development environment containing a suite of software development tools developed by Apple for developing software for OS X and iOS systems. Xcode takes advantage of all the newest Apple technologies by integrating all the tools needed to create source code, debug programs, and design user interfaces.

    MATLAB

    Matlab is a high-level language and interactive environment for numerical computation, visualization, and programming. MATLAB allows users to analyze data, develop algorithms, and create models and applications.

    Osirix/DicomRemap

    OsiriX is an image processing application for Mac dedicated to DICOM images. OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D, 3D, 4D and 5D viewers.

    Jira

    A web interface and bug-tracking package to allow users to create and modify bug reports in a simple database. This provides excellent feedback to our developers from users at any site.

    Confluence

    Web based wiki program that is used for project and information sharing and tracking.

    PET analysis

    A set of programs that provides capability for many types of analysis of PET data, including within-group analysis via techniques by Worsley et al. (the Montreal method), voxelwise correlational analysis and randomization analysis. Includes a sophisticated image viewer for easy review of results.

    Magnetic Resonance Research Facility

    The MR Research Facility (MRRF), one of the imaging centers of the Iowa Institute for Biomedical Imaging (IIBI), operates as a core university resource that provides research MR imaging facilities to the Institute for Clinical & Translational Science (ICTS). The facility manages research time on four MR scanners: 1) 100% allocation 3T scanner, 2) 50% allocation 3T scanner, 3) 10% allocation 1.5T, and 4) 100% allocation 7T whole body scanner. The MRRF currently supports 51 funded projects (40 NIH) from over 30 investigators across 6 colleges and 15 departments. The research dedicated 3T scanner was acquired through a High End Instrumentation Grant awarded in 2006 and serves as the primary system utilized for MR research studies at the University of Iowa. The College of Medicine invested $1.2 million renovating the space for this scanner, and we have continued to provide new technologies on this system for investigators. This has allowed us to have 20% annual growth in scanner utilization. A primary reason for this increased growth is the MRRF pilot grant program that supports acquisition of small datasets (~10 hours of scan time) to be used for grant applications. Presently, there are approximately 10 active projects acquiring pilot scans. Over the past five years, projects that have received pilot scans supported by the MR Research Facility have been awarded 10 R01s, 5 Program Project or Center Grants, 2 R21, and 12 grants from private foundations, the Veterans Administration, and the National Science Foundation. To support the growth of the imaging research, the University of Iowa is constructing the Pappajohn Biomedical Discovery Building (PBDB). The IIBI has been allocated over 26,000 square feet of space within the PBDB building to support both human and small animal imaging. This new space includes space for four whole body scanners and ten small animal imaging scanners including a 9.4T small animal MRI scanner. The 7T scanner will be installed in PBDB in November of 2013. To enhance exposure of this unique resource across campus, the MRRF is sponsoring a quarterly 7T lecture series.

    The MRRF provides support for translational research in animal models using a 4.7T small animal MR scanner for mice and rats as well as the human scanners for larger animal models (rabbit models for bone healing, goat models of osteoarthritis, and pig tumor models). In addition to support of projects across campus, the MRRF has been focused on MR technology development. A number of innovative projects are currently being undertaken and include 1) development and validation of pH sensitive MR imaging techniques, 2) new functional imaging techniques including magnetic source imaging, 3) accelerated imaging using compressed sensing, 4) lung imaging using hyperpolarized 3He and SF6, and 5) development of biomarkers for osteoarthritis. The facility has participated in a number of multi-center imaging studies including fBIRN, PREDICT-HD, Incyte, Direct-Net, and ADNI. Finally, the MRRF has contributed to the development of novel tools for analysis of brain morphology (BRAINS) and diffusion tensor imaging (GTRACT) as well as contributed to the development of 3D Slicer, ITK, and VTK open source software.

    UI PET Imaging Center

    The PET Imaging Center is a self-contained laboratory encompassing approximately 7000 sq-ft for production of radionuclides, synthesis of radiopharmaceuticals, quantitative PET scanning for research and clinical activities and analysis of PET imaging information.

    Radiochemistry Laboratories: The clinical radiochemistry laboratory has been recently modified to meet FDA mandated cGMP requirements. It houses a compact Class 7 Clean Room with three laminar flow hoods for aseptic processing procedures.

    The main production laboratory contains two large volume windowed hot cells, eight mini hot cells with remote video monitoring, a radiochemistry hood, and a laminar flow hood. The laboratory has a number of automated, computer controlled synthesis modules, including a Siemens Explora FDG quad-synthesis module, two GE FASTlab synthesis modulew that will be used for the synthesis of -[18F]FDG, anti-[18F]FACBC, and soon [18F]FLT, 2 Nuclear Interface synthesis modules for Fluorinated nucleophilic syntheses currently used to make [18F]FLT, a general purpose Nuclear Interface [11C]carbon synthesis module to make [11C] PIB and other [11C] compounds. We additionally have self- designed Lab-View controlled syntheses modules for [11C]choline, [11C]acetate, [18F]Fluoride, [13N]Ammonia. Two computers are used for master formulary tracking.

    A second research radiochemistry laboratory contains three custom-built Comecer hot cells equipped with laminar flow and gloved access for sterile radiopharmaceutical production. This lab contains 2 HPLCs equipped with variable wavelength UV and radioactivity detectors. Precursor development and developmental chemistry is performed in this lab.

    Quality Control Laboratory: The QC lab contains PC computers that control a Bioscan radio-TLC scanner and two Dionex BioLC HPLC systems complete with electrochemical, variable wavelength UV and radioactivity detectors. Three radio-GC systems are available for gaseous and liquid analysis. A Waters HPLC system equipped with electrochemical and conductivity detectors and a Waters EMD1000 mass spectrometer are also available. Other instruments include dose calibrators and NaI (Tl) well counters for accurate determination of radioactivity (dose) and gamma spectroscopy of labeled radiopharmaceuticals.

    Support Laboratories: The PET Center includes a physics and electronics lab with instrumentation for design, fabrication and repair of all devices in the PET Center, a complete machine shop, and multiple, networked computers for image display and analysis. Two full time, on-site engineers work within the PET Center, providing both repair and developmental services.

    Nuclide Production: GE PETrace 880 dual particle cyclotron (17 MeV protons, 8.3 MeV deuterons) for routine production of positron emitting radionuclides. The cyclotron is equipped with 5 primary target ports, with targetry designed for the production of F-18, O-15, C-11, and N-13. Attached to a sixth target port is an external beam line onto which is a four-target carousel, including a Comecer solid target system for the production of more novel positron emitting nuclides.

    PET/CT Scanners: Two PET/CT scanners are available: Siemens Biograph 40 PET/CT (3D only, LSO, 81 image planes, high-resolution, high count-rate options with 4.2 mm transaxial & 4.5 mm axial FWHM resolution, 4.4 cps/kBq sensitivity, 40 slice CT) and Siemens/CTI Biograph Duo PET-CT system (3D only, 45 image planes, 6.3 mm transaxial & 4.7 mm axial FWHM resolution, 925,000 cts/sec/μCi/cc sensitivity [scatter corrected], 2 slice CT). The Biograph Duo was installed in June 2003 and is primarily a clinical PET scanner. The Biograph 40 was installed in September 2006 and is available for both research and clinical uses. This scanner is equipped with Pico-3D electronics for improved count-rate performance and is capable of static, multibed, dynamic (list-mode) and gated acquisitions.

    PET Only Scanner: Siemens/CTI HR+ PET system (2D and 3D, 63 image planes, 4.6 mm transaxial and 3.5 mm axial FWHM resolution (3D), 900,000 cts/sec/μCi/cc sensitivity [3D, scatter corrected]). This system was originally installed in July 2002. This scanner is used for most research studies since it has a number of acquisition modes (static, dynamic, list mode, gated) useful for the investigation of brain function and tumor metabolism/response to therapy.

    Iowa Institute of Biomedical Imaging

    IIBI Facilities

    The Iowa Institute for Biomedical Imaging (IIBI) was formed in 2007 as an acknowledgment of a long history of interdisciplinary collaboration at the University of Iowa. The formation of the multidisciplinary institute reflects a strong institutional support to biomedical imaging and image analysis as well as to translational medical research. The IIBI brings together more than 60 faculty members (out of which over 45 hold faculty positions in the Carver College of Medicine, 15 hold faculty positions in the College of Engineering with a primary expertise in biomedical image analysis) and over 60 graduate students and postdoctoral fellows. The mission of IIBI is to foster efficient and cooperative multidisciplinary and cross-college research and discovery in biomedical imaging, and to improve training and education within the broader community at the University of Iowa. The Institute is finding its new home in two stories of a 100,000 sq.ft. University of Iowa Pappajohn Bioengineering Discovery Building that will be completed in June of 2014 – the floor plan and photographs are provided below. The IIBI space in this new building (30,897 sq.ft.) are devoted to human, large, and small animal imaging, image analysis, computational support, visualization, and biostatistical support. The IIBI space in the new building will become a new integrated home for a large number of image analysis projects that are currently ongoing at the University of Iowa and will therefore further enhance close interaction within the University of Iowa biomedical imaging community.

    The opening of the new facility, which is 100% devoted to research while located in an immediate proximity to the University of Iowa Hospitals and Clinics, represents a new chapter in IIBI’s existence and adds 30,897 sq.ft. of new imaging research space to IIBI, for a total of over 37,000 sq.ft. dedicated to small and large animal, and human imaging. The new facility brings together small animal housing; 1 floor of small animal imaging with 10 scanner rooms, behavioral rooms, as well as research staff office space; and another floor devoted to human and large animal imaging and translational medicine research with 4 large scanner bays, cardiovascular imaging suite, LINAC radiation delivery bay, virtual/augmented reality visualization suite, subject preparation rooms, meeting rooms and student/postdoc office cubicles. Research faculty/staff offices (2,627 sq.ft.) are adjacent.

    In the imaging space, a complete separation of human and animal access has been an important part of the programmatic design, animal and human research can be conducted simultaneously at different imaging bays with complete separation of access routes. Additionally, three of the four ground-level imaging scanner bays have been designed in a modular way with a removable wall to allow relatively easy way to install and/or replace whole-body imaging scanners as well as to allow installation of canners from different manufacturers. The fourth large scanner bay has been specifically designed for a 7T MR scanner which will be installed and operational in June 2014 – when the facility opens. Existing IIBI space in two adjacent buildings house a dedicated research 3T MR scanning facility (1,500 sq.ft.) and a dedicated dual-source CT scanning facility (1,800 sq.ft.). Additional 3,000 sq.ft. of computer-lab student cubicle space is available in a short walking distance. The IIBI facility is connected with a state-of-the-art Data Processing facility that houses file servers, compute-servers, data analysis clusters, and is connected to the IIBI space with ultrafast network connection (10 Gb/sec network speed).

    The remaining 6 floors of the Pappajohn Biomedical Discovery Building house translational research wet labs and will be occupied by research programs that require animal and translational imaging support. Among other research groups yet to be determined, the following research groups will find their new home in the wet-lab space of the Pappajohn Biomedical Discovery Building: Diabetes Research Center, Pulmonary Airway Biology Center, Neuroscience Institute.

    Computational and Informatics Resources

    The University of Iowa has two centrally managed enterprise data centers containing dedicated space, power and cooling for University of Iowa Research and a third server room entirely dedicated to research computing. Altogether, these data center spaces are ultimately designed to deliver 1.2 megawatts of power and associated cooling with approximately 4,800 square feet of securely managed and maintained raised floor capacity for research computing. The newest of these data centers, the Information Technology Facility (ITF), is located on the University of Iowa Research Park campus and utilizes multiple-10 Gigabit Ethernet circuits along diverse physical paths to connect to both the main campus network cores and the local-to-campus alternative data center. Distribution networks within data centers are a combination of multiple-10 Gigabit Ethernet circuits to data center-class network gear, providing 1 Gigabit and 10 Gigabit Ethernet service, and via direct fiber (e.g., for fiber-channel storage). Research computing within each campus data center is segregated from university line-of-business networks to provide isolation and performance-tuning optimizations.

    ITS Research Services manage High Performance Computing (HPC) resources available to UI researchers. The HPC system dubbed, Helium consists of 200, 8-core nodes with high speed Infiniband network connections and a combination of 24 GB and 144 GB memory nodes. Helium has a theoretical TFLOPS rating of 40. The University's newest HPC cluster, Neon, due to be operational in late 2013 will feature 157 nodes with a combination of 16 and 24-core processors and everything from 64 GB to 512 GB of memory. Neon's theoretical TFLOPS rating with processors and accelerators is estimated at 93. Both Helium and Neon are the result of researchers' pooling of funding in centrally managed and maintained HPC environments.