IU Health Neuroscience Center Facilities
The IU Health Neuroscience Center is a premier center that combines IU Health’s comprehensive neurological services into a single location for a more integrated approach to clinical care and research. The facility is located just south of IU Health Methodist Hospital and a few blocks north of the IUPUI campus. Phase I of the Neuroscience Center, an ambulatory care and imaging facility, opened in August 2012. The ambulatory care center includes outpatient clinics and office space for clinicians and researchers affiliated with Psychiatry, Physical Medicine & Rehabilitation, Radiology and Imaging Sciences, Neurology, Neurological Surgery, and Neuropsychology. This new state of the art facility also houses cutting edge imaging instruments for both clinical and research use. The dedicated research imaging facilities include a Siemens Magnetom Skyra 3T MRI, a Siemens Magnetom Prisma 3T MRI, as well as a Siemens Biograph mCT.
Siemens MAGNETOM Skyra 3T MRI. A research-dedicated Siemens MAGNETOM Skya 3T 70cm bore whole body scanner was installed in June 2012. Key features include: XQ-gradient providing gradient strength up to 45 mT/m (72 mT/m effective), slew rate up to 200 T/m/s (346 T/m/s effective), up to 50 cm FOV and AudioComfort noise reduction; RF system with 64 receive channels supporting up to 204 coil elements; multiple RF coils including a 32-channel dedicated head coil, a 20-channel Head and Neck Coil as well as an array of other anatomy coils (neck, cardiac, etc.); Syngo D11 software with InLine Automated Processing, Auto Align slice positioning, Phoenix image reproducibility, Intelligent Coil Control auto coil position detection, full suite of imaging techniques (inline 3D and SSH EPI fMRI, up to 512 direction DTI/DSI, 3D ASL, SWI, etc.), syngo advanced imaging applications, iPAT2 utilizing mSENSE and GRAPPA technologies to increase image quality and reduce susceptibility artifacts. IDEA and ICE development environment and analysis packages are also available.
Siemens MAGNETOM Prisma 3T MRI. A research-dedicated Siemens MAGNETOM Prisma 3T 60cm bore whole body scanner was installed in August 2014. Key features include: Zero helium boil-off technology, gradient strength up to 80 mT/m at slew rate up to 200 T/m/s, up to 50 cm FOV; RF system with 64 receive; Magnet homogeneity at 40 cm DSV – 0.25 ppm; multiple RF coils including the newly FDA approved 64-channel Head and Neck coil, a 20-channel Head and Neck Coil as well as an array of other anatomy coils (neck, cardiac, shoulder, knee, etc.); Tim 4G +Dot, Tim TX True Shape, Syngo D13 software with InLine Automated Processing, Auto Align slice positioning, Phoenix image reproducibility, Intelligent Coil Control auto coil position detection, full suite of imaging techniques, including multi-nuclear, advanced cardiac, Syngo advanced neuroimaging applications. IDEA and ICE development environment and analysis packages are also available.
Siemens Biograph mCT. A research-dedicated Siemens Biograph mCT PET/CT scanner was installed in June 2012. PET features include: TrueV technology for extended FOV up to 78 cm; HD?PET and ultraHD?PET/Siemens Time of Flight technology for 2mm intrinsic resolution and improved sensitivity; TrueC, model-based Compton scatter correction; patented high-density 4x4x20mm LSO detectors with decay time of 40ns and coincidence timing of 4.5ns; HI-REZ detectors; sinogram mode and dynamic listmode data acquisition capabilities; multiple filter selections and algorithms for reconstruction, including OSEM and FBP. CT features include 128-slice CT with STRATON X-ray tube with 0.3s CT rotation speed, Adaptive Dose shielding and CARE Dose4D, z-Sharp technology for 0.33mm isotropic resolution, and Adaptive 4D Spiral technology for full-coverage perfusion studies.
Tracer and Contrast Agent Development Facility
The Biomedical Research and Training Center (BRTC), houses our tracer and contrast agent development program. This facility consists of a cyclotron laboratory for the production of short-lived radionuclides, a radiation chemistry laboratory for the synthesis of drugs labeled with the radionuclides produced by the cyclotron, an analytical chemistry laboratory for measuring the sterility and pyrogenicity of the labeled drugs, and an automated pneumatic transport system for transporting PET radiopharmaceuticals to the imaging suite for measuring the 3D distribution of these drugs in the animal and human body following administration.
Cyclotron Laboratory. Housed within the cyclotron facility is a Siemens Radionuclide Delivery System (RDS), Eclipse RDS-111 cyclotron. This system consists of an 11 MeV proton cyclotron, irradiation target systems for the production of [11C], [13N], [15O], and [18F] radioactive material transport systems, and a series of computer-controlled synthesis modules for the production of radiopharmaceuticals.
Radiation Chemistry Laboratory. The 4 radiation chemistry laboratories at the BRTC consist of a series of shielded chemistry cells for the production of radiopharmaceuticals labeled with positron emitting radionuclides produced by the cyclotron. These cells are designed to hold several curies of radioactive material with minimal exposure to the personnel performing the syntheses. This laboratory also houses chromatography equipment for the isolation of radiopharmaceuticals from radiochemical contaminants produced in the synthetic process as well as analytical equipment for the measurement of radionuclide quantities.
Analytical Chemistry Laboratory. The analytical chemistry laboratory is used to assay small samples of the radiopharmaceuticals produced in the radiation chemistry laboratory. This laboratory contains assorted chromatography and sample assay equipment for these purposes. This laboratory is also used to assay human blood radiopharmaceutical concentrations and metabolites. Equipment used for the blood sample analysis includes an automated well counter system, centrifuge, and assorted separation columns for isolating radiopharmaceuticals from metabolites formed in the human body. The facility at BRTC houses 3 analytical chemistry laboratories.
Cold Chemistry Laboratory. The 6 cold chemistry laboratories in the BRTC are used for the synthesis of non-radioactive precursor compounds required for the synthesis of research radiopharmaceuticals.
Automated Pneumatic Transport System for PET Radiopharmaceuticals. A pneumatic transport system was established between our cyclotron/radiochemistry facilities and the PET imaging suites that are separated by a distance of ~2 km. Unique features of this system include a path which crosses a river, a 3-way networked computer control system, and novel carrier designs.
PET Tracer Production. PET [11C] and [18F] tracers, novel and potent enzyme-based and/or receptor-based brain, tumor and heart imaging agents are produced for PET to study brain, cancer and cardiovascular diseases. Numerous tracers are in various stages of development for support of research. The following list, although not exhaustive, illustrates the breadth of neuroscience, cancer, and cardiovascular-related radiopharmaceuticals at various stages of development, from initial evaluation in cell and animal models to evaluation in clinical trials.
- [18F]FDG Glucose metabolism
- [18F]Fluoride Bone Scanning
- [18F]Fluoromethane Perfusion
- [11C]CO Blood Volume
- [11C]Acetate Free Fatty Oxidation Rates
- [15O]H2O Blood Flow
- [15O]O2 Oxygen Consumption
- [13N]NH3 Blood Flow
- [11C]CFT and [11C]CIT Dopamine and Serotonin transporters
- [11C]Raclopride D2 receptors
- [11C]PIB b-Amyloid plaques
- [11C]DAA1106 Peripheral benzodiazepine receptor
- [11C]PBR28 Peripheral benzodiazepine receptor
- [11C]Flumazenil Benzodiazepine receptor
- [11C]Choline Brain Tumors
- [11C]Yohimbine a2 Adrenergic receptors
- [11C]DTBZ Vesicular monoamine transporters
10. a-[11C]Methyl-L-tryptophan (a-[11C]AMT) Serotonin synthesis
11. NK-1 Radioligands NK-1 receptors
12. D2/D3 Radioligands D2/D3 receptors
13. Glioma Radioligands Glioma
14. SKCa channel blockers [11C]NML SKCa channels
15. Arylbenzothiazoles b-Amyloid plaques
16. Stilbene derivatives b-Amyloid plaques
17. Tetrahydroisoquinoline derivatives AMPA receptors
Other Relevant Tracers (Cancer & Cardiovascular Programs):
- Radiolabeled MMP inhibitors Matrix metalloproteinase (MMP) enzymes
- Radiolabeled O6-benzylguanine analogues DNA repair protein MGMT enzyme
- Radiolabeled luciferin derivatives Luciferase gene
- [11C]Choline Choline kinase
- [18F]SU11248 Tyrosine kinase
- Stilbene derivatives Aryl hydrocarbon receptor
- Sulfonanilide analogues Aromatase
- Arylbenzothiazoles Tyrosine kinase
- Triphenylacetamides Nuclear factor k-B (NFk-B)
10. [18F]FES Estrogen receptors
11. Radiolabeled cyclofenil derivatives Estrogen receptors
12. Tetrahydroisoquinoline derivatives Glioma
13. Tetrahydroisoquinoline derivatives Selective estrogen receptor modulators (SERMs)
14. [11C]Neostigmine, Pyridostigmine Acetylcholinesterase (AChE)
15. [11C]HC-15, [18F]HC-15, [11C]HC-3, [18F]HC-3 High-affinity choline uptake (HACU)
16. Rivastigmine derivatives Acetylcholinesterase (AChE)
Image Processing and Data Analysis Computing
Super Computing and Massive Data Storage Systems:
We have access to the following supercomputers and storage systems:
- Big Red II. Big Red II is a new 1 petaflop supercomputer from Cray Inc., installed at IU the week of 8 April 2013. Big Red II has an aggregate peak theoretical capability of just over a petaflop, and an aggregate RAM of 47 TB. Big Red II consists of 1020 nodes total: 344 XE6 nodes, each with two 2.5 GHz AMD Abu Dhabi processors and 64 GB of memory; and 676 XK6 nodes, each with one 2.3 GHz AMD Interlagos processor and one NVIDIA K20 accelerator with 32 GB of system memory and 5 GB of GPU memory. The nodes are interconnected in a 3D Torus using Cray’s Gemini interconnect that provides 20 GB/s of bandwidth per node. This system will have more bandwidth to high performance file systems such as the Data Capacitor than ever before, as they will connect via a low-latency InfiniBand network that will provide an aggregate throughput to storage of 48 GB/s.
- Big Red. Big Red is an IBM e1350 distributed shared memory cluster with 4096 processor cores, 6 TB total memory capacity, and a peak theoretical processing capability of 40.96 TFLOPS. The compute nodes consist of 1024 IBM JS21 Blade servers, each with two dual-core PowerPC 970MP processors, 8GB of memory, a 73GB local SATA disk for scratch space, and a PCI-X Myrinet 2000 adapter for high-bandwidth, low-latency MPI applications. Four JS21 Blades are used as login and development nodes, and 16 p505 storage nodes are similarly configured. In addition to local scratch disk, the Big Red compute nodes are connected to the Data Capacitor via four shared 10Gbps Ethernet links.
- Karst. Karst is Indiana University's newest high-throughput computing cluster. Karst is equipped with 256 compute nodes, plus 16 dedicated data nodes for separate handling of data-intensive operations. All nodes are IBM NeXtScale nx360 M4 servers, each equipped with two Intel Xeon E5-2650 v2 8-core processors. Each compute node has 32 GB of RAM and 250 GB of local disk storage. Each data node has 64 GB of RAM and 24 TB of local storage. All nodes run Red Hat Enterprise Linux (RHEL) 6 and are connected via 10-gigabit Ethernet to the IU Science DMZ.
- Mason. Mason is an HP distributed shared memory cluster with 512 processor cores, 8 TB total memory capacity, and a peak theoretical capability of 3 TFLOPS. The compute nodes consist of 16 DL580 G7 servers, each with four eight-core Intel Xeon L7555 processors, 512 GB of memory, and a PCIe 10Gb Ethernet adapter for high-bandwidth data transfer. The cluster includes 16 TB of local spinning disk.
- The IU Data Capacitor II. The Data Capacitor II is a high speed/high bandwidth Lustre storage system that serves the high performance computing systems at Indiana University Bloomington. Installed in February of 2013, DCII includes a 5 PB Lustre file system (4 PB usable) from Data Direct Networks (DDN) with an aggregate 48 GB/s of data I/O capability. DCII includes sixteen Lustre object storage servers, two Lustre metadata servers, and eight Lustre routers all connected via full data rate (FDR) InfiniBand to two DDN SFA12000 storage controllers. The Lustre routers also have 10-gigabit Ethernet connections to allow systems without InfiniBand to access the system. The two metadata servers are connected to a DDN SFA6620 storage controller. The new Data Capacitor hardware is expected to provide 48-56 GB/s of bandwidth to IU research systems.
- The Research File System. The IU Research File System currently has a capacity of 80 TB (60 TB usable) and allows for group collaboration via file sharing. Users have a highly flexible system for granting access to files, and the underlying OpenAFS technology used for the system can enable users at multiple institutions to share files. Researchers can request dedicated project space for each project requiring dedicated storage and collaboration. In the first half of 2013, the RFS system was upgraded to a new DataDirect Networks (DDN) solution using GPFS that provides, on two IU campuses, 420 TB (336 TB usable) of storage synchronously mirrored for disaster recovery and availability. The new environment also provides home directory space for IU’s HPC systems, using GPFS as the underlying file system.
- IU’s Scholarly Data Archive (SDA). SDA uses High Performance Storage System (HPSS) software to make available to IU researchers a total storage capacity exceeding 15 PB. Data are written to a fast, front-end disk cache and migrated over time to IBM TS3500 tape libraries on the Indianapolis and Bloomington campuses. Data written to IU's HPSS system are copied simultaneously to both locations, providing highly reliable disaster protection.
The following computer systems and programs are available in the IU Health Neuroscience Center to aid us in the collection and analysis of data under the proposed project:
- Eighteen Linux Xeon 2 to 6 core 64-bit Dual CPU workstations (8 GB to 64 GB RAM, 500 GB Disk Space, DVD-RW)
- One Windows 7 Xeon 64-bit Dual CPU capable workstation (24 GB RAM, 4.5 TB Disk Space)
- One Windows 7 Xeon 64-bit Dual 6 core CPU workstation with NVIDIA Tesla GPU processing card (64 GB RAM, 200 GB Disk Space)
- 40 Windows XP or 7 Pro Intel Duo CPU computers (2 GB to 8 GB RAM, >250GB Disk Space, DVD-RW)
- Linux Dual Quad Core Web Server (4GB RAM, 900GB RAID5)
- Linux Dual Quad Core DICOM/LCMODEL Server (3 GB RAM, 900 GB SCSI RAID 5)
- LTO-3 11.2 TB tape library backup system
- LTO-4 45.8 TB tape library backup system
- 136 TB Raw Storage in Apple XServe/RAID NAS system with another 10.5 TB storage for scratch space and other testing
- “GenomeStudio”, “Plink/Haploview”, “Mach”, “Eigenstrat”, “PennCNV” packages for GWAS/CNV analyses
- “Pathway Studio” software package for pathway analysis
- “FreeSurfer” and “SPM5/SPM8” software packages for brain imaging phenotype definition
- "BRAINS" and “BRAINS2” software packages for brain morphology/volumetry
- “SLICER” software package for volumetrics and Diffusion Tensor Image processing
- “AFNI” and “FSL” software packages for neuroimaging processing and analysis
- “Amira” software package for 3D visualization and processing
- “LCMODEL” spectroscopy analysis package
- “SPSS”, “SAS”, and “R” statistical packages
- “Matlab” site license for method and tool development
MR Imaging and Stimulus Delivery Equipment
- 2 MRI compatible 4 button in-line response boxes with fORP interface (Current Designs)
- 2 MRI compatible 2 button trackballs (Current Designs)
- 2 fMRI Stimulus Delivery Systems
- Psychology Software Tools, Inc. – DLP Projector System
- Avotec sound system
- Resonance Technologies VisuaStim System with MRI compatible goggles and headphones
- “Presentation” stimulus delivery software
- “E-Prime” stimulus delivery software
- 4 Windows 64-bit desktops for running stimulus delivery software and equipment
- 2 Windows 64-bit laptops for task training and stimulus delivery computer backup