United States Department of Veterans Affairs
United States Department of Veterans Affairs

Center for Imaging of Neurodegenerative Diseases

Facilities

The Center for Imaging of Neurodegenerative DiseasesThe front view of CIND building

In March 2006 our research group moved into a newly remodeled building, CIND, located adjacent to our 4 Tesla MRI/MRS building. CIND houses our entire research group consisting of more than 60 faculty, postdoctoral fellows, technicians, computer support, and administrative staff. The 1.5 T Siemens MRI, which is part of CIND and is 100% used for CIND research remains in the main hospital building.


4T Bruker MedSpec MRI

In late 2003, a Bruker MedSpec 4.0 Tesla whole body MRI system was delivered to the CIND in a separate but adjacent 1000 square foot building containing a waiting room and bathroom in addition to the MRI instrumentation. The Bruker state-of-the-art MRI system is the result of a collaborative effort between Bruker and Siemens Medical Systems, and includes an actively shielded, whole body 4.0 Tesla magnet, 40 mT/m gradients (Siemens Symphony gradients) with a slew rate of 200 T/m/s. The system is equipped with an eight channel receiver and a number of transmit/receive headcoils including birdcage, TEM, and array coil headcoils. The broadband system uses a 4 kW RF amplifier at the proton frequency, and utilizes Siemens interface software for data collection, manipulation, and display. Also included is a high current (10 amp) shim power supply. In addition, echo-planar MRI, array coil reception with variable accelaration factors, and spectroscopy sequences are included with the system. Finally, orders have been placed for a higher power RF amplifier (8 kW) and body coil, an eight channel receive array coil, and auto-align software to automatically register repeat scans to the previous scan.


1.5T Siemens MRI/MRS Magnetom VISION

In addition to the 4.0 Tesla MRI system, the CIND also has a 1.5T Siemens MRI/MRS Magnetom VISION system equipped with 25 m T/m self-shielded gradients with rise times of 0.35 milliseconds providing echo planar imaging. The Siemens gradient amplifier booster package (‘Gradient Overdrive System’) giving a slew-rate approaching 80 mT/m/ms has been installed. The gradient performance comes close to existing FDA limits pertaining to peripheral nerve stimulation, but as this site is an accredited research center, such restraints will not be mandatory. These improved slew-rates, along with improved A/D converters, facilitate EPI with much better spatial resolution, with acquisition matrices of up to 128x256, and also greater temporal resolution. In addition to sequences for MRI and 1H magnetic resonance spectroscopic imaging (MRSI), the system has a 31P channel and 1H decoupling channel; a home built double-tuned 1H/31P birdcage head coil facilitates 1H decoupling during 31P acquisition. The system is operated by a SUN Microsystems SPARC 10 computer.


Computing Infrastructure

The CIND’s computing infrastructure is implemented primarily on a single subnet within the San Francisco Veterans Administration network. Most of the subnet is gigabit Ethernet which provides high throughput transfer of image files. The gigabit segment extends to the desktops of data processors.

The CIND has more than 80 additional PCs (Pentium III, IV), including single and dual processors with color monitors (up to 22") and 10 printers for image processing, word processing, spreadsheet, presentation graphics, and for computational programs (Python, R, Mathematica, Matlab, IDL, S-Plus). Operating systems for these computers include Windows 2000, Windows XP, Windows 2003 Server, and Fedora. Memory size on these systems varies from 512 MB to 4 GB.

For parallel processing applications the CIND has: 1) A 48 processor Beowulf system with 3 GHz Xeon CPUs, 4 GB of memory, and a fast (533 Mhz) on board bus; in addition the head node has a 1.0 TB RAID-5 disk array; the nodes are connected by a GigE internal network.

The CIND has a Medtronics computer for automated measurements of hippocampal volume and shape.

For data image and data analysis, CIND has 10 additional nodes running Linux containing two 3GHz CPU, 4GB of memory, a fast front side 400 or 800 MHz bus, and high resolution plasma and LCD screens for visual analysis.

For image storage and access by data warehousing and data mining applications, CIND has a Windows 2003 Enterprise Server Cluster consisting of 3 nodes each with dual 3 GHz Xeon CPUs and 4 GBytes of physical memory, and an attached Storage Area Network (SAN) with 20 Terabytes for large volume, fast access disk storage.

Files on the primary data stores are mirrored to systems sited in a physically different location within the VA campus from that of the primary data store. The mirrors are backed up to a Dell Power Vault 136T tape library attached to the Windows Cluster using Veritas backup software. Each tape is retained onsite and a copy of the tape is stored offsite in a secure vault.

The CIND database server has dual 3.2GHz Xeon's, 8GB of 800MHz DDR2, a 36GB RAID-1 SCSI system array and 144GB RAID-5 SCSI data array running Windows 2003 Server Enterprise Edition and Microsoft SQL Server 2000 Enterprise Edition.

The CIND intranet web application server has dual 600MHz P-III's, 1GB of memory, and a 12GB drive running Windows 2003 Server and IIS6.

The CIND source control server has dual 600MHz P-III's, 1GB of memory, and a 100GB RAID-5 SCSI array running FreeBSD 6.0, Subversion, and Trac.