The Research Imaging Institute (RII) has a total of 28,000 sq ft of space that houses the laboratories, computing facilities, and offices.

Human imaging suites (MRI, PET and TMS) are located on the first floor of the RII in a 10,000 sq ft area. Five MRI scanner suites (2 human and 3 animal – 2 scheduled for installation in 2008) are located on the first floor of the RII. The TMS laboratory (1 room), the PET area including rodent microPET (five rooms), one cyclotron (2 rooms), and the radiochemistry area (2 rooms) are also located on the first floor. The Biomedical Image Analysis Division (BIAD) (ten rooms), speech motor lab with sound booth (2 rooms), and ERP lab with sound booth (2 rooms) are on the second floor of the RII. A 5,000 sq ft addition that will house a 2nd cyclotron and additional radiochemistry laboratories was recently completed.

Electromyography (EMG) and nerve conduction studies are carried out in the TMS laboratory on the 1st floor. Neurocognitive assessments are carried out in 3 dedicated rooms on the 1st floor. Speech and motor assessments are carried out in a 800 sq ft laboratory on the 2nd floor.

A 10,000 sq ft laboratory animal facility is located on the first floor of the RII. This facility includes two MRI imaging suites, three large primate rooms, five preparation and recovery rooms, seven small animal rooms and two complete surgical suites.

The RII’s Biomedical Image Analysis Division (BIAD) provides computational support to all research projects and faculty. This division employs a technical director for computing systems, one faculty level programmer, two senior level programmers, one junior lever programmer, two consultants, and 3 system administrators. Three common-use rooms are available for researchers to analyze data, a server and HPC support area, and offices for staff and faculty. Each lab is equipped with computers appropriate with their applications. See below for major equipments.


The RII has 4,850 square feet of office space. Six administrative and secretarial personnel are dedicated to providing administrative support to the other 40 faculty, staff, and students.


Scanditronix MC17 dual particle, 17-Mev particle accelerator with automated chemistry modules for rapid line-delivery of 11C, 15O, and 18F - isotopes.

Siemens Eclipse HP cyclotron: a 11 MeV cyclotron will be operational by June 2008 for production of 18F-FDG, 11C, and 15O.

Radiochemistry Lab: is fully equipped for production, purification, and quality control of all needed isotopes.
PET: CTI/Siemens HR+, 63-slice, high-sensitivity, high-resolution (4.1mm in 3D mode). The PET camera and cyclotron are within 30 ft of each other.


Scanditronix 4096 high-resolution (5.5mm), 15-slice, high-peak-count-rate camera. The PET camera and cyclotron are within 30 ft of each other.

Concorde Rodent microPET, with 96 LSO detector blocks and 6,144 crystal elements. Bore is 10 cm in diameter; Axial field of view, 10 cm. Reconstructed volume resolution- <7.0mm3. System is fully portable.
Siemens Focus 220 Primate microPET, with 168 LSO detector blocks and 24,193 crystal elements. Bore is 26 cm in diameter; Axial field of view, 8 cm. Reconstructed volume resolution- <2.5mm3. System is fully portable and can be tilt up to a 45o angle for optimal placement of large animals. Bore size is sufficiently large to accommodate a human head. (scheduled for installation in 2008)

(NIH funds for the Focus 220 have been awarded; system to be delivered spring 2008)


Cadwell TMS: The transcranial magnetic stimulation system is a Cadwell High Speed Magnetic Stimulator (HSMS) (Kennewick, Washington).
Magstim BiStim Module (The Magstim Co. Ltd. Wales, UK).
NeuroMate Robotic System: The NeuroMate Robotic System includes a five-axis robot arm; robot base and head support frame; and (ActMate) workstation; CRS-Model F3 Robot

Neuromate image guided robotically controlled TMS planning and delivery system. Magstim and Cadwell high-rate stimulators with a selection of TMS coils designed for both human and animal use.



A whole-body 3T Siemens Trio MRI human scanner, high-field MRI, fMRI, and spectroscopy system. System will be upgraded to the TIM version in summer 2008.
A whole-body Siemens 3T TIM MRI full-bore scanner for primate imaging became operational in February 2008.
A small non-human primate and rodent Bruker Biospec 7T MRI scanner brought online January 2008. Bore size is 30cm diameter; 20/12/6cm free bore depending on gradient set.
A small animal Bruker Biospec 11.7T MRI scanner will be delivered by May 2008. Bore size is 16cm with a free bore diameter of 7cm with gradient.


68-channel SAI amplifiers; 64-channel BioSemi ActiveTwo electrodes and amplifier, Polhemus Scalp digitizer- and audio equipment.

Speech Motor lab: has Northern Digital: Optotrak with 2 infrared sensor bars for 3-D movement monitoring; Kay Electrometrics, Computerized Speech Laboratory for acoustic analysis; 3 Digital Video

Research Imaging Institute
The Research Imaging Institute (RII) is a department-level entity within the UTHSCSA. The mission of the RII is to develop non-invasive imaging and measurement methods and to apply these methods to basic and clinical research. The RII was created as a “Special Project of the University of Texas”, by an act of the State Legislature and receives annual infrastructure support from the State. The RII is composed of six divisions: 1) the Positron Emission Tomography Division; 2) the Magnetic Resonance Imaging and Spectroscopy Division; 3) the Translational Imaging Division; 4) the Human Electrophysiology Division (including the TMS and ERP laboratories); 5) the Biomedical Image Analysis Division; 6) and the Human Performance . The RII is directed by Peter Fox, M.D. and has 17 full-time faculty, 30 full-time technical lab staff, and 7 full-time administrative and secretarial staff. The following overview of the facility will focus only on those aspects of the RII which are apropos to the equipment grant application.

PET Division
Division Chief: Paul Jerabek, Ph.D.
The PET facility currently uses three FDA-approved radiotracers, which support 33 research protocols. Those include fluorine-18 labeled FDG to assess brain glucose metabolism in patients with depression, complex partial seizures, and myocardial ischemia and viability; oxygen-15 labeled water to assess changes in blood flow for human functional brain mapping and complex partial seizures. New tracers are being developed to investigate dopamine metabolism, improve the signal-to-noise in functional brain map studies, and to monitor hormonal-mediated receptor concentrations.
Positron Emission Tomography Laboratory.
Technical Director: Paul Jerabek, Ph.D.
Performance Monitor: Betty Heyl, BCNMT
CTI/Siemens EXACT HR+: a 63-slice, high-sensitivity, high-resolution (4.1mm in 3D mode) whole body scanner capable of 2D and 3D data acquisition. This scanner has 18,432 BGO detectors and has an axial field of view of 15.5 cm. The sensitivity of this scanner at the center of field of view is 5.24 cps/kBq in 2D and 36.57 cps/Bq in 3D mode.
Concorde Model Rodent microPET, 4-ring System, with 6,144 LSO detector elements. Bore 10 cm diameter; Axial field of view, 8 cm. Reconstructed volume resolution, 2 x 2 x 2 mm. Absolute sensitivity at the center of field of view is 5.62 cps/kBq @ 250 keV. Reconstructed volume resolution- <7.0mm3. System is fully portable.
Siemens CTI Focus 220 Primate microPET, with 168 LSO detector blocks and 24,193 crystal elements. Bore is 26 cm in diameter; Axial field of view, 8 cm. Reconstructed volume resolution- <2.5mm3. System is fully portable and can be tilt up to a 45o angle for optimal placement of large animals. Bore size is sufficiently large to accommodate a human head.
General Electric Model 4096 PET scanner. A whole-body 2D scanner containing 8 rings housing 4096 BGO detectors providing 15 slices. This scanner has a 10 cm axial field-of-view. In-plane resolution: 5.5 mm FWHM in the center of the field of view, axial resolution: 6.0 mm FWHM in the center of the field of view. True sensitivity is 4.5 cps/kBq.
Support Equipment
PET Stimulus Presentation Equipment: Stimulus presentation in the PET lab can be accomplished in several different ways. First, a Macintosh running SuperLab (Cedrus, Inc.) can present either auditory or visual stimuli and record behavioral responses. Second, for experiments where visual stimulus must be rapidly presented, a Macintosh running PsychStim (PsychStim v1.9, by David Darby, Australia) can be used. Third, a dual-PC computer system on a portable cart running software from the Electrophysiology Lab can also present either visual or auditory stimuli and record behavioral responses during PET studies. There is also a specially constructed, very wide field-of-view, PC-controlled, visual stimulation system using a Fresnel lens and a very large curved screen that can be used for studying peripheral visual processing. In addition, tape recorded video and auditory stimuli can be presented to the subjects. Finally, extremely versatile stimulus presentation software called E-Prime (Psychology Software Tools, Inc.) is being used. E-Prime is a new graphical experiment generator for the Windows 95/98/ME environment. E-Prime consists of a suite of applications to design, generate, run, collect data, edit and analyze the data. E-Prime includes: 1) a graphical environment allowing visual selection and specification of experimental functions; 2) a comprehensive scripting language; 3) data management and analysis tools. E-Prime is also capable of sending a signal through the printer or serial ports for interfacing with external devices. Thus, E-Prime can be used to trigger an event (e.g., signal an external device such as a pulse generator to begin and/or stop pulse sequences) or notify an external device of an event (e.g., in order to mark the event in the data collected by the external device).
Gas Delivery System. A gas administration system designed to deliver radioactive gases for continuous or bolus administration of 15O-labeled gases (15O2, 15CO2, and 15CO).
Automated Blood Sampler. An automated blood sampler can be integrated with the scanner host computer to provide blood sampling of radiotracer activity as a function of time for quantitative radiotracer modeling and quantitative analysis (e.g., blood flow and glucose metabolic rate).
Beta probe. An intra-arterial beta probe that can provide arterial concentration of the radiotracer activity as a function of time for quantitative radiotracer modeling and quantitative analysis (e.g., blood flow and glucose metabolic rate) is available.
Limited-Support Contract: There is a service contract with Siemens for CTI HR+ scanner. Service is provided by an independent contractor on as needed basis for the GE 4096 scanner. There is a continuing maintenance contract for the Concorde R4 microPET from Siemens/CTI.

Technical Director: Paul Jerabek, Ph.D.
Scanditronix Model MC17F Cyclotron. A dual particle (proton and deuteron), fixed energy (17.2 MeV protons and 8.6 MeV deuterons), isochronous accelerator. Five targets are available for production of 11C, 18F, 13N, and 15O. The accelerator is located in a concrete shielded vault adjacent to the radiochemistry laboratory and directly across the hallway from the PET scanner suite.
Eclipse HP cyclotron (Siemens): Siemens Eclipse HP cyclotron, an 11 MeV negative ion single particle accelerator, produces Curie levels of positron emitting radioisotopes — 18F, 11C, 13N and 15O. Its self-shielded, automated design offers fast, easy, and efficient production of PET radioisotopes. The four position automated target carousel can be installed on either of two beamlines. This cyclotron will be operation by January 2008. This cyclotron will not only expand the ongoing blood flow and metabolic studies in humans and animals, but also support new radio-ligand studies.
Support Equipment
Radiochemistry Laboratory. A fully equipped laboratory for providing a variety of positron-emitting radiopharmaceuticals to the PET scanner. Currently 15O-labeled water, 13N-labeled ammonia, 18F-labeled fluorodeoxyglucose, and 11C-labeled acetate are available for routine use. Synthesis systems include on-line production units, a laboratory robotics system, and a dedicated system for production of 18F-labeled fluorodeoxyglucose. The laboratory also hosts an array of equipment including gas chromatography and high performance liquid chromatography systems to support the radiochemistry activities.
A similar laboratory is being built in the new wing of the RII which will also house the cyclotron. This new radiochemistry lab will also be capable of providing providing a variety of positron-emitting radiopharmaceuticals to the PET scanner including receptor ligands.
Quality Control Laboratory. A fully equipped laboratory located adjacent to the radiochemistry laboratory is capable of providing in-house radiopharmaceuticals and quality control procedures for all of the PET radiopharmaceuticals produced.
Similar laboratory is being built in the new wing of the RII which will also house the cyclotron. This new quality control lab will also be capable of providing in-house radiopharmaceuticals and quality control procedures for all of the PET radiopharmaceuticals produced.
Limited-Support Contract: Service of the Scanditronix cyclotron is provided by an independent contractor on as needed basis. The new Eclipse cyclotron will be have a service agreement with Siemens.

MRI Division
Division Chief: Geoffrey Clarke, Ph.D.
The MR Division of the Research Imaging Institute currently has one magnetic resonance imager (MRI), a Siemens TRIO 3T MRI full-bore human scanner. Funding has been obtained to acquire 3 additional MRIs, a 3T MRI for large primate imaging, a 7T MRI for small non-human primate imaging and a 9.4T MRI for rodent imaging. These are expected to be installed and running within 2007 and early 2008. A large variety of volume and surface coils for imaging or localized spectroscopy are available. Facilities for constructing and testing radiofrequency and gradient coils are available.
Magnetic Resonance Imaging Laboratory.
Performance Monitors: Jinqi Li, M.D.
A whole-body 3T Siemens Trio MRI scanner has been installed at the Research Imaging Institute. This research-dedicated 3T system is funded by NCRR/NIH. This system provides the state-of-the-art techniques in performing functional MRI (fMRI), cardiac imaging, and in vivo NMR spectroscopy. It has 8 fast radio-frequency channels in supporting integrated parallel acquisition techniques (IPAT). A high gradient system (40mT/m) associated with this system enables us the ability in performing the diffusion tensor imaging (DTI). Based on the great improvements in signal-to-noise ratios, this scanner will provides higher spatial resolution as well as the scan speed.
A whole-body 3T MRI scanner capable of supporting human and primate imaging will be operational by the end of 2007. This system will provide similar the state-of-the-art techniques in performing functional MRI (fMRI), cardiac imaging, and in vivo NMR spectroscopy as the existing Siemens Trio scanner. System will be upgraded to the TIM version in summer 2008.
A whole-body Siemens 3T TIM MRI full-bore scanner for primate imaging became operational in February 2008.
A small non-human primate and rodent Bruker Biospec 7T MRI scanner brought online January 2008. Bore size is 30cm diameter; 20/12/6cm free bore depending on gradient set.
The Research Imaging Institute (RII) will be installing a new Bruker Biospec 11.7T/30 MRI scanner for animal imaging. This will be the first MRI of its kind in the Western Hemisphere. Funds for acquiring the MRI were recently awarded by the NCRR High-End Instrumentation Program (PI: Dr. Duff Davis, Chief of the Translational Imaging Division) for expansion of the RII’s Comprehensive Facility for Animal Imaging Research (CFAIR). The scanner is expected to be operational by the end of February 2008. Bore size is 16cm with a free bore diameter of 7cm with gradient. Commissioning of this instrument will help resolve a cross-institutional demand for a high-resolution animal MRI. This instrument will now enable users to perform such demanding studies as dynamic fMRI and cardiac imaging in small non-human primates. Scanning modalities yielding superior spatial and temporal resolution not previously achievable with our existing 2T and 3T human MRI's include anatomical MR microscopy (~100um resolution), BOLD (oxygen utilization), MR spectroscopy, contrast-perfusion MRI (blood flow) and diffusion tensor imaging (white matter connectivity). Along with the new Siemens 3T 90cm bore MRI and the Biospec 7T 30cm bore MRI, the addition of the 11.7T MRI is significant in that the RII will be able to accommodate both clinical and preclinical research on and a wide variety of animal species from transgenic mice and large non-human primates (e.g., rhesus and baboons) to humans.
Support Equipment: The images from MRI scans are transmitted and reproduced to a film copy via a fiber optic line to a 3M 969 laser camera and 5535 processor.
MRI Stimulus Presentation Equipment: Stimulus presentation in the MRI can be accomplished in several different ways. Visual stimulation can be presented by a projector connected to a PC. The subject can view the projector via a mirror attached to the receiving coil. In addition, motor behaviors can be video taped. Auditory stimuli can be presented by high quality head phones to the subjects. Reaction time and responses can be recorded by a button box connected to a PC. sensory stimulation such as vibration can also be presented. Extremely versatile stimulus presentation software called E-Prime (Psychology Software Tools, Inc.) is being used. E-Prime is a new graphical experiment generator for the Windows 95/98/ME environment. E-Prime consists of a suite of applications to design, generate, run, collect data, edit and analyze the data. E-Prime can be triggered by the MRI scanner for event related studies.
Limited-Support Contract: There is a service contract with Siemens.

Translational Imaging Division
Chief: Michael Duff Davis, Ph.D.
The Translational Imaging Division (TID) was created within the past two years as an initiative to strengthen translational imaging research opportunities at the HSC. It also serves other institutions locally, in the San Antonio area, as well as regionally across southern Texas where such capabilities are lacking. These include the UT San Antonio, the Audie L. Murphy VA Hospital, the Southwest Foundation for Biomedical Research and the Barshop Center for Longevity and Aging Studies, a satellite facility of the UTHSCSA, among others. It has a generous allocation of 1,820 square feet of laboratory space and, in addition, is supported by shared-instrumentation and computer labs, several offices, and administrative staff. The TID’s laboratory space consists of a wet-lab, surgery and animal prep suites, a microPET (see below) instrument lab and the new MRI magnet and console rooms. The TID is staffed by Dr. M. Duff Davis (Chief), Dr. Peter Kochunov( animal MRI director), Mr. David Lewis (PET technician) and Mr. Sean Buckley (animal technician). Though still in relative infancy, the TID has been able to make good use of the microPET and is presently supporting 7 full projects and 5 pilot projects. We expect that within a year after the new, second, cyclotron is installed that the availability of new radiotracers will capture considerably more interest, particularly from departments such as pharmacology, psychiatry and oncology where molecular imaging should have a big impact. Another important asset is the proximity of an expansive animal housing unit, neighboring the RII on the same floor. The designated 7T MRI and 9.4T MRI animal MRI rooms are even more strategically well-positioned, within the confines of the LAR satellite. Moreover, the TID’s close operational alliance with the Southwest Foundation for Biomedical Research and the affiliated NIH-commissioned Southwest National Primate Research Center (SNPRC) affords the investigator an enriched resource for working with numerous exotic animal and non-human primate species. These San Antonio based colonies are populated with several unique animal models of human disease as well as a large, unparalleled, colony of baboons. Research animals are made accessible to investigators through competitive in-house NIH funding for pilot studies or through other local, national and private sources. Both these centers provide logistical support and have an IACUC reciprocity agreement with the UTHSCSA, UTSA and VA, a relationship that expedites the mobilization of animal research protocols. The RII has several ongoing research projects with the SFBR and SNPRC.

Human Electrophysiology Division
Division Cheif: Shalini Narayana, Ph.D.

Includes two laboratories: 1. Transcranial Magnetic Stimulation (TMS), and 2. Event Related Potential (ERP).

Transcranial Magnetic Stimulation Laboratory
The focus of the Transcranial Magnetic Stimulation laboratory is to enhance the precision and ease with which TMS can be used for the diagnosis and treatment of neurological and psychiatric disorders and for neuroscience research. TMS is the newest and least invasive form of electrical brain stimulation. It is being developed for clinical application in pre-surgical mapping and in treatment of depression. It is also being used in neuroscientific applications to examine neural connectivity, reversible-lesion cognitive mapping, and chronometry of brain processing. Approximately 4/5 of the studies are in normal subjects; 1/5 of the studies are in patients.
Subject Testing Room: Room with state-of-the-art PC running Neuroscan (for electrophysiology) and E-Prime (for integrated control of TMS stimulus, psychological stimuli, and subjects’ responses); an examination table, color monitor for visual presentation, and headphones.
Cadwell TMS: The RII’s primary human transcranial magnetic stimulation system is a Cadwell High Speed Magnetic Stimulator (HSMS) (Kennewick, Washington). This stimulator uses a B-shaped coil. The peak energy transfer to the coil is 225 joules. The stimulator produces a symmetric bi-phasic pulse with a total duration of about 250 µs. It is capable of delivering pulses at a rapid rate of up to 25 Hz with no reduction in intensity. The maximum rate is 60 Hz at 40% of maximum intensity. We have 2 systems.
Magstim TMS: RII also has another transcranial magnetic stimulation system, Magstim BiStim Module (The Magstim Co. Ltd. Wales, UK). This stimulator uses a B-shaped coil. The stimulator produces a symmetric mono-phasic pulse with a total duration of about 500 µs. It is capable of delivering pulses at a slow rate of up to 0.25 Hz at maximum intensity. Two small animal coils (2 and 4 loop) are available for use with this system.
NeuroMate Robotic System: The NeuroMate Robotic System includes a five-axis robot arm; robot base and head support frame; and (ActMate) workstation. It was specifically conceived and designed for use by and with humans. It is the only robot approved by the FDA for use in neurosurgical application and the only device of its kind adapted to precise, safe, programmable positioning, with on-line co-referenced spatial coordinate systems. From 1989-1995, over 2500 neurosurgical procedures have been performed with NeuroMate. The NeuroMate Robotic System includes a five-axis robot arm; robot base and head support frame; and (ActMate) workstation. The tool holder contains sensors suitable for monitoring rotational movement of the tool in the holder. The NeuroMate has automatic self-blocking joints, sensor redundancy, and an embedded controller, which are key to its accuracy and safety. All joints are powered by worm gears, making them very stable (for tool holding) and absolutely rigid during power surges and loss. Once positioned, the NeuroMate can be de-powered with no change of position; it does not return to a home position. It is an automatic and extremely accurate positioning device. Its absolute accuracy (positioning 0.75 mm; orientation 0.125°) and repeatability (positioning 0.15 mm; orientation 0.02°) are well suited for accurate positioning of TMS coils at the scalp. Positions are achieved within 45 seconds, directly after trajectory validation on the image planner. The NeuroMate has no geometric limitations due to mechanics. The patient’s head always remains accessible. It has low EM emission, easy cleaning, and ergonomic design appropriate to experimental environment. Its inherent safety features and built-in controls will be efficiently integrated into a 2nd generation TMS- AHRM system in the future.
Microscribe Digitizer: The MicroScribe 3DLX, from Immersion Corp. (San Jose, CA) is a precision mechanical arm used to acquire 3D coordinates (see figure). The arm has five axes with precise encoders, which combine to track the position and orientation of the stylus tip. This particular version of the arm has a spherical workspace of 66" (1.67 meters) and an accuracy of 0.012" (0.30 mm). It supports RS232 serial interface to host computer, and has an internal sampling rate of 1000 per second.
E-Field Measurement: Currently we measure the electric field using both a custom-made dipole probe and a custom-made coil probe. The output from these probes is measured using a Tektronix TDS 320 100 MHz, 2-channel digital oscilloscope. We have calculated and verified comprehensive 3-D E-Field maps for all TMS coils.
Behavioral Apparatus: Research Imaging Institute investigators also conduct psychological experiments to develop the behavioral paradigms that serve as the basis for PET and TMS experiments, as well as for fMRI and ERP studies. In these experiments, a computer presents visual or auditory stimuli and collects either verbal, button-press, or joystick responses from a subject, which then can be analyzed for accuracy, reaction times, or other behavioral parameters. These computer experiments are conducted using either E-Prime (Psychology Software Tools, Inc.) on PC platform, SuperLab (Cedrus, Inc.) on an Apple or PC platform. Further the laboratory has audio and video recording capabilities during motor and speech studies.

Event Related Potentials Laboratory:
Technical Director: Nicole Y. Y. Wicha, Ph.D.
The focus of the Event-related potentials (ERP) laboratory is spatio-temporal mapping of information processing in the human brain in health and disease. Event-related potentials (ERPs) are the most frequently performed type of electrophysiological study. ERPs are scalp-recorded voltage fluctuations resulting from evoked neural activity. These are extracted from the background EEG by time-locked selective averaging and provide very high temporal resolution in the patterns of neuronal activity evoked by sensory, cognitive or motor events. Roughly 3/4 of the studies are in normal subjects and 1/4 in patients.
Facilities: The ERP lab consists of one audiometric examination room, a sound attenuated behavioral testing room and a workstation area. The examination room is a custom installed double-wall insulated, sound-attenuating, RF-shielded testing chamber (Industrial Acoustics) measuring 8’8”w x 8’6”l x 6’6”h. This larger testing room can comfortably seat two participants for any studies involving real-time human feedback or interaction and is equipped with adjustable interior lighting and a monitoring window (the integrity of the RF shielding is protected in all cases), as well as a participant chair, adjustable table and an intercom system communicating to outside the chamber. The chamber can be used as auditory recording booths, or for behavioral testing when a sound-attenuated environment is needed. The prep room includes locking storage cabinets for supplies and sensitive materials (e.g., completed consent forms) and a large sink for cleaning and disinfecting recording equipment. The workstation area houses computers for experimental design and testing, and data processing and analysis. The behavioral room has sound attenuated walls and is equipped with a computer and response devices for vocal and motor responses during behavioral tasks. In addition, engineers with access to mechanical and electronic workshop facilities for repair of ERP equipment or construction of custom-built equipment are available at the Research Imaging Institute.
Data acquisition:
The ERP chamber is equipped with a BioSemi ActiveTwo EEG/ERP system, which uses “active” electrode technology, with a preamplifier located at each recording electrode to increase the signal-to-noise ratio. The electrodes snap into an elastic cap (Electrocap) with preset labeled holes, and are connected directly to a battery-powered analog-to-digital conversion box (AD-box). Additional external electrodes for monitoring eye movement or physiological activity (e.g., GSR) can also be used. Each AD-box channel consists of a low-noise DC-coupled post-amplifier, with a first order anti-aliasing filter, followed by a Delta-Sigma modulator with an over-sampling rate of 64, and decimation filter with a steep fifth order sinc response and high resolution 24-bit output. The digital outputs of all the AD converters (capacity for up to 256 channels of data) are digitally multiplexed and sent to a PC via a single optical fiber without any data compression or reduction. The amplifiers have 4 user-adjustable sampling rates (2, 4, 8 or 16 kHz per channel). A receiver unit converts the optical data coming from the AD-box to an USB2 output. In addition, the USB2 receiver has a trigger port with 16 independent trigger inputs and 16 independent trigger outputs. This setup keeps the complete stimulation setup galvanically isolated from the subject. The trigger output signals can be controlled with an independent LabVIEW thread integrated in the BioSemi acquisition software. The trigger inputs allow easy setup of EP/ERP measurements, and event logging. Digital EEG/ERP data is stored on a PC running Windows XP and ActiView acquisition software (based on Labview). ActiView is a free open-source complete acquisition program designed to display all ActiveTwo channels on screen during recording and save all the data to (network) disk in BioSemi Data Format (BDF). The lab is also equipped with 2 analog amplifiers with 68 channels each (SAI). These units can be daisy chained to increase the number of recordable scalp channels.
Stimulus generation and behavioral responses:
Stimulus generation will be accomplished using Presentation or Eprime software running on a Windows XP platform PC. Presentation and Eprime have the capacity to display the stimulus, both to the participant in the chamber and the experimenter outside the chamber using a video splitter, as well as continuous real-time monitoring of performance (e.g., behavioral responses such as button press) in Presentation and upcoming stimuli (using a script dialog). Both report precise timing for each stimulus and response event (critical for ERP research) to the digitization computer and interfaces with standard low cost input devices (e.g., mouse, joy-stick or serial response box). Both have a powerful scripting language that allows ample flexibility for experiment design and stimulus generation. This chamber will be equipped with a 21-inch CRT color monitor with low distortion and high refresh rate for visual-stimulus presentation, headphones for auditory-stimulus presentation, an ergonomic finger-response pad and a table-mounted video camera connected to a monitor outside the chamber. A monitor switch is used to switch between stimulus presentation and real time data acquisition on the participant monitor when necessary. For psychophysical-level control of the stimuli in auditory experiments, the computer-generated acoustic stimuli will be funneled through additional equipment in an auditory rack containing special filters, a mixer and decibel-precision attenuators.
Data processing and analysis: A Linux platform (Red Hat Enterprise) PC runs EEG/ERP analysis software, including ERPSS (free open source software from the Hillyard lab at UCSD), which has sophisticated programs for artifact rejection, selective averaging to extract the ERPs, data manipulation, calculating topographic contour plots of both the voltage potentials and reference-free current-source densities (CSDs), and plotting of both the ERP waveforms and the various types of contour plots. The lab is also equipped with EEGLab (free open source software from the Makeig Lab at UCSD; Delorme and Makeig, 2004), another powerful software package that provides complimentary analysis tools to ERPSS using Independent Components for source localization, time/frequency for dynamic brain activity analysis and other methods. The lab also owns the Brain Electrical Source Analysis (BESA) software (M. Scherg) modules for data processing, time averaging and for dipole source localization. Additional software and strategies have been developed in-house to integrate the ERP data with data sets from the other brain imaging technologies at the center (i.e., structural MRI, functional MRI, and PET).
Scalp 3-D spatial digitization: The ERP lab is equipped with a handheld Polhemus Patriot 3D Digitizer system with stylus, for spatial mapping of the scalp electrodes. These spatial coordinates will be used when overlapping data collected from other imaging techniques, such as fMRI, for the same individual.


Animal Electrophysiology and Computational Neuroscience Division
Technical Director: James Bower, Ph.D.
The laboratory at RII is already equipped for in vivo EEG, evoked potential, extracellular single unit, and intracellular recording. The in vivo set up dedicated to these experiments includes a binocular (Zeis) surgical scope, amplifiers; various display devices, electrode pullers, isolation tables, etc. There is also a computer dedicated for data acquisition. Data is stored and backed up with a 3 Terraflop DaPowerEdge 2650, Intel Xeon 2.8 GHz RAID w/512K cache; multiple Graphics workstations-2 Sun Blade 2000 workstations are available for offline data analysis. Full sets of computer peripherals are also available (scanners, several types or printers, etc). The laboratory also has space and partial facilities for the unanesthetized recording preparation.

Human Performance Division
Division Chief: Donald A. Robin, Ph.D.
Human Motor Performance Laboratory (HMPL) & Neurocognitive Laboratory
The Division focuses on the development and implementation of measures of human performance that are used with various imaging modalities. For example, precise measures of motor performance and cognitive skills allows for correlations between imaging results and performance thereby providing an ability to model neural function for these tasks and applying these models to (1) understanding various patient populations and (2) developing treatments for various patient populations.

Human Motor Performance Laboratory (HMPL)
Laboratory Director: Donald A. Robin, Ph.D.
The HMPL is designed for the study of motor control and learning in limb and speech systems. The laboratory is structured to facilitate the study of healthy subjects and those with various neurological (e.g., Stroke, Parkinson’s Disease) and speech disorders (e.g., Stuttering, Apraxia of Speech). A focus of the laboratory is the development of new behavioral treatments for a variety of motor disorders and the integration of performance measures with different imaging modalities. The HMPL is actively involved in the development of new measures to capture human performance (e.g., application of 3-dimensional movement analysis during functional imaging). As such, data collection instrumentation has been made portable for use in other laboratories. Finally, the laboratory focuses on how humans learn to perform new skills (and regain those skills in the cases of patient groups) in relation to brain plasticity and changes in connectivity.

Subject Testing Rooms: Subjects are studied in one of two rooms. The first room in designed for the collection of kinematic data and also contains a number of data analysis stations. This room is housed with both PC and MAC computers; a movement capture system with applicability for limb and speech systems, and a robot arm. The inner room houses a sound isolated booth and outer technician area each with a PC computer. The sound room is designed for audio and video capture of speech and limb data and is used primarily for treatment studies associated with various motor disorders (e.g., stuttering, Parkinson’s Disease).

NDI Optotrak Certus (s-Type): This optical movement detection system that tracks the position and movement of infrared light emitting diodes with two sets of cameras (to minimize blind spots during movement). The system allows for representation of movements of any body part (e.g., arm, lips) in 3-dimension space in real time. The system contains a control unit that allows for synchronization with other signals (e.g., EMG; speech) and data collection from other signal sources. It also has triggering capability to time for example the onset of a TMS pulse with data collection. The system is highly accurate relative to position and time allowing for precise measurement of kinematic data. The system has a spatial resolution of 0.01 mm and a temporal accuracy that is < 1 ms.

Thermo CRS F3 Robot System: The F3 Robot system consists of the robot arm, controller, and umbilical cable (for powering the arm and communication between the arm and controller). The F3 arm has 6 joints for accurate spatial localization from any angle. The controller contains safety circuits, power and motion control for the arm. It stores feedback information from encoders located in the arm, and computes trajectories through storage of applications in memory. The controller detects any damaging situations (e.g., overheating, errors in communication) which when trigger cause an immediate shutdown. The arm has 6 axes and weighs 52 kg with a nominal payload of 3kg and a reach of 710mm. The system has a positional repeatability of 0.05 mm, a maximum linear speed of 4 m/s, and breaks on the first 3 joints. The controller has a dual microprocessor (133 MHz system processor and a 60 MHz DSP (motion control). It has 16 digital inputs, 12 digital outputs, 1 analog input, and 4 relay outputs. It weighs 31 kg. The robot meets FDA safety specifications and is used with both healthy subjects and those with motor disorders.

Acoustic and Perceptual Measures of Speech: The laboratory is fully equipped with microphones and digital video-recorders for analysis of speech and limb data (e.g., motor rating scales). Computers digitize audio signals at >22 KHz for acoustic and perceptual analyses. In general, in-house routines have been developed for analysis of the acoustic signal through the use of PRAAT.


Neurocognitive Laboratory
Laboratory Director: Donald A. Robin, Ph.D. (Interim)
The RII has three sound dampened rooms dedicate to neuropsychological testing, psychological assessments and medical screening. The rooms are equipped with a comfortable chair for the subjects, tables for the testing materials and adjustable lighting. Each room also has computers for computerized presentations. A third room is larger and equipped with additional tables and computers for technical staff to work and process data. Total square feet for all three rooms is 300 sq. ft. the first two are approx. 83 sq. ft., the third is approx. 125 sq. ft. In addition, the RII has two certified nuclear medicine technologists, Betty Heyl and David Lewis, on full time staff. Both are trained and certified to draw blood. The samples will be stored at 40°C in a refrigerator designated for this purpose in the larger of the three testing rooms.


Biomedical Image Analysis Division (BIAD)
Division Chief: Jack L. Lancaster Ph.D.
The Biomedical Image Analysis Division (BIAD) broadly supports each of the Research Imaging Institute’s (RII) divisions through collaborative scientific research and image processing and data management services. BIAD is also a scientific research division in its own right, collaborating with the RII’s other divisions in all areas of data analysis. Through these collaborations, BIAD creates software for conducting complex data analysis and visualization. Because the software can be customized to meet the needs of a wide variety of research protocols and imaging equipment, researchers are free to experiment with unique new data formats.
Research Data Archive - The Research Data Archive includes all of the biomedical images, image descriptor files, and other auxiliary data required for the analysis of the RII data. Software has been developed for the preprocessing, archiving, and retrieval of research data. The archive consists of a Sun Blade 2500 interfaced to a 1TB SCSI to IDE RAID system and a Dell Power Edge 400SC with a 1.5 TB SCSI to IDE RAID system. All MR and PET images acquired under research protocols at the RII are maintained in this active image archive.
Data Analysis Facility - The Data Analysis Facility consists of Unix, Macintosh and Windows workstations housed in two computer labs for the use of faculty, staff, and visitors of the RII. The printers that display biomedical data include a large format printer for producing posters. The facility includes the following hardware:
1 single processor Sun Blade 2500 Workstation
1 single processor Sun Blade 1200 Workstation
2 Macintosh G5 Workstations
2 Dell 3.0 GHz Workstations
1 dual processor Ultra SPARC 60 Workstations
4 single processor Ultra SPARC 30 workstations
a range of magnetic tape storage units (8mm, 4mm DDS-2, DLT, SDLT) including 2 high-speed, high-capacity SDLT 600
Biocomputation High Performance Computing Cluster - The High Performance Computing (HPC) Cluster which processes large numbers of biomedical images and calculates biomedical simulations consists of 40 Pentium 4 systems (>2.4 GHz) managed by a master node with Sun Grid Engine software. The HPC Cluster includes access to over 2 TB of disk storage on SCSI to ATA RAID.
Server and HPC Support Facility - All of the servers and the HPC Cluster are housed in the Server and HPC Support Facility, which provides a physically secure location with adequate environmental controls and power for the systems.
Research Database Support - Two systems, one for production (Sun Blade 2500) and one for development (Sun Ultra 10), provide support for the following research databases:
The RII subjects and protocol databases
The ICBM databases
The BrainMap database systems
World Wide Web Support - Support for the Research Imaging Institute's Website, BrainMap web applications, and the Genesis Genera Neural Simulation System website in supported by 2 Sun Blade 2500 systems.

Computers Supported
42 Red Hat Linux HPC Cluster systems
8 Red Hat Linux systems
40 Macintosh OS X systems
36 Windows systems
16 Sun Solaris system
Personal Access Systems - The Personal Access Systems exist at each individual's desk and provide access to electronic mail, file services via NFS and ftp, and the Data Analysis Facility via X11 or terminal emulation software. In many cases, these systems have sufficient computing power to provide personal data analysis. These systems consist of 8 Linux Workstations, 34 Windows Workstations, 2 Solaris, and 38 Macintosh Workstations.

Data Communication Networks - Every computer system is interfaced to a modern fully switched 100 base-T Ethernet network. File sharing is accomplished with the Network File System (NFS) for the UNIX and Macintosh systems and ftp for the Windows systems. We support Gbyte ethernet networking within isolated subnets and are planning on moving to this higher-speed alternative for all systems within the next several years.

BrainMap™. BrainMap (http://brainmap.org) consists of a results database and content-based indexing system for the human functional brain mapping literature. The purpose of BrainMap is to provide rapid, comprehensive access to the human brain-mapping literature and its data in a manner facilitating the understanding of study design and results and to promote quantitative meta-analysis of related studies. To this end, a multi-dimensional, multi-level indexing scheme for the context (how and why) and content (results) of brain-mapping studies has been developed. BrainMap contains >600 papers which collectively report on >2500 functional brain-mapping experiments which activated a total of >20,000 locations. For each paper, full citation information, subject populations, cognitive domain, methodology, and locations of brain activation are archived. Mental operations are characterized using a multi-dimensional coding strategy. Experimental conditions are described, including stimuli, responses and instructions for task and control states. Experimental paradigms are classified, for example, as a Stroop paradigm, an attention shift paradigm, a saccades paradigm, and so forth. Cognitive domains are also classified, for example, as Cognition.Attention or Emotion.Sadness. Locations are reported as centers-of-mass in Talairach's coordinate space (above). In addition, cortical locations are assigned Brodmann area names. Sub-cortical activations are named according to nuclei.

"Raw" data are not stored in BrainMap's database. Three-dimensional image volumes are extremely bulky and require extensive post-processing to be interpreted. For this reason, BrainMap stores highly processed data, but includes pointers to the originator, location, nature, and robustness (number of subjects, level of significance, etc.) of each study.

BrainMap's™ Database. BrainMap's data is managed with Oracle, a commercial relational database management system. BrainMap's database resides on a Sun Microsystem’s workstation at the Research Imaging Institute, UTHSCSA, San Antonio, TX. BrainMap software is written using the Java programming language and the targeted computer systems are PC, Macintosh, and UNIX. The use of Java makes updating and distributing these applications simpler for both developers and users. BrainMap's™ database is publicly accessed through three interfaces: BrainMap™ Submit (Windows, Macintosh, UNIX), BrainMap™ Search&View (Windows, Macintosh, UNIX) and BrainMap™ Online (web-based application). All interfaces access BrainMap's™ database via the network using TCP/IP, even when operated within the RII intranet.

BrainMap™ Scribe. A multi-platform, Java version of BrainMap™ Scribe is currently available for free download (http://brainmap.org). This application includes a user interface that mirrors the organization of the database structure and allows for the input of information on each paper contained in BrainMap.

BrainMap™ Sleuth. A multi-platform, Java version of BrainMap™ Sleuth is currently available for free download (http://brainmap.org). This application includes extensive graphics, query, and analysis features interfacing with the BrainMap database.

BrainMap™ GingerALE. This Java application performs meta-analyses via the activation likelihood estimation (ALE) method (see ALE below); also converts coordinates between MNI and Talairach spaces using icbm2tal.

BrainMap™ Online (WWW). This interface was developed using the Hypertext Markup Language (HTML), Java server pages (JSP), and Java servlets. It operates on any platform with internet access and browsing tools such as Mozilla Firefox, Safari, and Internet Explorer. Special scripts were written using JSP to access the BrainMap™ database server via SQL calls. This interface can access all the search streams available to BrainMap™ Search&View. Atlas graphics and the associated plotting routines are not available from this interface. BrainMap™ Online can be accessed from the main menu at BrainMap’s website or through the direct url (http://apps.rii.uthscsa.edu/bmapWeb/).

ALE (Activation Likelihood Estimation) Meta-Analysis Software. The original ALE algorithm was written in C++ and obtained from Georgetown University (http://csl.georgetown.edu/software/). This code was imported into Java and a graphical user interface was added that allows the user to navigate input files, select analysis parameters such as FWHM and number of permutations, and select output file prefixes. Statistical inference is performed using a permutation test of randomly distributed foci with a correction for multiple comparisons using the false discovery rate (FDR) method. ALE output file formats are either AFNI (.brik and .head) or Analyze (.img and .hdr) format. A cluster search algorithm was added to searches for clusters within the output ALE map, and gives the coordinates of their weighted center-of-mass, extent, and anatomical label (as assigned by the Talairach Daemon). An anatomical ICBM template is also provided with the software package for overlay purposes.
Mango. Mango is a multi-platform Java application with an extensive set of image processing tools and display features, i.e. those commonly used by researchers at the RII (free download at http://rii.uthscsa.edu/mango). Mango provides comprehensive support for region of interest (ROI) generation (manual and automated), editing, and analysis. ROI tools are provided for 1-4 dimensions to support processing needs of the many imaging technologies at the RII. Analytical tools include cross-section profile graphs, histograms (image or within ROIs), and general statistical summaries (also by image or by ROI). Mango supports a variety of image formats including the DICOM and the recently developed NIFTI standard. An image browser is provided to preview images and helps organize images in a project-oriented manner. 3-D surface extraction and rendering features provide users full control of viewing 3-D images, including integrating multiple 3-D objects and freeform rotation, translation, and zooming. Mango provides image capture and layout features for the image-based figures submitted for publication by researchers at the RII. Mango supports addition of plugins for specialized processing and the SN software described below has been fully implemented as a plugin. Mango is freely distributed and we are presently developing screencasts (short videos of computer screens with audio) with examples of how to properly use its major features.

SN (Spatial Normalization). This software was written in C as an X-window/Motif application and is readily portable to most UNIX platforms. For the last several years it has existed as a stand-alone software package. However, in the future, SN will exist as a subset of DIVA, the newest image processing envisionment. SN's chief design goal was to normalize images from any tomographic modality into Talairach's space (above). This flexibility was achieved by a structured interaction with the user (see SN manual in appendix) . The user is relied upon to visualize and identify a pre-defined set of planes and points. As the operations are non-commutative (order specific), the user is guided through the proper sequence. Landmarks were chosen to be identifiable in both anatomical (CT and MRI) and functional (PET and SPECT) images. As visualization is an integral component of the normalization procedure, SN has a comprehensive set of visualization tools. Irrespective of the plane of acquisition, images are continuously viewed in three orthogonal planes: axial, coronal, and sagittal. The user has full control over translation, rotation and scaling of the images.

SN can save images (before, during, or after spatial transformation) in a large variety of formats. One commonly used format is to store the transformation matrix that can be used later by SN to view a spatially normalized image or by MIPS to spatially normalize images prior to processing. Another commonly used format is to store spatially normalized volumes. Images stored in this manner can be overlaid (e.g., PET activations onto MRI) in various display formats to better visualize the location and extent of findings. These subroutines (or modifications thereof) will be used by FVM to place FVM objects and systems into the Talairach space as 3D volume models. FVM models can be logically contrasted with data from functional neuroimaging experiments and visualized by overlay on MRI or by 3D rending. This software was validated by Lancaster, et al. (1995).

CH (Convex Hull). A fully automated application for UNIX platforms (Sun Solaris 2.5 and greater) for global spatial normalization. This software can perform and entire spatial normalization operation on PET images in seconds. This software was validated by Lancaster, et al. (1999).

DIVA (Digital Image Visualization and Alignment)., This addition to the Research Imaging Institute’s software resources provides tools and utilities which cover a wide range of uses. In addition to numerous features unavailable in other packages, many existing software package capabilities (SN, MIPS, Alice, Imaging Toolkit) have been or will be incorporated into DIVA. These features include alignment tools (including the controlled-environment SN package), MIPS pre-processing and analysis tools, 3-D visualization utilities, masking and ROI tools, multiple image visualization, Talairach Daemon interface, MIPS post-processing analysis tools, direct statistical analysis utilities, basic formula and arithmetic image manipulation, reslicing and other output tools, multi-slice layout capability with hard copy and selectable graphic output formats, image overlay processing, and time series visualization with displayed clock times.

DIVA also provides advanced internal processing features that enhance the compatibility between images of differing modalities and sizes. A highly intuitive user interface reduces the learning/training time for new users as well as streamlining image processing for the advanced user. A panel-based window hierarchy (as opposed to a menu-driven system) provides immediate visual feedback with embedded histogram, image, color, and other visual cue data. Windows are designed to leave a geographic “afterimage” in the user’s mind so that the experienced user can always tell “at a glance” the current state and hierarchy position during processing.

Image Toolkit is used to co-register image data when motion is detected during imaging or to simplify spatial normalization of images from the same subject acquired on different imaging systems (e.g., MRI and PET). We are using the head-and-hat method of Pelizzari, et al. (1992) and the automated image registration (AIR) method of Woods, et al. (1992, 1993). Image Tool kit is an X-window/Motif application that includes display, interactive image input/output and parameter selection, as well as file and spatial transformation compatibility with other software applications at the RII.

MIPS. MIPS is coded in C as an X-Window/Motif application for UNIX platforms. The MIPS analysis software used at the Research Imaging Institute uses a modification of the Change Distribution Analysis routines reported by Fox, et al. (1988) to extract coordinates in the Talairach format that relate to the centroid of extrema sites within activated brain regions. It is highly integrated with the SN application and uses the same coordinate transforms to guarantee spatial normalization of images prior to analysis. MIPS provides routines for extracting brain masks to isolate the brain from non-brain regions, performs spatial filtering with operator-selected 3-D Gaussian filters, provides the mathematical routines for addition and subtraction, and performs statistical evaluation of images.

The general scheme is to average functional images from different task states and to provide output that presents the difference in task states as statistical parametric images. The output images may be z-score images, penetrance images, or logical images. Penetrance images (Fox, et al., in review) indicate prevalence of findings across subjects while logical images provide a method to view correlated brain activities. CDA is applied to the z-score images and the results summarized in reports and stored in data files for viewing or further analysis. This analysis uses a gamma 1 statistic as an omnibus test. Also under development are more sophisticated and sensitive omnibus tests. The z-score, estimated cluster size, and p-value are reported for each point detected using CDA. The results of the MIPS processing can be easily viewed using the SN application, including overlaying of activation sites onto the images and direct readout of Talairach coordinates.

An additional feature of MIPS is the ability to analyze statistical parametric images with regions of interest (ROIs) throughout the brain volume. The ROIs are defined using Talairach coordinates and readily apply to any spatially normalized data. ROI’s can be specified in any shape or size in a variety of formats. Cross-correlation analysis is a powerful feature that was implemented in for use with ROIs or on a pixel-by-pixel basis. The base correlation pattern can be derived from a user-designated ROI or external signals/measurements. While many of the capabilities of the MIPS software are available in the SPM software, this feature is one of several available only in MIPS.

Talairach Daemon. The Talairach Daemon is a database and data retrieval system returning anatomical labels (traditional, feature-based terms) when queried with a Talairach coordinate. The entire brain has been anatomically labeled using a five-level, volume-based, terminological hierarchy. Level One (“hemisphere”) has six components: left and right cerebrum; left and right cerebellum; left and right brainstem. Level Two (“lobe”) divides each hemisphere into lobes or lobe equivalents. In cerebrum and cerebellum, lobes are as traditionally defined. In brainstem, three lobe-equivalents are defined: midbrain, pons and medulla. In both cerebrum and cerebellum, brain areas lying deep to traditionally defined lobes are termed sub-lobar. Level Three (“gyrus”) divides each lobe into gyri or gyral equivalents. Nuclear groups, such as thalamus or striatum, are gyral equivalents. Level Four of the hierarchy is tissue type. Each gyrus or gyral equivalent is segmented into grey matter, white matter and CSF. Level Five of the hierarchy is cell population. Cerebral cortex is labeled by Brodmann area. Nuclear groups are labeled by subnuclei. Cytoarchitectonic labels for cerebellar cortex and tract labels for white matter are being developed but are not yet available.
The Talairach Daemon’s labels are stored as a volume array (1 mm isometric voxels) spanning the extent of the brain in Talairach 1988 atlas. This corresponds to approximately 500,000 voxels. Each voxel in this array contains a pointer to voxel-specific brain information. This information is called a relation record and is managed as a linked list. A relation record can store any information that is recorded using Talairach coordinates. To eliminate the need for storing duplicate information in relation records, each record contains pointers to the information rather than the information. This scheme offers the potential for extremely high-speed access to information within the relation records. To realize this high performance computing capability the application code, the array of relation pointers, and the relation records are maintained in physical memory on a Sun SPARCstation 20. Although this memory-resident approach is costly—it currently requires a system with 256MB of RAM— and would not have been attempted even a few years ago, the practicality of such high-performance solutions to computational problems in neuroimaging is now justified. Talairach Daemon is accessed by remote applications over the Internet using TCP/IP sockets. When Talairach Daemon receives requests from a remote client application, it searches, retrieves and transmits the requested information to the requesting client. Talairach Daemon is a multi-threaded application to better manage multiple users and memory efficiently. Preliminary testing indicates that response rates are often in excess of 25 transactions per second. Within a single transaction, it can retrieve records at a rate of tens-of-thousands of coordinates per second. This provides near real-time responses for those with high-speed connections to the server at the RII. The Talairach Daemon’s use in automating the labeling of functional brain sites was reported by Lancaster, et al 2000.
The Talairach Daemon has been incorporated into several common software packages including AFNI, MEDx, TurboFIRE, and the FSL application distributed by Oxford University.

MEDx. A commercial software package for functional image visualization and analysis from Sensor Systems, Inc. This package, written for Unix/X-Windows, features a wide range of statistical, visualization, and image registration functions. MEDx features a fliexible and open scripting language (Tcl) and a modular design to allow for rapid prototyping. Several of the RII’s in-house data standards, image formats and software tools are included in this package.

Machine and Electronics Shops
Technical Director: John Roby, M.S.

Machine Shop: The machine shop is well equipped to support the needs of RII instrumentation. Major machinery includes a drill press, band saw, mill, lathe, surface sander, and TIG welder. Smaller hand held power tools and general shop tools complement the equipment available for use.
Electronics Shop: The electronics shop houses electronics parts and diagnostic equipment to support the needs of RII instrumentation. Major equipment includes an oscilloscope and waveform generator.
Administrative Division.
Division Chief: L. Jean Hardies, Ph.D.
The Administrative Division assists the Center Director in the guidance and facilitation of all Center activities, in accordance with the objectives of the Center’s mission.
Center technology resources are extensive, complex, and costly. Potential applications of Center technology are very broad, already serving an international cachement area. Close management of this resource is needed to assure its preservation, expansion and for access to scientists worldwide. As the Center is a cooperative undertaking of many highly skilled scientists, they are actively engaged in administrative processes. As Center activities presume inter-institutional administrative cooperation, as well as scientific cooperation, special attention is given to the coordination of financial agreements and institutional review of research on human subjects.


The University of Texas Health Science Center at San Antonio is the leading research institution in South Texas and one of the major health sciences universities in the world. With an operating budget of $536 million, the Health Science Center is the chief catalyst for the $14.3 billion biosciences and health care industry, the leading sector in San Antonio’s economy. The Health Science Center has had an estimated $35 billion impact on the region since inception and has expanded to six campuses in San Antonio, Laredo, Harlingen and Edinburg. More than 22,000 graduates (physicians, dentists, nurses, scientists and allied health professionals) serve in their fields, including many in Texas. Health Science Center faculty are international leaders in cancer, cardiovascular disease, diabetes, aging, stroke prevention, kidney disease, orthopaedics, research imaging, transplant surgery, psychiatry and clinical neurosciences, pain management, genetics, nursing, allied health, dentistry and many other fields.

The Greehey Family recently donated $25 Million to the Health Science Center, the largest outright cash gifts from a private donor in the history of The University of Texas System, and one of the most significant gifts in the history of San Antonio philanthropy. This landmark gift will impact the Health Science Center in a number of ways. The Greehey Academic and Research Campus (previously know as the North Campus) and the Greehey Children’s Cancer Research Institute will be permanently identified with the Greehey Family, one of the most respected names in business, humanitarianism and philanthropy in the United States.
This gift will establish the Greehey President’s Endowment for Excellence in Children’s Health Sciences and will support construction of our new South Texas Research building. Each of these endowments will enable us to build upon, in a very substantial way, the founding endowment approved by the Legislature to create the Children’s cancer Research Institute.

The Greehey President’s Endowment will establish five Greehey Distinguished Chairs to help the University continue to recruit and retain the best academic clinician-scientists in the world.
Budget: $499.4 million/yr.
Endowments (September 2005): $ 319 million, market value.
Research Grant, Contracts, and Awards (2005-2006): Only Tier One research institution in South Texas, with more than $175 million

Nearly $1 billion a year contributed to the South Texas economy
Chief catalyst for the $14 billion biosciences and health care industry in San Antonio
Accounted forproximately 12,000 jobs both on and off campus

The vision of community leaders, combined with the energy, talent and dedication of UTHSCSA students, faculty and staff, make the Health Science Center a major force in the biosciences today and for the 21st century.