Resource for Magnetic Resonance and Optical Imaging

Resource for Magnetic Resonance and Optical Imaging

Research Emphasis

The focus of this resource is on developing instrumentation, methodologies, and data analysis techniques for the quantitative assessment of functional, structural, and metabolic parameters in humans with the use of multinuclear magnetic resonance, novel spectral, perfusion, functional, and optical imaging techniques.

Current Research

In conjunction with our collaborators, the resource is pursuing the following four broad areas of core research. The first core deals with the development of novel magnetic resonance (MR) techniques for studying the structural, biochemical, and metabolic aspects of cartilage, brain, and tumors, with direct application to arthritis, stroke, Alzheimer's disease, and cancer. This core also develops novel image reconstruction strategies to quantify high temporal contrast agent dynamics in breast and other tissues. In the second core, research is being undertaken to improve quantitative perfusion imaging at high fields and in pediatric patients as well as methods for concurrent imaging of blood flow and glucose metabolism. It also develops strategies for correlation of functional magnetic resonance imaging (fMRI) with optical imaging. The third core's subprojects deal with MR of hyperpolarized gases and development of a comprehensive approach for the study of pulmonary and sinus diseases. This core also develops strategies for improving the efficiency of hyperpolarization of 129Xe. The fourth and final core focuses on combining optical and MRI techniques, development of methods of two-photon optical metabolic imaging and image reconstruction strategies in diffusion tomography for the study of neurophysiology, and breast cancer. The facility's core sections provide research and computing resources for numerous user, collaborative, and training projects.

Resource Capabilities

1.5 T Siemens Sonata, a 3 T Siemens Trio, and a 2 T, 1-meter bore, magnet system with a versatile spectrometer for multinuclear spectroscopy and imaging with in-magnet exercise capability; 4.7 T (30 cm diameter) and 9.4 T (10 cm diameter) vertical magnets for animal imaging; specialized radiofrequency probes for various nuclei; local magnetic field gradient sets; Workstations for data analysis; electronic test equipment; physiological monitoring equipment; in-magnet exercise apparatus; and bioelectric amplifiers and recorders. Metabolic spectroscopy including (but not limited to) ¹H, ¹³C, ¹⁵N, ²³Na, ⁷Li, ¹⁹F, 31P, and 17O, equipped for physiologic synchronization (gating) and decoupling, magnetization transfer experiments, two-dimensional, multiple quantum spectroscopy, and in-magnet exercise. Software and hardware support for all nuclear magnetic resonance experiments, including sodium and phosphorus imaging, chemical shift imaging, Hadamard spectroscopic imaging, ³He, and ¹²⁶Xe imaging, and high-resolution proton imaging and flow. Facilities and expertise for generating hyperpolarized helium and xenon gases, specialized coil design, and construction are available, as are body-positioning devices for specific experiments (e.g., in-magnet exercise and heart, brain, and liver studies). Expertise and infrastructure for state-of-the-art functional perfusion imaging and integrated optical and MRI experiments.

Instruments

Whole-body MRI Scanners: 1.5 T Siemens Sonata whole-body clinical scanner, 2 T custom-built whole-body system, 3 T Siemens Trio whole-body clinical scanner with multinuclear capability, 4.7 T/50 cm Varian small-bore MRI system, 7.1 T Bruker AMX-300 Spectrometer, 9.4 T/8.9 cm Varian small-bore MRI system, and 11.8 T Bruker AMX-500 Spectrometer.

Software

MATPULSE—Shinnar-LeRoux radiofrequency pulse synthesis: MATPULSE is a graphic user interface written in the Matlab programming language designed to generate amplitude modulated radiofrequency pulses for a desired spectral response. The program implements the Shinnar-LeRoux (SLR) algorithm for pulse sysnthesis.

Extractor —three-dimensional volume segmentation: EXTRACTOR is a graphic user interface written in the IDL programming language. The program is a tool for the extraction and segmentation of subvolumes from a three-dimensional image data set.

BreastPro—rapid bilateral breast imaging: MRI pulse sequences and analysis software for simultaneous three-dimensional bilateral back-projection imaging of dynamic contrast-enhancement in the breasts.

TIMESERIES—fMRI Hemodynamic response analysis: TIMESERIES is a plugin for the EXTRACTOR program (see above) and is designed to perform parametric analysis of the hemodynamic response of fMRI data. It can be used to produce parametric maps of such metrics as the time-to-peak, latency, and FWHM of the hemodynamic response function (HRF). It also includes regression to and unbiaseded HRF function, ideal for event-related designs.

CYLINDER—electrode recording cylinder visualization: CYLINDER is a graphical user interface-driven program that uses MRI to quantitatively determine recording electrode trajectories and their intersection with desired brain anatomy. This program can be used to guide electrode placement specific to the anatomy of an individual subject.

O²Analysis-pro—analysis software for ³He MRI: This software calculates regional V_A/Q ratios from the regional measurements of P_AO₂ by a variation on methods used to calculate P_AO₂ from a known V_A/Q ratio.

Pulse sequences—novel MRI pulse sequences: Customized pulse sequences for commercial Siemens, GE, and Varian scanners are developed here at the Metabolic Magnetic Resonance Research and Computing Center (MMRRCC).

Hardware

Hardware designs for T/R switches and radiofrequency coils are also available. For more information, please contact Ari Borthakur at ari@mail.mmrrcc.upenn.edu.

Facilities

Facilities exist for building radiofrequency and gradient coils based on the demand of projects. The MMRRCC houses an electronics lab and has access to dedicated coil building facilities in both the Department of Radiology and an adjacent NMR facility. Personnel are available for coil building and consulting in coil design.

The MMRRCC also maintains a chemistry laboratory, required for biological MR research and a mechanical shop for fabrication of custom, non-magnetic components for various specialized needs.

The MMRRCC also has facilities for producing hyperpolarized noble gases using various lasers and other equipment. Associated centers and laboratories include the Center for Advanced Magnetic Resonance Imaging and Spectroscopy, the Center for Functional Neuroimaging, the Laboratory for Multinuclear Magnetic Resonance Imaging, and the Laboratory for Molecular Imaging.

Training Opportunities

Trainees and researchers come from a variety of backgrounds, including medicine, bioengineering, biophysics, chemistry, physics, engineering, and mathematics. The resource center excels at educating future scientists on the fundamentals of magnetic resonance theory and applications. Both new and established researchers are aided in learning about new developments in the field and to hone their skills for applications within their own research programs. Investigators may be trained on an individual basis by resource staff or through group mechanisms such as seminars, courses, and workshops. The resource facility houses more than 40 desks in a wall-less, cubicle-free environment that promotes open communication and discussion among the Principal Investigator, faculty members, predoctoral and postdoctoral fellows, and visiting and senior researchers.

Publications

1. Borthakur, A., Hulvershorn, J., Gualtieri, E., Wheaton, A. J., Charagundla, S., Elliott, M. A., and Reddy, R., A pulse sequence for rapid in vivo spin-locked MRI. Journal of Magnetic Resonance Imaging 23:591-596, 2006.

2. Fernandez-Seara, M. A., Wang, Z., Wang, J., et al., Continuous arterial spin labeling perfusion measurements using single shot 3D GRASE at 3 T. Magnetic Resonance Medicine 54:1241-1247, 2005.

3. Fischer, M. C., Kadlecek, S., Yu, J., et al., Measurements of regional alveolar oxygen pressure using hyperpolarized ³He MRI. Academic Radiology 12:1430-1439, 2005.

4. Chen, Y., Intes, X., and Chance, B., Development of high-sensitivity near-infrared fluorescence imaging device for early cancer detection. Biomedical Instrumentation and Technology 39:75-85, 2005.