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Center for Magnetic Resonance and Optical Imaging

Ravinder Reddy, Ph.D.

Center Overview

The primary goal of the Center for Magnetic Resonance and Optical Imaging (CMROI) is to develop state-of-the-art core Magnetic Resonance and Optical biomedical imaging technologies for solving important problems in biomedical research with a special emphasis on the rapid clinical translation. These technological developments are driven by collaboration with scientists from within and outside University of Pennsylvania, the primary institution. Specifically, the Resource is focused on the development of quantitative, noninvasive MR and optical imaging based biomarkers for studying tissue metabolism and function, with an eye towards clinical translation through early diagnosis. The Center also provides support in the development and evaluation of new therapies in a variety of diseases.

Impact on Human Health

Imaging technologies developed by the resource will have substantial impact on fundamental understanding, early diagnosis, and development of novel therapies for several diseases including Alzheimer's disease, arthritis, heart disease, cancer, stroke, and chronic obstructive pulmonary disease (COPD).

Current Research

The Research Resource has made major technical contributions to diagnostic medicine over the years. SLR pulse synthesis algorithm, ASL MRI for the measurement of perfusion, and T1-rho MRI are some examples of technologies that led to patents and subsequent technology transfer to many NIH-funded labs as well as licensing by the healthcare industry.

The Resource maintains an extensive training and dissemination program in biomedical imaging. The Resource, within the auspices of the Radiology department at the University of Pennsylvania, remains committed to intellectual interchange and the interdisciplinary pursuit of basic and clinical medicine.

The research capabilities of the CMROI are distributed into three distinct divisions called Technology Research and Development cores.  While each TR & D is semi-autonomous in their individual research goals, extensive collaboration exists among the groups as well as within the external scientific community.

TR & D 1 - Rotating Frame Imaging Methods:
The first TR & D project deals with the development of novel rotating frame MRI techniques for studying the structural, biochemical and metabolic aspects of cartilage, brain, and tumors, with direct application to Arthritis, Alzheimer's Disease and cancer.

TR & D 2 - Perfusion Imaging: The second TR & D focuses on the development of quantitative perfusion MRI at ultra high field (7T) scanners, real time fMRI as well as methods for integrating perfusion MRI with optical imaging for the study of stroke and neurodegeneration.

TR & D 3 - Optical Imaging: The final TR & D develops multi-modal state-of-the-art instrumentation combining optical imaging and MRI, and develops diffuse correlation spectroscopy (DCS) for blood flow monitoring/imaging of diseased tissues in stroke and breast cancer.

The Resource emphasizes clinical translation of its TR & D work and actively collaborates on ongoing research projects. It provides service in the use of state-of-the-art MRI including a whole-body 7T research MRI scanner, optical imaging and hyperpolarized gas imaging systems, and software resources developed by the Resource.

Resource Capabilities

All of our systems of the Research Resource are available to aid in technology development and transfer.

The University of Pennsylvania provides an optimal environment for our resource, combining an outstanding medical school with a strong foundation of research and world-renowned faculty. The greater Philadelphia area is also the home of four other medical schools, each the source of substantial biomedical research. In addition, the University of Pennsylvania Health System has associations with both the Childrenâ??s Hospital of Philadelphia and the Fox Chase Cancer Center. MR facilities exist at both of these locations, and the resource has transferred technologies to many related projects at these institutions.

Another important aspect of the CMROI is the broad knowledge base of its staff, ranging from basic physicists to medical clinicians. The resource has developed numerous new technologies in areas as diverse as RF and gradient coil design, pulse synthesis, spectroscopic imaging, perfusion imaging, mathematical models of metabolism, and optical imaging. Furthermore, numerous clinical experts complement resource staff in solving clinically relevant problems. Our commitment to intellectual interchange and the interdisciplinary pursuit of science has proven a fertile medium for interaction among scientists and clinicians, promoting the application of basic research to clinical medicine.


For a complete list of instruments available at the Resource, please visit the website.


Please visit the Software website for information on CMROI software available for download.

Please visit the Pulse Sequence website for information on obtaining MRI pulse sequences.

Other Facilities

Facilities exist for building radiofrequency and gradient coils based on the demand of projects. The CMROI 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. Hardware designs for T/R switches and radiofrequency coils are also available. The Center 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 Center also has facilities for producing hyperpolarized noble gases using various lasers and other equipment.

A list of associated centers and laboratories is available here.


All human research is performed under guidelines set by University of Pennsylvania's Institutional Review Board (IRB) with full accreditation by the Association for the Accreditation of Human Research Protection Programs. Accreditation standards establish the highest expectations for the conduct and oversight of human research.  Further oversight of all MRI-based research on the clinical scanners is provided by the Center for Advanced Magnetic Resonance Imaging and Spectroscopy (CAMRIS), located within the Department of Radiology of the Hospital of the University of Pennsylvania and staffed with MRI technologists skilled in imaging research protocols. In addition to these research personnel, an on-call Radiologist is available and the scanners are equipped with full physiological monitoring capabilities, crash carts, and are accessible to Hospital code teams. An on-site engineer is available to maintain the scanners in the event of technical malfunction.

Animal care at the University of Pennsylvania is maintained by a fully licensed, NIH-approved University Laboratory Animal Resource (ULAR). Facilities provided by ULAR include boarding, routine inspection for disease, treatment, surgical facilities, and assistance from veterinarians. This facility is fully accredited by AAALAC, demonstrating compliance with NIH Guidelines. The University of Pennsylvania's Institutional Animal Care and Use Committee (IACUC) approves all protocols for animal use. The Department of Radiology provides further support and oversight through its Small Animal Imaging Facility (SAIF). In addition to the Animal Resource Center facilities, a surgery room equipped with complete surgical facilities and monitoring equipment is available with equipment such as anesthesia equipment, animal respirator and ventilator, EKG, transducers and hemodynamic monitors are available.

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.



ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
Center for Magnetic Resonance and Optical Imaging

This package includes a 3D simultaneous bilateral back-projection sequence for dynamic contrast-enhanced imaging of the breasts. Data from both breasts are acquired simultaneously using a 3D hybrid sequence in which data are acquired radially in-plane and the slices are phase-encoded. The signal from each breast is saved separately and residual slice aliasing from one volume into the other is removed using SENSE reconstruction. An effective temporal resolution of 15 seconds for both breast volumes is...

Linux, Mac OSX, Windows N/A N/A
Center for Magnetic Resonance and Optical Imaging

CYLINDER is a GUI 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.

Center for Magnetic Resonance and Optical Imaging

EXTRACTOR is a graphical user interface written in the IDL. The program is a tool for the extraction and segmentation of sub-volumes from a 3D image data set. The program permits the interactive selection of standard image processing operations, including pixel intensity threshholding, seed growing, boundary tracing, and morphological dilation and erosion.

Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
Center for Magnetic Resonance and Optical Imaging

ImScribe is a Matlab program designed to automate the specification of the acquisition Field-of-View with Siemens MRI scanners. The program is particularly suited for neuro-imaging, including fMRI.

DICOM, GE, Philips, Siemens,...(more) N/A N/A
O2 Analysis - Analysis Software for 3He MRI
Center for Magnetic Resonance and Optical Imaging

This software calculates regional VA/Q ratios from the regional measurements of PAO2 by a variation on methods used to calculate PAO2 from a known VA/Q ratio.

DICOM, TIFF (.tiff, .tif,...(more) N/A N/A
Center for Magnetic Resonance and Optical Imaging

SequenceTree is an open-source pulse programming environment with a large user community which is growing every day. Many pulse sequences are available for download, including: Spoiled Gradient Echo, Balanced Gradient Echo, Fast Spin Echo, Diffusion, T1p.

Linux N/A N/A
T1-rho and T2 processing GUI
Center for Magnetic Resonance and Optical Imaging

This MatLab GUI will assist in processing T1rho- or T2-weighted images to create T1rho or T2 parametric maps. Includes 2D in-plane co-registration Affine algorithms to correct for rigid-body distortions between data sets.

Linux, Mac OSX, Windows DICOM N/A N/A
Center for Magnetic Resonance and Optical Imaging

TIMESERIES is a plugin for the Extractor program (see above) 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 HRF. It also includes regression to an unbiaseded HRF function, ideal for event-related designs. The software accepts a timeseries of 3D AVW (Analyze) image files as input.

Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A