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Magnetic Resonance Imaging (MRI) and Solution Phase NMR

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Penn State College of Medicine’s Magnetic Resonance Imaging (MRI) Core is a magnetic resonance imaging facility for animal and human research, providing state-of-the-art MRI methodologies and expertise for in vivo studies to internal and external investigators.

Through the Center for NMR Research, the core provides a number of services, including advanced MRI modalities and Solution Phase NMR services.

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Instrumentation and Services

MRI Modalities Expand answer

MRI allows for in vivo imaging studies for humans and animals. In addition to the conventional anatomical imaging methods, the Center for NMR Research at Penn State College of Medicine provides these new MRI modalities for advanced research:

  • Functional MRI
  • Quantitative parametric mapping
  • Quantitative morphological measurement
  • Diffusion imaging
  • Tractography
  • Magnetic resonance spectroscopy

Functional MRI (fMRI)

Functional MRI is used to examine brain functions or activations. The active areas of the brain for specific tasks will show enhancement from the increased oxygen in those areas of the brain. A given brain activation map can be elicited with a task paradigm designed by the researchers.

Functional MRI requires post-processing techniques after MRI data are collected.

Quantitative Parametric Mapping (qMRI)

Quantitative parametric mapping uses MRI parameters to quantify the associated pathological changes such as tissue iron concentration, edema, cortical thickness or atrophy.

Quantitative Morphological Measurement

MRI provides versatile and superior contrasts (T1 and T2) between various tissues. For example, T1 can be used to locate tumors in the brain in vivo or to observe changes in the abdominal fat pad, while T2 can be used to examine bone regeneration and hydrocephalus regions in the brain.

Diffusion Imaging

Diffusion weighted imaging contrast is based on the rate of water diffusion in the tissue described by a parameter called apparent diffusion constant. It is used for evaluation of stroke and many other diseases. Areas which are injured during a stroke show up darker on an apparent diffusion constant map than healthy tissue does.

Diffusion tensor imaging is used to map the anisotropy of the water diffusion in the tissues. This provides a powerful tool to visualize the brain white-matter tracts and to assess the changes due to diseases or trauma. Fractional anisotropy is used to characterize the diffusion tensor imaging changes.


Tractography is used to examine the white-matter tracts and the changes associated with brain diseases with diffusion tensor imaging. It is also used for studies of the brain activation network.

Magnetic Resonance Spectroscopy

Magnetic resonance spectroscopy is used to study neurochemicals and their changes due to diseases in a tissue with NMR spectrum in vivo.


MRI Facility and Equipment Expand answer

MRI Facility

The MRI Core and Center for NMR Research have 6,500 square feet of laboratory space, which includes:

  • Biochemical, electronic and surgical suites
  • A fully equipped machine shop with a Universal X2-600 computer guided 2-axis laser manufacturing system

The laser cuts, drills and engraves plastics (delrin, polycarbonate, nylon) to an accuracy of 0.002 inches on a 32- by 18-inch working surface.


The MRI Core has two MRI systems and an EEG MRI-compatible system dedicated for research.

  • 3T Siemens PRISMA-Fit scanner equipped with True 2 Channel Tx and 128 Channel Rx
  • The latest RF coil set including a 64-channel head coil and software packages with full clinical capability
  • 7T Biospec 70/20as small-animal imaging system (Bruker Biospin, Ettlingen, Germany)
  • 128-channel high density geodesic MRI-compatible EEG system
  • Full sensory fMRI stimulation systems
    • SenSaVue System for visual and auditory stimulation (Invivo Corp, Florida), which includes an LCD visual display, audio system, button response unit and software (E-Prime) for paradigm creation, patient management, protocol planning, precise delivery of brain stimulation and behavioral analysis
    • ETT olfactometer with full-programmable six independent channels for odor and trigeminal stimulation (ETT, Hershey, Pennsylvania)
    • Olfact Smell Test System (Osmic Enterprises, Cincinnati, Ohio), a computerized instrument to test the smell functions of human subjects; functions that can be tested are odor threshold, odor identification and odor memory
    • ETT gustatometer with full-programmable seven independent channels for taste stimulation (ETT, Hershey, Pennsylvania)
    • Eye Link 1000 Plus Host PC system via SR Research: Performs real-time eye tracking at 250, 500, 1000 or 2000 samples per second while computing true gaze position on the display viewed by the participant
      • Host PC also performs online detection and analysis of eye-motion events such as saccades, blinks and fixations
      • In addition to sample data, events are stored in data file on host PC and can be sent through the ethernet link to the display PC with a minimal delay, or output as analog signals
      • From host PC, operator performs participant setup, monitors performance and can communicate with applications running on display PC

Additionally, the facility also has an Agilent E4991A RF Impedance material analyzer, an HP 4195A Network Analyzer, an HP 8452A Diode Array Spectrophotometer, an Orion EA920 pH/ion analyzer, balances, a LeCroy 9450A 300 MHz dual digital oscilloscope, two analog oscilloscopes, two Morris Model 505 RF Sweepers and an HP 4263A LCR Meter.

Solution Phase NMR Expand answer

Penn State College of Medicine’s Solution Phase NMR Core supports multiple modern NMR applications, including structure elucidation of small molecules, triple resonance experiments for biomolecules, and metabolomic and tissue analyses.

Solution Phase NMR instrumentation includes a 500 MHz Bruker Avance II and a 600 MHz Bruker Avance II.

The Solution Phase NMR facility is located in Room C2818 of the College of Medicine’s Biomedical Research building.


All probes are equipped with a z-gradient coil.

Other Capabilities Expand answer

The following information may be used in grant submissions or to orient investigators to other support available for research at the College of Medicine.

3-D Printer via Form Labs

This instrument is used for prototyping parts and customized devices of MRI peripherals requested by researchers.

Animal Capabilities

The Animal Resource Facility includes central animal quarters in the Medical Sciences Building, and Animal Research Farm and a large dairy farm. The unit features an experimental surgery area, holding area for most species, and full radiological, histopathological, chemical and microbiological supports.

Computational Power

The MRI core includes a 32-processor (3.0 GHz) cluster with 16 GB RAM and 1830 GB RAID storage, eight Dell multiprocessor workstations with an array of software packages for image processing and electromagnetic field calculations, a large-format Mitsubishi dye sublimation printer and an Opal digital slide maker.


Office space and secretarial support are provided to the faculty by the Department of Radiology, with the support of one current full-time administrative assistant.


In addition to the machine shop operated through the Center for NMR Research, the medical center is equipped with both machine and electronic shops. Both of those shops are fully available for projects and operate on about a one-week turnaround.

Procedures, Protocols and Forms

MRI Protocol Submission Process (Facility Utilization Form) Expand answer

To use MRI facilities for research or clinical trials, users must first submit a protocol via the online application form.

The application requires basic information to be completed, as well as the submission of an abstract and relevant consent forms or letters of approval.

The abstract should clearly and concisely describe aims and hypotheses, background and significance and the experimental plan, and include sufficient detail to allow for evaluation on scientific merit.

Any materials or equipment that an investigator proposes to take into the magnet area must be described as part of the application.

Upon receipt of the application, the Center for NMR Research Protocol Review Committee will evaluate the protocol in terms of scientific merit, feasibility and safety.

Protocol Review Process Expand answer

The Protocol Review Committee holds overall responsibility for scientific quality and safety assurances for the project utilizing Center for NMR Research resources.

Following review, each protocol will be considered:

  • approved;
  • approved pending revisions;
  • disapproved; or
  • deferred.

Protocols approved pending revision must be resubmitted to the chair of the Protocol Review Committee, who may approve the revisions without convening the entire committee. Deferred protocols must be resubmitted to the committee with additional information appended.

Investigators may be invited to clarify their protocol to the committee. Their presence is not required unless requested for these committee meetings.

Solution Phase NMR Service Request Form Expand answer

To receive Solution Phase NMR services, investigators must complete a service request form.

Investigator Responsibilities Expand answer

It is the responsibility of investigators to follow strictly all guidelines established for conducting research in the Center for NMR Research, including the maintenance of logs for all systems and the filing of screening forms, informed consent forms and exit questionnaires where applicable for human participants.

Citation Expand answer

Investigators should cite Penn State College of Medicine MRI Core or Center for NMR Research and list the names of the instruments that were utilized either in the Materials and Methods section or the Acknowledgements section of any article.

Work With MRI and NMR

Fees Expand answer

For current scanner rates and data analysis fees, contact Research Project Manager Jeff Vesek at

Scanner usage charges will be calculated following the reserved time slot in the scanner scheduling system or the time actually used, whichever is larger. Data analysis fees are charged for things including but not limited to FMRI, DTI, MRS, volumetric and morphologic data processes.

Payment will be due upon receipt of the invoice issued by the Center for NMR Research.

In case of the inadequate quality of data collected due to MRI system problems, the scanner charge will be waived.

The center will not be responsible for the inadequate data quality due to the experimental design, execution of the experiment, subject movement and statistical errors.

In case of cancellations due to unforeseeable events, it is the user’s responsibility to notify administrators at least 48 hours in advance to reschedule the study time, as follows:

Otherwise, the usage will be charged as scheduled.

Scheduling Expand answer

Investigators will be provided with information on procedures of booking the scanner time for proposed studies after their information is reviewed by the Protocol Review Committee.

Publications Expand answer
Contact the Core Expand answer