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 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
- 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 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.
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.
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.
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.
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.
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
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.
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 pending revisions;
- disapproved; or
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.
To receive Solution Phase NMR services, investigators must complete a service request form.
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.
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.
The following boilerplate language can be used in grant applications when referencing the College of Medicine MRI Core or Center for NMR Research.
Penn State College of Medicine’s MRI Core has 3,000 square feet of laboratory space, which includes biochemical, mechanical, electronic small-animal handling and surgical suits and a fully equipped machine shop with CNC. The CNC CM-1 Compact Mill is a small-footprint, high-accuracy solution for producing and prototyping small, high-precision 2D and 3D parts. More information about the core is available at https://research.med.psu.edu/core-facilities/mri-nmr.
The College of Medicine MRI Core has two MRI systems and an MRI-compatible EEG system dedicated for research.
- 3T Siemens PRISMA-Fit scanner with a bore size of 60 cm equipped with True 2 Channel Tx and 64 Channel Rx. This can be used for human and large-animal MRI studies. The latest RF coil set includes 16 coils and software packages with fully clinical capability, which can provide high-SNR images of the whole body.
- 7T Biospec 70/20as small-animal imaging system with a bore size of 20 cm (Bruker Biospin, Ettlingen, Germany), equipped with the latest hardware and software (Avance NEO with Paravision 360).
- 128-channel high-density geodesic MRI-compatible EEG system.
The core also has multi-sensory fMRI stimulation and monitoring systems:
- SenSaVue System for visual and auditory stimulation (Invivo Corp., Florida), which includes an MRI-compatible 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 (Hershey, Pa.) features an easy-to-use, interactive interface with a touchscreen control. The Olfactometer connects to an odorant carrier that can hold up to 12 different odorants. Paradigms can be programmed and saved to a computer. Stimulation can be sequential or simultaneous and can be set to either monorhinal or dirhinal. Respiration can be monitored and recorded. Additionally, odorant delivery can be triggered by respiration or MRI-TTL pulses. This makes it convenient to simultaneously run visual prompts and record feedback. The Olfactometer can run independently or be paired with fMRI and EEG studies. Research proposed in this R01 will not be possible without this computerized and highly versatile olfactometer.
- The Olfact Smell Test System (Osmic Enterprises Inc., Cincinnati, Ohio) is a computerized instrument to test the smell functions of human subjects. The smell functions that can be tested are odor threshold, odor identification and odor memory.
- ETT Gustatometer with seven fully programmable independent channels for taste stimulation (ETT LLC, Hershey, Pa.).
- Eye Link 1000 Plus system via SR Research. The EyeLink 1000 Plus Host PC performs real-time eye tracking at 250, 500, 1,000 or 2,000 samples per second while computing true gaze position on the display viewed by the participant. The Host PC also performs online detection and analysis of eye-motion events such as saccades, blinks and fixations. In addition to the sample data, these events are stored in a data file on the Host PC. They can be sent through the Ethernet link to the Display PC with a minimal delay or output as analog signals (if the optional analog/digital I/O card is installed). From the Host PC, the operator performs participant setup, monitors their performance and can communicate with applications running on a Display PC.
- Olfactory Threshold and Identification devices (Osmic Enterprises Inc.). The OLFACT family of instruments delivers computerized, self-administered tests for assessing odor thresholds, odor identification and odor memory. The tests are currently being used by physicians, researchers and commercial businesses to test for anosmia, hyposmia and many aspects of normal olfactory function. Additionally, the tests are being used to evaluate personal preferences for various fragrances, odor interactions/masking and the relationship between taste and smell. Scientists are also discovering unique relationships between neurodegenerative diseases like Alzheimer’s and Parkinson’s diseases and the sense of smell.
- Patient Monitoring System/Invivo Precess MRI Compatible. SPO2, ECG, NIBP and ECG recordings.
- BioPac wired and wearable wireless physiology measurement and interpretation solutions. The main hardware and software are the 16-channel data acquisition system and the MP160WSW EDA100C-MRI amplifier used for the electrodermal activity. The INISO-TRIGA: TTL Trigger Isolation Adapter is ideal for recording trigger signals produced by MRI scanners. The NIBP-MRI is a wireless and noninvasive physiological monitoring system that tracks blood pressure, using pulse-decomposition analysis technology as well as heart rate.
The core 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.
A 3-D printer via Form Labs is being used for prototyping parts and customized devices of MRI peripherals requested by researchers. This is the Fusion3 High Performance 3D (F410 3D Printer) via Fusion3 Design LLC.
Penn State Health operates the 548-bed Penn State Health Milton S. Hershey Medical Center on a 550-acre campus in Hershey, Pa., that is also home to Penn State Children’s Hospital and Penn State College of Medicine. Learn more about the health system at https://pennstatehealth.org.
The Animal Resource Facility includes central animal quarters, the 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, as well as an on-site 187-square-foot vivarium with clean room preparation.
The MRI Core includes:
- 16-core server (i9-7960X) with 64 GB RAM, two NVidia Titan V GPUs (12 GB VRAM each) and 10 TB RAID storage
- 16-core server (Xeon Gold 6242) with 96 GB RAM, two NVidia Quadro GV100 GPUs (32 GB VRAM each) and 20 TB RAID storage
- Three Dell multiprocessor workstations with an array of software packages for image processing and electromagnetic field calculations
- A dedicated research PACS system with 11 TB storage and fiber optics network for real-time image data access and distribution to eacH individual investigator’s personal data folder
Office space and secretarial support are provided to the faculty and staff, with the support of one current full-time administrative support staff member. Office space is also available to external MRI Core users upon request.
In addition to the Center for NMR Research’s machine shop, Hershey 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.
Detailed system information
OLFAC Smell Test System: The Olfac Smell Test System (Osmic Enterprises Inc., Cincinnati, Ohio) is a computerized instrument to test the smell functions of human subjects. The smell functions that can be tested are odor threshold, odor identification and odor memory. The odor threshold test measures a person’s ability to detect an odor. Thirteen concentrations of an industry-standard odorant are used. The participant smells two samples, one blank and one with an odorant. They are then asked to determine which of the two samples is the stronger. The concentrations are decreased or increased depending on whether the stimulus is identified correctly. The Odor Identification Test tests a person’s ability to identify a series of 20 different odors. During the test, after smelling the odor, the subject selects the correct odor from four choices on a computer screen. The Odor Memory Test assesses a person’s ability to remember the odors that were presented earlier. The test begins with a presentation of 10 odors. After a 10-minute break, 20 odors are presented, including the 10 original odors. The subjects need to identify whether each is a new odor or one of the earlier 10 odors. A tutorial is built into the program so the subjects can easily learn the task procedures.
ETT Olfactometer: The ETT Olfactometer (Emerging Tech Trans LLC, Hershey, Pa.) is a computerized instrument for odor delivery. It is MRI-compatible and features an easy-to-use, interactive interface with touchscreen control. Its odorant carrier can hold up to six different odorants or six different concentrations of the same odorant. Odor delivery paradigms can be programmed to be sequential, simultaneous, monorhinal or birhinal and can be saved to the Olfactometer directly or in a separate control computer. The execution of the odor-delivery paradigm can be synchronized with functional data acquisition (e.g., fMRI and EEG) and the execution of instructions, other task or stimulation paradigms. The subject’s respiration activity and subjective response can be monitored and recorded. The odor delivery can also be triggered by the respiration activity.
ETT Gustatometer: The ETT Gustatometer (Emerging Tech Trans LLC, Hershey, Pa.) is a computerized instrument for taste delivery. It is MRI-compatible. It hosts eight channels, each with an input and output port. The execution of the taste-delivery paradigm can be synchronized with functional data acquisition (e.g., fMRI and EEG) and the execution of instructions, other task or stimulation paradigms.
Work With MRI and NMR
For current scanner rates and data analysis fees, contact Research Project Manager Jeff Vesek at firstname.lastname@example.org.
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:
- For Siemens 3T, contact Jeff Vesek at 717-531-0003, ext. 285782 or email@example.com.
- For Bruker 7T, contact Patti Miller at 717-531-6895 or firstname.lastname@example.org.
Otherwise, the usage will be charged as scheduled.
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.