MRI Scanning
The CfN utilizes MRI scanners within the Center for Advanced Magnetic Resonance Imaging and Spectroscopy (CAMRIS) in the Department of Radiology within the Hospital of the University of Pennsylvania (HUP). CAMRIS currently operates two whole-body human MRI scanners fully dedicated for research protocols, a 1.5 Tesla Siemens Sonata and a 3.0 Tesla Siemens TIM Trio. Limited access to clinical scanners for research protocols is also possible through special arrangements with CAMRIS.

The CfN also manages a Siemens Prisma 3 Tesla whole-body MRI with a 64-channel head/neck array and Siemens 7 Tesla whole-body MRI with a 32-channel head array. These MRI resources, along with testing and exam rooms, are located in the basement of the Stellar Chance Building in the Perelman School of Medicine.  All of these research-dedicated MRI systems at HUP and Stellar-Chance Bldg. are capable of multi-band EPI and include ancillary insrumentation for stimulus delivery and biobehavioral response monitoring including eye-tracking, noise cancelling bidirectional audio, visual stimulus delivery, and fiberoptic response monitoring with button, trackball, joystick, and grip force devices.  Capabilities for concurrent EEG are also available. Please visit the Resources page for details on 3T Prisma and 7T MRI scanners.


Extensive expertise in pulse programming, radiofrequency coil design, and pulse sequence design is available within the CfN and the Department of Radiology. Access to research scanners requires regulatory approval and scheduling through the CfN on-line calendar. The calendar website is https://cfn.upenn.edu/calendar/ Please contact the calendar administrator, Margaret Ryan, to set up a new account once your protocol has been approved by Penn's IRB and the CAMRIS Committee. Phone: 215-573-8486 E-mail: ryanm@mail.med.upenn.edu.

Stimulus and Response monitoring
Both 1.5T and 3T research scanners within CAMRIS at HUP are equipped with stimulus delivery and monitoring systems for fMRI research. These include Sanyo SXGA 4200 lumens projectors with Sanyo Long Throw zoom lens for rear-view/rear-projection onto Mylar screens. Video signals are carried into the magnet room using a Lightwave FiberLynx optical-fiber VGA connection. Both the projector and the FiberLynx units are housed in custom RF shield boxes with filtered power receptacles. Images are viewed through mirrors mounted on the head coils. Audio stimuli may be presented via air-conduction headphones available on both the Siemens Sonata and TIM Trio 1.5T and 3T systems, or alternatively via Avotec audio systems Responses are monitored using FORP fiberoptic button boxes installed at 1.5T and 3T. Low pass filters in the magnet room penetration panels allow custom interfacing of other stimulus and monitoring equipment using DB-9 connectors. for HUP6, click here for instructions on how to use the scanner microphone At HUP6 (3T Tim Trio MRI) and the 3T Prisma and 7T MRI machines in Stellar-Chance Bldg. have an MR compatible in-bore video camera (from MRC Systems GmbH) available for subject monitoring during fMRI experiments.

Data Analysis

The CfN makes use of distributed resources throughout the University of Pennsylvania, but also houses two data analysis facilities. The CfN HPC cluster consists of:

* 576 dedicated compute cores, from 21 compute nodes with dual 8-core Intel Xeon E5-2450 2.10GHz CPUs and 64GB RAM, and 30 compute nodes with dual 4-core Intel Xeon 2.83GHz E5-440 CPUs with 16GB RAM.

* A dedicated 16-core head node (running Rocks and SGE) manages cluster operations.

* Three dedicated file servers managing high-speed (6GB/s and 4GB/s) RAID-6 devices for over 200TB of formatted storage.

* A high-speed 10GbE internal cluster network and a Gigabit external network connection.

* A dedicated tape backup system with 100TB capacity.

The cluster is located in a University-run commercial-grade server room with redundant power supplies, UPS power backup systems, fire suppression system and 24-hour restricted access and security.

A lab (B19 Stemmler) has both public and private workstations and a 50-inch plasma screen for meetings and presentations.

Software and expertise to run a broad range of data analysis procedures is available, including SPM, fixed and random effects analyses, nonparametric analyses, time series extraction, both automated and manual segmentation into regions of interest, Brodmann areas, vascular distributions, BrainVoyager, FMRIB Software Library, MRIcro, AIR, AFNI, FSL, Free Surfer, SNAP, Matlab, VoxBo (developed at Penn), and others additional capabilities for large-scale processing are available in the Gee Lab. The CfN also hosts and maintains an MRI scheduling calendar for all MRI research instrumentation.

Additional capabilities for large-scale processing are available through the Department of Radiology in the form of a 16 Xeon processor cluster with 5 TB RAID that is optimized for cutting edge methods, including high-resolution spatial normalization, population-specific template construction, deformation/tensor-based morphometry and quantification of cortical geometry and shape, as well as customized analysis of pediatric and elderly populations, brains with lesions and diffusion tensor images.(Gee Lab)

Mock Scanner
The CfN's original mock scanner was located in Room B19, Stemmler Hall Basement. Due to construction, this resource has been decommissioned. It was fabricated from our old GE scanner shell and closely replicates the subject's experience during fMRI including a realistic scanner face and bore, head coil, stimulus presentation and response, scanner sounds, and triggering with each mock TR. Subject head movements are monitored with an inertial device and displayed in real time.

As of October 1, 2015, we have a new mock scanner/MRI Simulator purchased from Psychology Software Tools, Inc. It is model # PST-100355 and equipped with MoTrak (motion tracking) and SimFx (sound simulation and presentation) Software, also from Psychology Software Tools, Inc.

This new mock scanner was installed in Room C512 of the SOM Richards Bldg. but has recently moved. The current location of the CfN mock scanner is Room 304, Levin Building. The key for this room is located in a lock box outside of Room 301, Please contact Margaret Ryan for the code to the lock box. Kindly return the key to this location when finished.

The mock scanner creates a realistic fMRI environment so that subjects may be desensitized and focus more easily on the tasks they are to perform.

This resource can be reserved by individual protocols or labs by calling 215-573-8486 or contact Margaret Ryan (ryanm@mail.med.upenn.edu) for calendar access.