Perelman School of Medicine at the University of Pennsylvania

Center for Magnetic Resonance & Optical Imaging


Regulatory Agencies


All research involving human subjects require approval from the Institutional Review Board. Take the online exams in KnowledgeLink as soon as possible.


All research that involves animals require approval from the Institutional Animal Care and Use Committee. Take the online exams in KnowledgeLink as soon as possible and sign-up for any hands-on training sessions you require.


Following IRB or IACUC approval for your protocol, you’ll need Center for Advanced Magnetic resonance Imaging and Spectroscopy (CAMRIS) approval for all research on the clinical MRI scanners.  For the non-clinical smallbore scanners, all experiments need or Small Animal Imaging Facility (SAIF) approval.

CAMRIS & SAIF meet once every two weeks on a Tuesday to review all applications. At the end of that day, they will give you an account (either a PRODEV account for unfunded protocol development projects or another name if the project is funded) and time on the appropriate MRI scanner you requested on the application. TECHDEV accounts are also available but restricted to pulse sequence development and testing only.

Becoming an Approved User

Approved User status is given to those individuals that have completed the following:

  1. Complete MRI Safety Training (KnowledgeLink)
  2. Complete CITI Patient Oriented Research course and HIPAA (KnowledgeLink)
  3. Complete Basic User Training (On-site training 60-90 minutes)
  4. Completion of all required paperwork
  5. Approval from individual responsible for your training (mentor)

MRI scanner account setup


New MRI pulse sequences and/or coils are continuously being developed. These accounts are for testing of such experimental magnetic resonance techniques. These technical developments are typically phantom experiments of limited scope. Limited human scanning is allowed to further access the results of such techniques.


A protocol development account is required to scan human subjects including patients for a unfunded project.  The results should serve as preliminary data for a grant or a publication (manuscript, abstract, talk etc.).  CAMRIS/SAIF approval for these unfunded projects usually means that a prodev account will be created with 10-15hrs of free scan time.

Funded projects

A funded project will have its own set of consent form(s) and a CAMRIS/SAIF account name with MRI scanner time as budgeted.

Research MRI scanners

After CAMRIS approval and account creation, scheduling time on these scanners is possible via an online whose access will be provided to you. Visit our Resources page for more details of human and animal MRI scanners.

Computing Center

There are a several PC and Mac desktop computers in the lab. If you have your own computer, please ask the appropriate personnel below for software and hardware requirements.

Pulse Programming

Some dual-boot (Linux & Windows XP) Dell PCs are for pulse sequence programming for the Siemens clinical scanners. The software for this is called IDEA and the latest version is installed . The computers may be used for non-pulse programming related work as well such as data processing. Please contact Dr. Hari Hariharan at the CMROI with any questions.

Data Processing

Several dual-boot Dell PCs also have the Matlab software. Software licenses must be ordered via the Office of Software Licensing. To process images obtained from the scanners, two post-processing steps must be performed : (1) pre-processing and (2) image analysis.

(1) Pre-processing

Unsorted DICOM-type images obtained from the clinical MRI scanners must be sorted using IDL software prior to analysis. To obtain a copy of IDL for your PC, contact Ari Borthakur. Conversely, images may be downloaded directly to your PC laptop from the scanner itself and need not be sorted using IDL. For more information on how to obtain sorted DICOM images directly from the scanner, please contact Dr. Hari Hariharan.

(2) Image Analysis

Sorted Siemens images are of type DICOM (.dcm). For mapping (T2ρ, T1ρ, T2, T1, etc.), a series of DICOM images may be processed using software in IDL. To obtain custom-written mapping programs in either language, please contact Dr. Hari Hariharan

Scheduling MRI exams on clinical scanners

Please see the Center for Advanced Magnetic resonance Imaging and Spectroscopy (CAMRIS) website for details.

Contact Information:

CMROI MRI-related issues:
Dr. Hari Hariharan, PhD
Associate Director, CMROI

CMROI administrative issues:
Susan Colleluori
Associate Director. CMROI

CAMRIS administrative issues:
Shannon Long
CAMRIS Manager

SAIF administrative issues:
Marcia Shinn
Research Application Administrative Coordinator