Scanning: Information for Users

This page contains vital information on becoming a scanner operator, gaining access to BIC, scanner reservation policies and other administrative matters. Please read this page in its entirety before contacting BIC staff with your questions.

Getting Information

The primary vehicles for communication between BIC staff and scanner users are the scanner mailing lists. All training courses are announced on these lists (amongst many other things). If you have a email address you may sign yourself up via the "bConnected Lists" link at We use three main lists for BIC activities:

The list specific to the 3 T is for scanner-specific practical and administrative issues only. Post slot cancellations here, look for announcements of training courses, etc. The fmri list is reserved for non-scanner-specific discussions, such as general acquisition questions, discussion of MRI data processing issues, etc. The mock scanner list is for, well, I'm sure you can figure that out!

If you aren't a Berkeley student or employee and therefore don't have a email account, contact Ben to get added to the mailing list(s) of your choice. Note also that you can use any email address to register for the lists - you don't have to register using your Berkeley address once you're logged in - but you must post to the lists using the registered account. So, if you are in the habit of using gmail, say, instead of your Berkeley address when you read/send mail, I suggest you register the gmail account for the list.

Safety Training

Anyone who plans to spend any significant time at the scanner (i.e. other than to be a subject or an occasional, accompanied visitor) must pass a safety quiz after attending a safety orientation class. Classes are announced on the 3 T list and occur approximately monthly, depending on demand and staff schedules. The current safety syllabus is downloadable here.

Next safety training session:

11 am to 1 pm, Thursday 10th August, 2017.

Meet at the BIC elevator. Please read the safety syllabus/SOP document beforehand. Instructions on how to find the BIC elevator are on the Contact page.


It is important to note that there are dual objectives for the safety training: your safety and the safety of your subjects. The latter objective requires that you not only understand the safety information you are taught, but can impart that same information to your subjects, most of whom will probably never have been around an MRI before. You may also be interested to read a report on MRI Research Safety and Ethics produced by the NIMH Council Workshop on MRI Research Practices. If you intend to set up and run your own experiment you will be discussing subject safety extensively with the Berkeley Committee for the Protection of Human Subjects (CPHS), which is the Institutional Review Board by another name. So, reading this document should provide useful suggestions when you are developing your CPHS protocol, and the information contained therein will help you make decisions when screening subjects and working in the MRI suite. Note that these documents are not required to pass the safety quiz, however.

User Training for the Scanner

Introductory and Intermediate level user training classes happen every 3-6 months or so, depending on demand. The Introductory level class consists of a two-hour demonstration followed by an optional (but strongly advised) hands-on tutorial a few days later, and covers basic scanner operation only. Intermediate level classes are an interactive 2-3 hour session dealing with general fMRI acquisition topics; attendees are expected to know scanner operation basics already. There is usually one demo class and one interactive/tutorial class a few days later. Advanced classes for users with intermediate-level fMRI experience will be customized to specific topics based on interest. Advanced classes also form the basis of annual user re-certification. All class dates and times will be announced to the scanner3t mailing list.

To attend ANY formal scanner training classes you must first have passed the 3 T safety quiz (see above), and have a current CPHS approval to scan. You should also have sufficient funding to cover the scanning you intend to do. For most people, your principal investigator (PI) will be responsible for getting CPHS approval and funding for scans. Please discuss with your PI before you try to initiate scanner training. If you (or your PI) don't have a current CPHS approval and/or funding, contact Ben Inglis and we will try to figure out what you can do. Once you have the CPHS, funding and safety quiz requirements satisfied, please complete the Request for Scanner Training form and submit it to Miguel Perez. There is no charge for training classes.

Please note that you may learn to scan by apprenticing under an experienced operator in your group, or you may already have experience from a prior lab. There is no requirement to attend the formal classes, only to pass the user quiz. See the description of the user quiz below to determine whether you might need the formal training or not. A user training guide/FAQ is available to assist you. Note that this guide is mandatory reading for the user quiz anyway.

Next User Training Classes:

Last training was May, 2017 so the next training will be late summer or early fall this year.

Introductory Training

Intermediate Training:

Peripheral Equipment Training:

Please submit a Request for Scanner Training Form to Miguel Perez to register for training.

Peripherals Training

Peripherals training is treated separate from scanner training. Please contact Miguel Perez to set up a time to learn how to use the peripheral stimulus equipment. He may be able to tailor the peripherals training to your particular requirements. There are documents for setting up the mirror, a guide to the peripherals and separate guides for the eye tracker and Biopac physiological recording.

Becoming a Qualified Scanner Operator - the User Quiz

Prior to taking the user quiz it is expected that you have attended the Introductory and Intermediate level scanner training sessions, or have received equivalent education by apprenticing under an experienced operator in your group, or have suitable experience from another facility. (Note: Advanced training is beyond the level of the user quiz.) The litmus test for knowing when you are ready to become a qualified operator is straightforward: you should be able to run an entire scan session, from subject screening through image acquisition to data transfer, without needing significant assistance from anyone.

The user quiz covers the following broad areas: scanner operation, peripherals equipment operation, subject screening and safety, and some background physics of fMRI. To pass the user quiz you should have a good idea of why you do what you do, not just be able to make pretty pictures in rote fashion!

You must read/review the following documents before taking the user quiz:

1. The specific CPHS protocol and screening form you'll use for your subjects. (Contact your PI for these.)

2. The CPHS Policies governing MRI examinations at Berkeley.

3. An explanation of how to screen subjects for 3 T MRI.

4. Re-read the 3 T safety syllabus you read for the safety quiz. (Contact Ben Inglis if you need a new copy.)

5. Chapters 4,5,6,7 and 8 from the book by Huettel, Song & Mccarthy, "Functional Magnetic Resonance Imaging." If you have already taken PSY214, Mark D'Esposito's Intro to fMRI Methods class, then a lot of this material should be review. If not, you should read through these chapters carefully. It is important to have a solid understanding of the basic physics and physiology underlying fMRI. Otherwise you will find it difficult, if not impossible, to know how best to set up an experiment, how to recognize and avoid/reduce common artifacts, etc.

6. The user training guide/FAQ.

7. Review the basic use of peripheral equipment for displaying stimuli in the scanner.

Scanner Access Policies

Once you have passed the user quiz you'll be placed in a regular booking group on the scanner scheduler and will be allowed card key access to Zones III and IV. Your scanner access privileges will remain current provided you maintain a current CPHS approval and provided you have funding to scan. Anyone who is found to be scanning under an expired CPHS protocol will be barred from the scanner and will be reported to the CPHS.

Billing is done based on the reservation schedule. Our goal is to maximize the amount of science that can be done, not maximize revenue. Thus, if you delete a reservation for any reason, even at short notice, you won't be charged provided you email the 3 T list announcing the cancellation so that someone else might use the time.

Charges will not apply if you cannot scan because of a legitimate scanner or peripherals issue. Note, however, that lack of experience or training does not constitute a legitimate problem! It is rare that a real scanner issue arises. More often a user creates a problem for himself by rushing, or by trying to scan solo without sufficient practical experience.

As a general rule, only funded studies may be conducted on the scanner. However, there are a few occasions when scan slots can be reserved without charge. If you are about to start a new experiment and need to set up a protocol with the assistance of BIC staff, or you are installing a new piece of equipment with the assistance of BIC staff, scan slots should be reserved with the appropriate BIC staff person such that your group won't get the bill. Note also that these "free" slots can happen only if they are the segue to a funded experiment. Anybody needing scanner time for an unfunded, pilot project should contact Mark D'Esposito.

Card key access to the BIC

Access to BIC in Li Ka Shing Center is restricted to those people who have passed the safety quiz. Access to the 3 T scanner (Zones III and IV) is further restricted to those people who have passed the user quiz. Having passed one or both quizzes, download and complete the BIC Card Key Access Request Form to request activation of your UC Berkeley card key. Note that passing the safety quiz alone grants Zone II access privileges while passing both the safety and user quizzes grants Zones II-IV access privileges. Please mark the appropriate zone request on the form.

You may submit the form electronically or drop it off as a printed copy. Check to see if your card key has been activated 2-3 working days after receiving notification that your card key request form has been received and processed. Once it is active, contact Rick Redfern to receive an LKS sticker to go on your card. This sticker is required for after hours access. The LKS security guards (and UCPD) are authorized to eject anyone from the building whose card key doesn't have the sticker.

3 T Scheduler

The 3 T scheduler is accessible via the Scheduler menu item at the top of the page. To get an account on the scheduler (called Calpendo) you must have passed the safety quiz and submitted a Request for Scanner Training form, or have already passed the user quiz. You will be assigned Trainee status, allowing you to view the schedule but not make reservations. Your status will be changed to a regular user, allowing you to make reservations, once you pass the user quiz (assuming you have a current CPHS and your PI wants to pay for your scans!).

Bookings may be made up to two calendar months ahead of the current date without prior approval. If you need to make a reservation that is more than two calendar months away, please submit a Request for Scanner Reservation form to Ben Inglis or Mark D'Esposito. The instructions are on the form.

Peripheral Equipment

A brief overview of the scanner's peripheral equipment may be found on the Stimulus page. Most of the peripheral equipment in the 3 T suite is owned by BIC and is for general use (subject to suitable training). However, some users need equipment that is not deemed necessary for general use but is essential for a specific experiment. In those situations, a user group or multiple groups may purchase equipment and have it installed in conjunction with BIC staff, and the use of that equipment is prohibited without express permission from its owner(s). You will learn what equipment is general use/access when you take peripherals training. And if in doubt about a specific piece of kit, please ask BIC staff.

If you want to use a device that isn't presently available at BIC and would like BIC to purchase it for general use, please complete and submit a BIC Equipment Purchase Request form to Ben Inglis or Mark D'Esposito. If you already own the device, or you will purchase it without BIC assistance, please contact BIC staff to discuss how it can be installed in the scanner suite.

Mock Scanner Access

Anyone with a Cal ID can get access to the mock scanner that is housed in the old 4 T building. You do not need to have passed the 3 T safety or user quiz. Please complete the Mock Scanner Access form and submit it to Rick Redfern.

User QA Procedures

Users are requested to run a simple check of the scanner's operational status after startup and prior to shutdown, and may be requested to perform the check if certain problems are encountered. A full list of the situations necessitating the "User QA" procedure is included in this document, along with a complete description of the procedure itself.


Forms and Training Documents


Mock Scanner Access Request Form
BIC Card Key Access Request Form
Request for Scanner Reservation Form (for reservations > 2 months away)
Request for Scanner Training Form
BIC Staff Assistance Request Form
BIC Equipment Purchase Request Form

Scanner Training:

3 T Safety Training Syllabus (Last updated: 08 Oct 2016)
User Training Guide & FAQ (Last updated: 08 March 2012)
CPHS Policy for MRI Research at Berkeley
How to Screen Subjects for MRI

Peripherals Training:

Guide to The Peripherals
Setting Up The Mirror
Guide to The Eye Tracker
Peripherals Setup Schematic
Peripherals Checklist
Guide to Acqknowledge and Biopac

Supporting Human Subjects Documents:

NIMH Report on MRI Research Safety and Ethics
Full UC Berkeley CPHS Policies and Procedures