Getting Started

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The CNI facility has been designed to reflect the experimental needs in social science and related disciplines. The core instrumentation provided by the CNI is a research-dedicated 3T MRI scanner. In addition to the scanner, there is a mock scanner for training, experimental testing rooms, and MRI integrated experimental equipment such as visual displays, audio presentation equipment, and MR-compatible EEG. See the MR Hardware page for more details.

If you are interested in an introductory tour and access to the facility please email Laima Baltusis or call her office phone (5-8382).

User Access & Training

The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.

The CNI imaging facility is available to researchers by arrangement with the Facility Manager. Each individual investigator using the MRI facility must obtain basic magnet safety training and must also obtain additional training to use the MRI lab and to operate center equipment.

The first step in safety training is to complete the CNI online training module that explains key issues concerning safety and MR operation. This module can be found at Stanford's CourseWork site. Please note that starting December 21, 2016 Coursework will be retired and no longer available. The CNI on-line training has been migrated and is available as a Canvas module. the link to this module is

To get to the Coursework module go to This should bring up the course module. If you are not yet a member of this site a prompt will pop up asking if you want to join (after you enter your SUNetID and password into the login page). You can sign up for the course and follow the instructions. If there are any questions about the CNI CourseWork module you should contact Laima Baltusis

Access status is organized into three categories:

  • Level 1: Safety Trained User. This individual works with a Level 3 MR operator and may enter the magnet room to assist. Level 1 investigators must have passed Safety training, but they need not have experience operating the scanner; Level 1 investigators cannot schedule or operate the scanner.
  • Level 2: Apprentice Operator. This individual may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.
  • Level 3: Operator. This individual has permission to run the MRI Scanner when CNI staff members are not present and to supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on test administered by the CNI Facility Manager. Level 3 operators are given full privileges to the facility and can enter the facility at any time.

Project Review and Approval

Before using the MR scanner, you must have IRB approval and identify an account for billing.

Projects cannot be initiated without IRB approval. PI’s must provide written documentation of the initial IRB approval(s) and annual IRB renewal(s). The PI must make sure that the protocols list all personnel who will be conducting MRI research.

Researchers requesting authorization to use the scanner for human studies should submit their request and IRB approval to CNI Research Director, Robert Dougherty.

Scheduling MRI Scanner Time

All scanner time is booked via the CNI on-line scheduling system.

To schedule time you must have adequate safety training.

Setting up a CNI account

To start carrying our your study and scheduling time, should request an account from [1]. To set up an account requires the following information

  • Project title (ex. Neural Basis of Visual Pattern Appearance)
  • Funding source (ex. NIH, NSF)
  • Grant number(s) (as per funding source)
  • Grant Expiration Date
  • IRB approval dates
  • Abbreviated title: one or two word description. (This will be used along with the PI name and funding source to allow appropriate users to select a project when scheduling scanner time on the web-based scheduler, e.g., Smith- NIH Pattern).
  • A list of researchers associated with this project

The Facility Manager will contact the PI via email once the accounts have been set up.

Billing and Cancellation Policies

Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The Facility Manager sends an e-mail at the beginning of each month to all users including each PI containing all the hours scanned for the previous month and the accounts used. PI's must verify that the information is correct and send a reply, or charges are automatically be submitted at the end of the month. Users also have an opportunity to dispute charges during this time.

CNI users will be able to cancel their scanning sessions 20 hours or more in advance of their scheduled scanning time without penalty. When a scanning session is canceled with less than 20 hours of the scheduled time, the session will be removed from the scheduler (calendar) but a record of it will be retained. If nobody uses the time, then it could result in a charge. Information about the previous month's cancellation policy is included in the e-mail sent by the facility manager to all users at the beginning of the new month. Please contact the Facility Manager with any additional questions.

Update - please note:

New cancellation policies are in effect as of Monday March 1, 2013. Due to increasing time demands on the CNI MRI system we have found it necessary to modify the center's booking and cancellation policies. These changes were presented at the recent CNI Town Hall meeting. We hope that these policies will minimize scanner idle time and allow fair access for all users to schedule the scanning time that they need. We expect these changes will have little or no effect on most users.

To avoid being charged for canceled time, you must:

(1) Cancel time at least 48 hours in advance of the scheduled start time (rather than 20 hours)

(2) Cancel no more than 4 hours per week per PI (Lab)

If you fail to meet both conditions, you will be charged for the canceled time unless another funded user uses that time.

Here are some typical booking scenarios:

(1) You scan 3 hours each week. Sometimes you cancel 48 hours in advance. Consequence: No charges for canceled times.

(2) You scan 10 hours each week. Mostly you use at least 6 hours. In one week, five subjects are no-shows and the canceled hours go unused. Consequence: You will be charged for 1 hour of unused time, subject to staff judgment.

(3) You scheduled 8 hours over a weekend, two months from now. You cancel 4 hours, 48 hours in advance. Consequence: You are annoying for holding that time for so long, but you will not be charged.

(4) You schedule 20 hours three weeks from today. You cancel 10 hours, 48 hours in advance, and you use 10 hours. Consequence: You will be charged for 6 hours of the canceled time unless someone else uses that time.

Additional information regarding these policies is available in the CNI Standard Policies and Procedures Guide in the Safety Policy section at

User Etiquette

Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:


  1. Please make sure that you show for scan time that you have booked, and start and stop your scan session on time.
    • If your scan is running late please contact the CNI staff to determine the best course of action for your scan and for the experimenters who are scanning after you. Do not assume that you will be able to finish your scan if you are starting to run overtime. Other researchers may not have flexible schedules.
    • Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. Research labs are limited to 4 hours per week of late cancellations. Additional cancellations may be charged if those times are not rebooked.
    • Please book your scans with valid grants.
    • Please e-mail IRB approval letters for new and extended studies to Laima Baltusis (

  2. After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.
    • Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.
    • Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.
    • The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.
    • Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.
    • If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.

  3. Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.
    • After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.
    • Food consumption is discouraged in areas of CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.
    • If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.
    • Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.
    • Ink stains, coffee stains, and food stains on furniture, counters and floors are very difficult to clean. If an accident occurs please let staff know as possible.
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