Getting Started

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The Stanford Center for Cognitive and Neurobiological Imaging (CNI) research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the MR Hardware page for more details.

If you would like an introductory tour of 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 used to be on Stanford's CourseWork site. Please note that starting December 21, 2016 Coursework has been retired and no longer available. The CNI on-line training has been migrated and is now available as a Canvas module. the link to this module is

Please note - to access the CNI module you must click on the link above. The CNI Canvas module cannot be accessed by first logging into Canvas and then searching for the CNI module. If there are any questions about the CNI Canvas module you should contact Laima Baltusis CNI Facility Manager.


Access status to CNI is organized into three categories:

  • Level 1: Safety Trained User. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators.

  • Level 2: Apprentice Operator. Level 2 operators 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. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time

We have found that most individuals are interested in becoming Level 2 users to fully participate in the research projects done at CNI. It is most efficient, therefore, to have combined Level 1/Level 2 orientation sessions rather than two single (Level 1 or Level 2) orientation sessions Please schedule that session by contacting the CNI Facility Manager, Laima Baltusis, once you have completed the Level 1 and Level 2 on-line training.

Late night scan sessions approval policy

New policy: Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.

IRB Approval for Project

Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval.

Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.

Scheduling MRI Scanner Time

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

Only researchers who have completed Level 2 on-line training and attended the CNI orientation session can book times. Once you have completed such training, you can request (via email) that the CNI Facility Manager enter your information into the CNI scheduler database. Please include your e-mail address, your SUNetID, and the research grants of your research group that you are permitted to access.

Setting up a CNI account for research studies

To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [1].

  • Full project title (ex. Neural Basis of Visual Pattern Appearance)
  • Funding source (ex. NIH, NSF)
  • PTA assigned to this project
  • Grant (PTA) Expiration Date
  • IRB approval letter
  • Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).
  • A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.
  • Name, e-mail, and SUnetID of the person, who will be receiving the invoice notice for this grant each month. The invoice contains the listing of all the bookings to the grant. This can be either the PI, finance manager for the grant, or any other designated person for these funds. Please note that only one person can be set up in the system to receive the invoice. The invoice e-mail can, however, be forwarded to others to additionally to review if needed.

The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.

"Protocol Development" Policies

Some new grants require Protocol Development time to establish scan parameters. Each project may request some development time, but the amount is limited to 10 hours (preferably off-peak). Protocol development time should be used to setup and test the protocol and stimuli related to the project. We recommend that users preserve some development time in the event that a problem develops during the course of a study. The reserved time can be used to trouble shoot the problem.

If there is a need to book more that 10 hours of protocol development time due to the project complexity, please contact the CNI Facility Manager to discuss those issues. For approved projects there will a project associated protocol development PTA set up with an agreed to hour/dollar value.

Beginning in FY18, there will be no protocol development for Seed Funds grants.

Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.

Billing and Cancellation Policies

Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month are included in the invoice or usage summary cover letter.

Current rates for scanning are:

8:00AM to 6:00PM weekdays (Monday-Friday) - $420/hour

6:00PM to Midnight weekdays (Monday-Friday) 8:00AM to Midnight weekends (Saturday-Sunday) - $315/hour

Midnight to 8:00AM weekdays (Monday-Friday) and Midnight to 8:00AM weekends (Saturday-Sunday) - $100/hour

EEG usage charge is an additional $50/hour at any time

Rates as of March 1, 2018 through August 31, 2019 will be:

8:00AM to 6:00PM weekdays (Monday-Friday) - $425/hour

6:00PM to Midnight weekdays (Monday-Friday) 8:00AM to Midnight weekends (Saturday-Sunday) - $325/hour

Midnight to 8:00AM weekdays (Monday-Friday) and Midnight to 8:00AM weekends (Saturday-Sunday) - $100/hour

EEG usage charge is an additional $50/hour at any time

Cancellation Policies

CNI users can cancel their scanning session 48 hours or more in advance of their scheduled scanning tine without penalty. When a scanning session is canceled with less then 48 hours of the scheduled time, the session will be removed from the scheduler (calendar) but a record of it will be retained in the CNI scheduler. If nobody uses the time, then the cancellation could result in a charge.

To avoid being charged for canceled time, you must:

(1) Cancel time at least 48 hours in advance of the scheduled start time (not 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 typical booking scenarios:

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

(2) You typically scan 10 hours each week. For a particular week you have 6 hours booked. On this 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 or less in advance. Consequence: You are annoying for holding that time for so long, but you will not be charged.

(4) You scheduled 20 hours three weeks from today. You cancel 10 hours, less than 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.

User Etiquette

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


  1. Please show up 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. Given how busy the scanner is, any overtime may impact the next group.
    • 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 the CNI Facility Manager 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 at 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 difficult to clean. If an accident occurs please let staff know as possible.
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