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).


CNI has been cleared to reopen by the university as of Wednesday June 10, 2020.

Upon re-opening, the CNI facility is operating with procedures that include frequent cleaning and that reduce the number of people in the facility at any one time. All users will be required to complete additional training (recertify) prior to resumption scanning at the CNI. The steps for recertification are listed here:

  • Review the CNI Standard Operating Procedure (SOP). The CNI SOP covers procedures for participant screenings, enhanced cleaning procedures and other general required behavior during a research session as well as Stanford’s recommendations for employee screening as to whether they can come in to work. Please also review the CNI SOP Slideshow illustrating the main processes of the CNI SOP.
  • Complete the quiz/verification form
  • Complete the EHS training (STARS course code EHS-2470-WEB) on COVID19 information

For each time you come to perform an experiment at the CNI, each of your participants and any other visitors must complete the COVID19 screening form and deposit it with the CNI team.

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 new user orientation sessions rather than two single (Level 1 or Level 2) orientation sessions. After March 1, 2020, please register for a CNI new user orientation session listed in the next section (CNI Orientation session registration forms) below on this wiki page.

CNI New User Orientation Session Registration Forms

The combined Level 1/Level 2 new user CNI orientation sessions have typically been held on Thursdays 8:30AM to 10:30AM at CNI. Enrollment to any in-person session has been limited to eight people. Currently in-person sessions are now cancelled. Until further notice CNI orientation sessions will be scheduled as Zoom meetings. Please fill out the registration form for the Zoom session you would like to attend below. To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form Etiquette Form.

Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions. (1) (2)

Past and Upcoming Zoom new user orientation sessions currently scheduled

  • Nov 16, 2023 09:00 - 10:30AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

  • Dec 14, 2023 09:00 - 10:30AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

  • Jan 18, 2024 09:00 - 10:30 AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

  • Feb 22, 2024 09:00 - 10:30 AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

  • Mar 14, 2024 09:00 - 10:30 AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

  • Apr 18, 2024 09:00 - 10:30 AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

  • May 16, 2024 09:00 - 10:30 AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

  • Jun 13, 2024 09:00 - 10:30 AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

  • Jul 18, 2024 09:00 - 10:30 AM Pacific Time (US and Canada) Register in advance for this meeting: After registering, you will receive a confirmation email containing information about joining the meeting.

Note: Please complete the Level 1 and Level 2 CNI on-line training modules in Canvas (the link to this is ) prior to attending the CNI New User Orientation Zoom session.

CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing

For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [1]

  1. The PI's must complete the verification form [2], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the CNI Standard Operating Procedures (SOP). I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.
  2. All team members of the group must read the SOP for urine testing at CNI Media:CNI - Urine Test - SOP.pdf
  3. All team members of the group must take the quiz for urine testing after reviewing the SOP document [3]

Late night scan sessions approval 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 [4].

  • 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.

Scheduling Policy

Overview: We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours.

The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.

Advance Booking Policy: The CNI scheduler opens up for slots 8 weeks in advance. The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When a slot for a date and time 8 weeks in advance opens, you may book a scan time period that extends beyond the just-opened slot. When booking time, please avoid leaving single ½-hour slots idle between your time and any immediate neighbors.

If you have exceptional study requirements that require booking further in advance than the 8-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible.

Protocol Development Policy: The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully.

Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant.

Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted.

Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during normal weekday hours (M-F 8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant.

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.

Cancellation Deadline: The late cancellation deadline is 2 weeks before the scheduled time.

Late Cancellation Policy: A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.

To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability.

We will of course not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials.

Cancellation limits: Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed.

Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.

Short-term reserve time: As of February 2019, CNI has started reserving some blocks of time that are labeled CNI_Short_Term_Reserve. These times will be manually released once they move fully within the two-week cancellation window. That is, a block of time reserved from 2-5pm on February 15 will be released on February 1 at 5pm. The intent of opening this time up within the two-week window is to address the needs of researchers who have only limited advance notice of acceptable subjects. If your research project has a more flexible subject population, we ask you to be considerate and leave these time blocks open to those whom are less fortunate.

Billing 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 will be included in a separate invoice.

Rates for scanning effective September 1, 2023 - August 31, 2024 will be:

8:00AM to 6:00PM weekdays (Monday-Friday) - $503/hour

6:00PM to Midnight weekdays (Monday-Friday) - $410/hour
8:00AM to Midnight weekends (Saturday-Sunday) - $410/hour
8:00AM to Midnight University Holidays or Closure - $410/hour

Midnight to 8:00AM any day (Monday-Sunday) - $115/hour

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

Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.

Cancellation Policies

See above

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.
    • 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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