Staglin MR Suite

From Center for Cognitive Neuroscience
Jump to: navigation, search

General Policies

All policies of the Staglin One Mind CCN aim to ensure participant and experimenter safety and to foster a community of respect, consideration and co-operation. If not followed, the Staglin One Mind CCN reserves the right to review and possibly revoke scanning privileges.

CCN Space

  • Restricted Areas: Only safety certified users are allowed to enter the scanning suite (control room & scanner room) unless granted an exemption by CCN. This is for the safety of the individuals and liability of the center. If an exemption is granted, it is for a single instance. It is paramount that uncertified users do not touch any research equipment while shadowing.
  • MR Suite: It is the responsibility of all experimenters to maintain the facility in a clean and orderly state. This includes all surfaces, linens, cabling, computing and other equipment in both the MR room and the scanner operation room of the MR suite.
  • Equipment and Peripherals: Users must obtain consent from CCN Tech or Mark Cohen to add, change, and/or remove equipment in the control room or magnet room. USB flash drives must be properly scanned for viruses before connecting to console.
  • Phlebotomy: CCN has gone through the necessary review and approval to open C7-439C (EEG Prep Room) to its users as a make-shift blood collection site. Strict adherence to guidelines must be followed. Please see Blood Collection SOP for details.


  • Safety Certification and Recertification: CCN safety certification is done using a combination of in-person sessions and remote work via the Staglin Safety and Training Course on Bruinlearn. Please ask your lab manager/research coordinator for enrollment information. All links and resources necessary can be found on the BruinLearn course. Recertification is also done via the BruinLearn platform, with no password necessary. Please only email the MR Tech if you are experiencing trouble enrolling in the course or you have questions with the materials.
  • Operations Training: The MR Tech offers multiple trainings per month to familiarize individuals with operations in the MR suite. Please enroll in the BruinLearn course and look at the calendar to sign up for available sessions. Additional training opportunities on more advanced or specialized topics will be arranged as appropriate.


  • User Rights: All users have equal rights and privileges to perform projects at the center. All users will be treated with respect; failure to do so may result in suspension of scanning privileges. Any user can ask questions and suggest policy changes/additions by reaching out to Executive Committee.
  • Scan Personnel: For the safety of both the participants and the investigators, all scans must have two MR-safety certified investigators in the facility for the entire duration of the scan. In case this cannot be achieved, please make arrangements with one of our MR Technicians to provide support. MR Technicians are not required to be on the premises during all scans, and cannot be assumed to provide backup support without prior notice. Please note that at least one individual present is required to be a full-time/part-time staff, graduate student, post-doc etc. Part-time paid undergraduate researchers cannot presently act as primary users unless submitted to CCN for review.
  • MR Technician Services: The Staglin One Mind MR technicians maintain the MR facility and are available to support experimenters in all aspects of MR imaging, including assisting during scanning. If there is an anticipated need for support during scanning, experimenters must contact the technicians well in advance of the scheduled scan. Contact information is posted in multiple areas throughout the center (e.g., on the control room wall, by the Eyetracking computer) in the event of unanticipated issues during the scan.
  • Observers: Persons who have not completed safety certification are not allowed to observe scans or enter the magnet room for training or other purposes. For case-by-case exceptions with respect to scan shadowing, see the sections regarding CCN's Restricted Areas policy and Common Personnel Questions on this page.
  • Volunteers: All volunteers who would like to join a lab and gain valuable research experience at the Staglin Center are required to undergo the full on-boarding process with the UCLA Health Sciences Volunteer Program. Please read through the Staglin Volunteer Addendum for duties and responsibilities. Please understand that volunteers are not allowed to handle CCN research equipment without supervision of a user who is full-time staff, graduate student or faculty, and may not operate the scanner unless dealing with an emergency.
  • Visitors: As per Staglin One Mind CCN safety protocol, visitors are not allowed in the MR suite without prior approval. Please contact our MR Technicians to arrange a visit for a group or individual.

Scan Procedures

  • Infection Control: Current guidance for infection control policies can be found here. Please make sure you are administering the Pre-Appointment Screening Form to your participants before they arrive to UCLA.
  • Participant Arrival: Please make sure that your study participants have a direct contact and that lab personnel will be available to take calls and/or respond promptly to texts/emails as the time of the scan approaches. Study participants should not wait inside of CCN unattended. If a participant arrives early and you are part of the research team, make sure someone is available to communicate with the person and direct them to wait on the bench right outside CCN. If you are in CCN and not part of the research team expecting this participant's arrival, it is up to you if you have the time to ask questions and help figure out who their research contact is. Regardless, still ask them to wait on the bench outside CCN.
  • Pilot Program: The Center will consider proposals by members of the UCLA community to access both the scanning and analysis core services for pilot studies without charge to the investigator. Priority will be given to junior investigators and to proposals for novel cognitive neuroscience projects that have a high likelihood of achieving extramural funding. To submit such a request, email the completed application to the CCN Managing Director. The proposal will be reviewed by the Executive Committee members and CCN personnel will contact you regarding the status of the submission.
  • Protocol Testing: Each new protocol is granted off-hours time to test and refine the scanning protocol, at no charge. All such scans must be booked directly through the MR Technician.
  • Scheduling: The center does not mandate a strict limit on when scans can be booked relative to the scanning date. However, to foster cooperation and consideration within the community, booked scan times are assumed to be filled (assigned a participant) promptly and booked on an as-needed basis. Scans that are booked in advance, above and beyond the current scheduling norms, will be reviewed by the CCN staff and potentially canceled. Investigators whose experimental needs do not fit these guidelines are encouraged to contact our MR Technician to make other arrangements.
  • Scan Time: All scans are expected to start and end promptly at the scheduled time. It is the investigators’ responsibility to communicate with the CCN staff and/or other investigators if these times cannot be met. Please note that CCN and/or other investigators may not be able to accommodate requests for change of scheduled time when these are communicated less than 24 hours prior to the appointment.
  • Scan Start and End: All users have the right to start their scan on time, no questions asked. Start and stop time includes setup and cleanup--users must build this into their scanner scheduling (i.e., scanner must be ready for next group by their scheduled start time). When possible, try and be flexible. However, if the next group is adamant about starting their scan at the scheduled time, then it must be so. If the current scan is running behind, the current group must make an effort to inform the next group. The next group may then, at their discretion, allow the current group to scan into their allotted time, but this is done as a courtesy and not out of expectation that the next user will provide the same. Projects that continually run over time will be required to book more time for future scans.
  • Cancellations: Scans must be cancelled >24hrs prior to the scheduled time to avoid scan charge. Scans cancelled within 24hrs of the scheduled appointment may be charged the full scan fee. Please fill out this scan cancellation form in order to inform CCN Tech of issues leading to cancellation. Each funded project has 2 free cancellations assigned when it starts and accrues another free cancellation after every 10 completed scans.
  • Data Transfer: All f/MRI data are transferred automatically to a dedicated server. In cases where data must be transferred manually from any of the computers in the MR suite, please notify the MR Technician to make arrangements. No external storage devices (flash drives, hard disks, etc.) are to be connected to the scanner without prior approval. If data is not visible in the DICOM server 24 hours after acquisition, please contact MR Technician immediately to resolve. Due to high scan load, only 3 days of scan data can be guaranteed to be kept on the host machine at any given time. It is not CCN's responsibility to check that data has transferred to data server without issue.
  • Incident Reporting: Users are responsible for communicating with CCN staff any equipment malfunction or software irregularities that occur during the course of the scan session. This may include scanner error messages which do not allow users to continue with their session, the breaking or malfunction of peripheral equipment etc. Emergency incidents, such as injuries, natural disasters or magnet quench, should be relayed to the MR Tech immediately and CCN's Incident Reporting Form should be filled out in a timely manner.

Billing and Refunds

  • Scan Time: All scans must be paid for. CCN will pay for pilot scans as appropriate (see previous section: Scan Procedures > Pilot Program), but all others are paid for by users. Free scan hours are not permitted by Sales & Service, with the exception of specific technical testing and protocol development purposes, which must first be approved by CCN Tech.
  • Refunds: Refunds are provided only for events beyond the users' control.

Project Management at Staglin

The figure below presents a general flow chart for starting a project at Staglin.
Project Startup Flow Chart
  • The study PI or co-coordinator is responsible for initiating an account (creating a new project) at CCN.
  • Flow chart and instructions for project startup can be found here
    • After reviewing instructions, if you still have questions, please reach out to Marlo Duran


Information about lab members can be found under General --> My Profile | My Personnel.

Personnel Page

Adding a New User

Before CCN Techs can activate a user for scanning in the scheduling system, an account must be created for them by a member of their lab. Your lab study PI or co-coordinator should have administrative privileges to add new users to the lab.

  1. Navigate to "General" → "My Profile | My Personnel"
  2. Under the "User" dropdown menu, select "Create Passport For New User"
    Create Passport
  3. Input the new users information (bolded fields), and the new user will receive an email with their login credentials
  4. Once the account is created, please reach out to CCN Techs to activate their account and input their certification information

DICOM Accounts

CCN has a DICOM server that stores raw data under each group's directory. To apply for a DICOM server account:

  • Send an email with the following information to the CCN Programmer Analyst Jonathan Hernandez
    • Your Hoffman2 account ID if you have one
    • CC your request to the PI whose group directory you need access to for approval
  • If you have an account with the Brain Mapping Center and want access to the CCN DICOM server, you will still need to apply for an account. CCN and the BMC are separate organizations and require separate accounts and policies.

Study Team & Personnel FAQ

Can an uncertified person shadow my scan?

  • As per the information above (see CCN's Restricted Areas policy), uncertified individuals are not allowed in the control room unless granted an exemption by CCN. Contact CCN for such an exemption if it's necessary for someone to shadow your scan. Regardless, the uncertified person is prohibited from touching any research equipment and any exemptions granted only apply to a single instance. Users who have started but not finished the certification process are considered uncertified until the full certification is completed. If you have questions about this, please ask.

Can I be a primary user?

  • See "Scan Personnel" above. Current CCN policy stipulates that primary users need to be full-time in some capacity (staff, faculty, postdocs, etc.). Also, Primary Users are required to have significant scanning experience. Primary Users typically start as Secondary Users (safety seconds) and work through numerous scans and trainings with their team before being granted Primary User status.

Primary User (Responsible User) Definition

  • Allowable Roles: Full-time staff, Post-doc, Graduate student, or Faculty member
  • Can perform all scan related responsibilities independently without the need for supervision
  • Will serve as the primary scan operator
  • Responsible for assigning tasks to and providing oversight for the secondary user, especially if secondary user has volunteer status

Secondary User Definition

  • Allowable Roles: Any of the aforementioned full-time roles, Part-time paid/work-study students, volunteers
  1. Full-time roles
    • Allowed to perform all responsibilities independently without supervision of the primary scanner
    • May serve as scan operators
  2. Part-time paid undergraduate/work-study
    • May perform responsibilities explicitly defined in their UCLA approved job description independently without supervision
    • This can include operating the scanner, handling scanner and peripheral equipment, interacting with participants
    • May not serve as primary user
  3. UCLA volunteer
    • May not independently handle participants, coils, or operate MR beds/controls
      • Must ALWAYS perform these tasks under strict supervision of the primary scanner/responsible user
    • This can include handling scanner (coils, mirrors) and peripheral equipment and directly interacting with participants, e.g. assisting in placing them into head coil
    • May not serve as the scan operator
    • In the event of an emergency where the primary scanner is unable to perform their duties, volunteer personnel should be trained on stopping the scan and removing the participant
    • Required to undergo full CCN safety training
    • Must be officially onboarded via UCLA Health Sciences Volunteer Office
    • Please refer to the Staglin CCN Volunteer Addendum


Add Fund

  • Funding sources can be added under "Financial" → "Add Fund"
    • New projects must be linked with Active funds
  • Adding a fund requires:
    1. Funding agency
    2. Active FAU
    3. Start and End date
    4. Fund manager overseeing this fund

Project Documents

  • CCN requires new projects to upload approved IRB documents before scanning can commence.

Facilities & Equipment

MRI Facilities

The Staglin IMHRO Center for Cognitive Neuroscience operates a Siemens 3 Tesla Magnetom Prisma Fit MRI Scanner running VE11C software, equipped with 20, 32, and 64 channel head coils.

  • Sequences: Standout sequences include full CMRR multi band package, Siemens simultaneous multi slice with physio logging, 3D multi-delay pCASL, T1 and T2 structural with navigator technology, multi shell, multi band diffusion, MEGAPRESS and HERMES multi voxel spectroscopy.

Scan Simulator

An MRI simulator that gives subjects a realistic sensory experience.

  • Includes Mo-Track software, and a dedicated laptop to play movies and recorded scanner noise

Quality Control

Staglin runs a daily stability check via the Siemens Service Platform to check signal intensity and drift. A weekly QA protocol and a more in-depth monthly routine is also acquired for advanced analysis, including QA for each coil, and RF spectrum analysis for each peripheral device.

Multimodal Data Collection

Testing Facility

A dedicated private room for screening, pre-testing, interviews, and post-tests. Each group is allowed use of the room for 30 minutes before or after their paid scan, at no additional charge.

Electronics and Machine Shop

Facilities for fabrication of specialized devices required by the users, such as radio receiver coils, stimulation and response devices, holders and stabilizers for subjects.

MR Suite Supplies

Extra supplies can usually be found in the tall grey cabinets to the left of the sink. In general, please contact CCN staff if something is running low.

Where to order supplies

Support and Peripheral Equipment

Peripheral Equipment

Peripheral equipment available for projects include:

iMac Computer

The MR suite is equipped with a dedicated iMac computer running Mac OS High Sierra with a dual-boot Windows 10 partition capable of running:

  • Psychophysics Software:
    • Psychtoolbox,
    • PsychoPy,
    • E-Prime,
  • MATLAB 2015b
  • AcqKnowledge 4 (for BioPac MP150)

For new software, please contact the MR Technician before installation.


A tool for measuring the prescription on an eyeglass lens.

  • This is stored in a small, rectangular box in the cabinet with the MR glasses. It is a white box under the cleaning wipes (Image 1 below).
  • Open the box and remove the components within (2).
  • Stand the largest piece upright and slot it into the divot on the outer shell of the box (3).
  • Slide the reflective rectangular piece horizontally into the small slats. This may take a bit of wiggling (4). If one end doesn't seem to want to slide in, turn it around and try inserting from the other end.
    • You can leave this piece aside unless you want to measure a pair of glasses. Its purpose is to provide a stand to stabilize the glasses on.
    • Once the stand piece is in, you can slide it up and down as needed to provide a stable resting place for your glasses.
  • Squeeze the silver trigger on the back and hold the lens in question in the resulting aperture space. Release the trigger and the lens will be held firmly in its position (5).
  • Look through the eyepiece and find the green, starry shape that will be defining the focus. If it's off-center or totally missing, adjust the position of the lens in its measurement position. Once you find it and it's centered, turn the black dial on the right until it becomes clear and focused.
  • Read the little window on the left of the tool to see what the corresponding prescription is (6). Red and black numbers correspond to positive and negative.

CCN MR Documentation

  • Safety Manual
    • Topics include: MR safety concerns, hazards, common and adverse reactions etc.
  • Operations Manual
    • Topics include: Running QA, standard reboot procedures, saving log files, editing subject info after a scan etc.

Common Questions and Concerns

(In Progress)

Implants & Devices

Is my participant's implant safe?

  • The simple truth is, we don't know yet! Please refrain from emailing CCN personnel without acquiring documentation, records, or official communications from a medical professional.

I have received information, now what?

  • If you receive manufacturer information (make/model number etc.) about your participant's implant, please go one step further by searching the web for implant safety information. Oftentimes there will be documentation published by the manufacturer or the FDA.
  • If you are unable to get specifics about the manufacturer/model of your participant's implant, please forward as much information as is available to CCN Technical Staff. This is often in the form of communication from your participant's surgeon, radiologist or medical team.

My participant can't find any information about their implant from authoritative sources, but has had previous MRIs and assures us it's MR safe. Can they scan?

  • Having previous MRIs does not automatically clear their implant to scan at CCN. Most MRIs will be clinical, and there are many meaningful differences between clinical scanners/sequences and research scanners/sequences. Plus, because your participant is receiving no clinical benefit from this scan, CCN and your scanning team should aim for zero risk to protect yourselves and the center.

Safety Status of Common Implants & Devices - Coming Soon

Certification & Training

I am BMC certified. Will I need to get re-certified to be allowed in the CCN scanner and/or to access the CCN server?

  • Yes. CCN and BMC are separate organizations, so you will need to be safety certified at CCN to access the scanner and server.

Why am I not in the user dropdown list when scheduling a scan?

  • The most likely reason is that your safety certification has expired. You can see certification expiration dates in the My Profile | My Personnel page. Users also receive an email a few weeks before expiration.
  • The Re-certification Exam can be found on the Staglin Safety and Training Course on BruinLearn. If you are not enrolled in the course, please talk to your lab manger or email CCN Tech for an enrollment link.

Scheduling & Administrative

Why isn't my project showing up on the system?

  • The most likely reason for this is because your project has run out of funds. If you navigate to "Projects" --> "Summary of Existing Projects", you'll find information about all your labs projects. Projects with balances in parenthesis i.e. ($1200.00), are overdrawn and more funds need to be encumbered.
Projects Dropdown
Summary of Existing Projects Attn: Project Balance

How do I transfer my scanning protocols from the BMC scanner to the CCN scanner?

  • Please export a copy of the .exar1 files of the scanning protocol from BMC scanner computer and email the .exar1 to CCN Technical Staff, who can import the protocol. Alternately, you can also copy the DICOM data of a subject directly from the BMC scanner computer (or from a server) onto a CD, which can be converted in the exam interface. Please contact CCN lab manager with requests and files for transferring protocols. Note: CCN scanner computer does support data/protocols stored on flash drives, but drives must be virus scanned every time before being connected to the host machine. Sophos anti-virus is available on the CCN iMac next to the scan computer.

Can I Film at CCN?

  • Filming is allowed at CCN, but only through proper channels:
    1. Reach out to UCLA Media team in order to fill out appropriate paper work and acquire proper permits.
    2. Once approved by UCLA Media team, email CCN Staff to discuss scope of work and logistics (who will be involved, will an actual scan with a human subject be needed? etc.).
    3. CCN Staff can block off time for the shoot free of charge, but every effort must be made to use off-hour times, such as early morning (before 8am), or evening (after 7:00pm) availabilities.
    4. Film crews may film inside the control room, but under no circumstances are they to enter the scanner room.
    5. A sign reading "Filming In-Progress", must be posted on the outside of the CCN entrance, in order to alert users entering that there is a possibility they might unintentionally be caught on film.


CCN Staff and Contacts

  • Director: Dr. Susan Bookheimer (
  • Technical Director: Dr. Robert Welsh (
  • Managing Director: Dr. Agatha Lenartowicz (
  • Administrator: Marlo Duran (
  • Server Administrator: Haiyan Wang (
  • Technical Support: Jon Hernandez (
  • Research Support Tech: Dr. Melodie Yen (
  • Lab Manager/Technician: Jared Gilbert (
    • First point of contact