Getting Started

The University of Connecticut provides a world-class environment for conducting research in the Cognitive Neurosciences. The 3,200 square foot Brain Imaging Research Center (BIRC) offers the resources for nearly any human MRI, EEG, or neuromodulation study. The BIRC houses a 3 Tesla Siemens Prisma MRI Scanner. Additional systems allow for in-scanner eye tracking (SR-Research Eye Link 1000 Plus), EEG and simultaneous MR-EEG studies using dense EEG (Electrical Geodesics, Inc.) with 256 channels. A MagVenture TMS (X100) is available for use to all researchers. Advanced TMS Navigator software allows for the precise targeting of the TMS pulse on individual subjects with a high-resolution MRI scan. Additional systems allow precise measurement of heart rate and respiration. In addition, the center houses multiple behavioral testing rooms, a sound-attenuated testing chamber, and a Mac-based data processing lab, for researchers to analyze their data using standard software (AFNI, FSL, FreeSurfer, SPM, MATLAB, R).

This page provides an overview of the steps involved in beginning your MRI, EEG, or TMS study at BIRC and some of the resources available to support your research. Please feel free to contact us at any stage. We are happy to meet to discuss the direction of your grant proposal or design of your study. Meetings with the Associate Director can be scheduled online.

Steps to starting a study

  1. Join the listserv
  2. Bookmark our online documentation and guides
  3. Write a budget and secure funding
  4. Obtain IRB approval
  5. Get trained
  6. Obtain BIRC approval
  7. Reserve BIRC resources
  8. Get your data

Capabilities

BIRC provides access to:

  • 3T human MRI
  • Standalone high-density EEG
  • In-scanner high-density EEG
  • In-scanner eye-tracking
  • TMS

More details are available on our Equipment & Resources page.

Support Resources

BIRC provides online and in-person resources to support every step of your project. Please email us if you have any questions not answered below!

BIRC listservs

MRI_CENTER-L

Important BIRC announcements are distributed via the MRI_CENTER-L listserv. All BIRC users or interested parties should subscribe to this list. To subscribe, send an email to listserv@listserv.uconn.edu with the body:

SUB MRI_CENTER-L Firstname Lastname

BIRC_HELP-L

The BIRC_HELP-L listserv is intended to be a community support service where users can ask questions or share other relevant information, off of the main MRI_CENTER-L list. If you are actively conducting neuroimaging research, we encourage you to join the BIRC_HELP-L listserv to share and answer questions.

To subscribe, send an email to listserv@listserv.uconn.edu with the body:

SUB BIRC_HELP-L Firstname Lastname

Once you have subscribed, you can post to the list by emailing birc_help-l@listserv.uconn.edu.

Additional documentation

  • The BIRC Wiki (campus or VPN required) has additional documentation for each BIRC resource. All users can view the wiki and encouraged to contribute after NetID sign in.
  • The BIRC Computing Guide (under construction) provides support for high performance computing and containerized processing pipelines.
  • Background readings on MR, EEG and TMS topics are available in the BIRC Zotero group.

IBRAiN Fellows

The CT Institute for the Brain and Cognitive Sciences (IBaCS) offers IBACS-BIRC Research Assistantships in Neuroimaging (IBRAiN). After formal training, IBRAiN fellows provide a teaching resource to help BIRC users design and implement experimental procedures for fMRI, EEG, TMS and other methodologies, provide resources for data analysis, and oversee use of equipment by others. IBRAiN service to BIRC users is intended to be focused on educating BIRC users, rather than deliverable results. Click here for information about the scope of IBRAiN activities and associated policy. Click here for more information about applying to this program.

IBRAiN fellows hold weekly office hours to help users with their projects and provide short tutorials. Click here to request an appointment with an IBRAiN fellow.

Budgeting and Funding

Fees for the use of MRI, TMS, and EEG equipment at BIRC are detailed in the rate table. When developing your budget, make sure you base your calculations on the rates announced for your anticipated funding period. Investigators should contact the Director for advice on their proposed budget prior to submitting a grant proposal. The following points should be kept in mind when developing your budget:

  • When estimating the time needed for each session, include setup and cleanup time in addition to the expected length of your experimental procedures.
    • EEG sessions generally require at least 30 minutes of prep time and 15 minutes cleanup.
    • MRI sessions require at least 10 minutes total for setup and cleanup. Additional time may be needed for physiological monitoring or pediatric or clinical populations. Each scan in your session may require 30-90 secs to setup, with additional time needed for MRS setup. For example, a typical 1-hour MRI session will provide only 45-50 minutes of usable ‘table’ time for actual scanning.
  • Round your time estimate up to the nearest 30-minute billing increment (e.g. a 75-minute MRI session must be budgeted for 90 minutes of scan time)

BIRC provides seed grants to support pilot data collection and a Trailblazer Award to support innovative, high-impact research. Both award mechanisms are expected to lead to extramural funding.

IRB Approval

All studies must have current UConn IRB approval. For investigators submitting applications to the UConn IRB, IRB-approved IRB-1 and consent form template language is available and covers the use of MRI, EEG, eye-tracking and/or tDCS at BIRC. Investigators are strongly encouraged to use the appropriate template language whenever possible to facilitate IRB review. IRB submissions should also include the standard MRI screening form, tDCS screening form, and/or TMS screening form. All IRB and screening materials can be downloaded here.

Training

General MRI safety training and hands-on equipment training is required prior to using any equipment at BIRC. Click here for more information.

BIRC Approval

New studies are reviewed by the Associate Director for feasibility and compliance prior to implementation, as well as to keep track of projected usage at BIRC. To begin the approval process, please complete the study request form. This form will collect some detailed information about your study design, timeline, staffing, and equipment needs. If you are conducting an MRI study, you will be asked for your preferred scan parameters. Some common, tested options are available, or you can paste in your own. If you are unsure of your scan parameters or are new to MRI, please schedule a meeting with the Associate Director to discuss your needs.

When your study is reviewed and approved, you will be given access to scheduling and data management systems, scan protocols will be setup for MRI studies, and you will receive an approval email with important information. Among other things, your project will be assigned a BIRC billing code, which will be used for scheduling, data collection, and later data retrieval. Sadly, you cannot buy anything with this code; it is entirely used for internal bookkeeping, billing, and IRB compliance with data access. Please contact the Associate Director if you have questions about this process.

Scheduling BIRC Resources

All resources must be reserved using the online scheduling system (campus or VPN required). Scheduling limits, cancellations policies, and fees are described in more detail on the rates and policies page.

Key points

  • Reservations are made (and billed) in 30-minute increments.
  • Your reservation period must include any needed setup and cleanup time.
    • EEG sessions generally require at least 30 minutes of prep time and 15 minutes cleanup.
    • MRI sessions require at least 10 minutes total for setup and cleanup. Additional time may be needed for physiological monitoring or pediatric or clinical populations. Each scan in your session may require 30-90 secs to setup, with additional time needed for MRS setup. For example, a typical 1-hour MRI session will provide only 45-50 minutes of usable ‘table’ time for actual scanning.
  • MRI reservations cancelled within 24 hours prior to the scan time are subject to a 100% charge. However, we encourage all unfilled scans to be cancelled 2 weeks prior to the scan time.

The use of some equipment requires reserving multiple resources (e.g. both the EEG system and EEG/Sound Room) or adding an accessory (e.g. out-of-scanner button box), described below:

  • Testing rooms A and B—For behavioral experiments, assessment, or interviews
  • Conference room—For small meetings (up to 8 people), with display and videoconference ability.
  • EEG/Sound Room—A sound attenuated room housing a high-quality recording setup and EEG system. This can be booked alone for behavioral experiments or recording sessions.
  • EEG NetAmps 400 GTEN (30-120 minutes)—The out of scanner EEG system. You must also reserve the EEG/Sound Room resource. This EEG system cannot be moved to another room. The 2×2 non-MR button box can be added as an accessory.
  • MR-Conditional EEG System (30-120 minutes)—The in-scanner EEG system. This should generally be booked concurrently with an MRI session, but the system may also be moved to other locations when required. Please contact the Associate Director to discuss plans for using the system outside of the MRI.
  • TMS/Photogrammetry Room—This room houses the EGI photogrammetry dome, Biopac recording system, and TMS system. If you are using the photogrammetry system, please reserve the room only for the time you expect to be using the dome during your EEG session.
  • TMS System (30-120 minutes)—The MagPro X100 system. You must reserve the TMS/Photogrammetry Room for at least the time you will be administering TMS. If you do not reserve the room, others may enter, e.g. for photogrammetry. Use of the Biopac and Localite systems is included. The 2×2 non-MR button box can be added as an accessory.
  • MRI (30 minute minimum)—The Siemens 3T Prisma and all peripherals (except MR-EEG). MRI reservations will be confirmed by a technologist.
  • Mock Scanner—The mock scanner/MRI simulator. The 2×2 non-MR button box must be added as an accessory if needed.
  • MR Stimulus PC—During some hours that are not available for MRI, you may book this resource to come in and test your scripts. You do not need to book this during normal MRI reservations.

If you cannot access a particular resource that you wish to schedule, please email the Associate Director.

Required reservation details

For all reservations, provide the following information:

  • Billing Code: The three digit number provided when your study is approved. The conference room may be booked using the code 000, if it is not being used for a specific study. All other reservations should be associated with a study/billing code. Do not enter additional information in this field.

For billable reservations (EEG, TMS, MRI), provide the following information:

  • KFS #: The account to be billed for your reservation.
  • Development scan: Check this box if this reservation is part of your permitted protocol development time.

For MRI reservations, please provide the name of your study (acronym acceptable) under Title of Reservation.

Please do not enter anything in the internal use box.

Scheduling Development Time

Each project can reserve up to two development sessions to ensure that your experiment works as expected on the equipment at BIRC. Prior to using your development time, please make sure that:

  • You have tested your stimulus presentation outside of BIRC and verified that the presentation and response collection work as expected. MRI triggers and button boxes can be emulated by keyboard presses, as described on the equipment page. After you have tested your scripts in your lab, you can verify that they work on the computers in the MR console room. You can come in and test scripts during open periods in the MRI schedule, or book the MR Stimulus PC resource.
  • For MRI studies, you have worked out how long each run of your task is.
  • You have drafted a protocol for operating your experiment.
  • You have identified a patient participant, such as a member of your lab group, ideally one who provide feedback on the experiment.

To schedule your development time, create your reservation online (campus or VPN required) and check the Development scan box.

Scheduling Experimental Sessions

Archiving and Accessing Data

MRI data

BIRC provides automatic storage and backup of original MRI data only. Researchers must copy any behavioral or eye-tracking data files to a USB drive after their session. BIRC does not provide storage for processed data. Once your MRI data is collected, it will be automatically sent to NiDB (campus or VPN required). You will be asked to login with your NetID and Password. If you select the Projects link from the top of the screen, you should be able to find your project listed. If you do not have access to that project, please make sure that you are listed on the corresponding IRB application and email Roeland Hancock to gain access to the project.

For downloading data, it is often preferred to click on the “Search” button at the top of the page. Choose your project under the “Enrollment” option. Select the series that you wish to download from the list, and then set options as follows:

Option Recommended Selection
Download Type Web
Data Imaging, Behavioral
Format DICOM – No anonymization necessary
Directory Format Primary Alternate Subject ID
Series Directories Preserve Series Number
Behavioral Data Place in beh directory in root

EEG data

EEG data must be copied off the recording computer after your session.