User Information

  1. Information for MRI Users
    1. Help and Documentation
    2. Information for Users
    3. IRB Template
    4. Experimental Design and Implementation
    5. Services Offered
    6. Scheduling a Development Scan
    7. Participant Protocols
    8. Gaining Access to Data
    9. Scanner Stability and QC
    10. Simultaneous Systems (EEG, Eye Tracking)

Help and Documentation

Additional in depth documentation and information is available on the Wiki

The BIRC_HELP 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 list. If you are actively conducting neuroimaging research, we encourage you to join the BIRC_HELP listserv to share and answer questions.

To subscribe, send an email to with the body:

SUB BIRC_HELP-L Firstname Lastname

Information for Users

We have setup a web portalfor your convenience. Here you can find applications for accessing your data after it has been collected, a scheduling software for scheduling scans (and other BIRC resources), and MRI safety training.

Please take a moment to sign into both the “Data Access” and “Scheduling” applications using your UConn NetID and Password. Once you have signed into each application, please email Elisa Medeiros with your NetID and the name of the project that you are working on. If you have multiple members of your team who will use these applications, please include their names and NetIDs as well.

Next, make sure that you and everyone on your team has completed MRI Safety Training. This consists of watching three videos and completing a short quiz. Projects involving children may have some additional training so that the researchers (or designated RAs) can accompany the participant into the scanner room. If desired, we can activate your UConn ID to enter the BIRC after completing safety training.

Before beginning a study, complete the study request form. Your application will be reviewed for feasibility and you will be contacted with questions or study approval. After you have completed these steps, your project will be assigned a “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 bookkeeping, billing, and IRB compliance with data access.

We also offer training opportunities to help you become familiar with our equipment.

IRB Template

IRB-approved template protocol and consent language is available online to facilitate IRB submissions. The template covers the use of MRI, EEG, and tDCS at BIRC.

Experimental Design and Implementation

The BIRC offers experimental presentation using a variety of software packages. We have licenses for E-PRIME, Experiment Builder, PsychoPy, and Presentation. For visual presentations, we offer theCambridge Research Systems BOLDscreen. For auditory presentation, we make use of a Avotec Silent Scan.

For the most part, all of these software products work the same inside of the scanner as they dooutside of the scanner. However, there are some nuances that you will want to take into account. First and foremost, the scanner sends either a “5” or a “t” whenever the TR begins. This is relevant because you likely want to have your programbegin after it receives the first TR marker. Your programs may use subsequent TR markers to synchronize with the scanner.

Occasionally we run into issues with version compatibility with E-PRIME. For reference, we have E-PRIME 2 version Due to compatibility with several devices, we cannot upgrade versions at the same pace that PST releases them. If you need to develop on this version of E-PRIME, we have a copy in the BIRC Data Analysis room. Other software packages are kept up to date with the most recent version.

We have a number of response boxes available to users (made by Current Designs). The most popular is four buttons (two in each hand) shown below.


The readout of the buttons corresponds to either of the following sequences:

Readout Trigger Pulse
Blue = 1, Yellow = 2, Green = 3, Red = 4 5
Blue = b, Yellow = y, Green = g, Red =r t

You will want to ensure that experimental control softwareaccepts those as key presses. We recommend that you test these as much as possible before showing up for your development scan. For Psychtoolbox users, the KbName of the codes are 1!, 2@, 3#, 4$ and 5% when the box is in numeric mode.

Services Offered

In addition to standard structural and functional MRI imaging, we are pleased to offer Human Connectome Project (HCP) compatible sequences for collecting multiple slices (e.g. multi band) for both functional (e.g. BOLD) and diffusion (e.g. Diffusion Tensor Imaging).

Scheduling a Development Scan

To facilitate your research, we offereach project up to two hours of project development time for 1) setting up pulse sequences and 2) verifying that your E-PRIME (or other stimulus presentation system) works as expected inside of the scanner. We strongly encourage you to use these two scans to verify that your stimuli are visible (or hearable) to the participants inside of the scanner and that responses are correctly being recorded.

We recommend that you bring the following information with you to your first development scan (you can also email it ahead): Outline of protocol, common parameters for each sequence (e.g. BOLD with TR timing and total duration of the scan). Other common terms for functional sequences include FOV (field of view), matrix size, resolution, flip angle, TR, TE. If necessary, we are able to assist with the selection of pulse sequences based on your experimental design and hypotheses. To facilitate the process, we encourage you to identify common sequences used in previously published research in your area for guidance on parameters.

All MRI scans are scheduled through our online scheduling system. Please login to the system using your UConn NetID and Password. You will then be able to see existing reservations on all of our facilities (e.g. MRI, Mock Scanner, EEG, Behavioral Testing Rooms). If for some reason you cannot see a particular resource that you wish to schedule, please emailRoeland Hancock.

When scheduling a development scan or regular MRI, the system will ask you for a date and time as well as both a title and description of the reservation. Under the “Title of Reservation”, please provide the name of your Study (acronym acceptable). Under the “Description of Reservation”, please provide us with the billing code that you were issued for this particular study. The presence of the billing code will ensure that you have access to the data after the scanning session.

As part of your development scan, we can program the necessary pulse sequences for your experiment into the system. This can take between 30 minutes and an hour, depending on how complicated your requirements are. You are welcome to send your criteria for MRI scan sequences to us prior to the development scan or wait until your scheduled time. Regardless, we anticipate modifying the pulse sequences during the development scan time, so we recommend having a very understanding participant, such as a member of your lab group. We cannot provide you with participants.

Participant Protocols

When the day of any MRI scan arrives, please meet your participant at a previously agreed upon location. You are welcome to have them come to the center directly, but please note that you or your designee will need to facilitate the participant through the setup process. That includes filling out all IRB required forms (e.g. consent form) and a metal screening form.

In addition, you should allow participants (if they wish) to change into scrubs using our changing area. We have lockers with locks that will keep valuables safe for the duration of the scan time. Also, we recommend you ask participants to use the restroom prior to entering the scanning area.

Once in the control room, expect the MRI Technologist to review the MRI screening form with the participant prior to entering the MRI room. Once the participant is cleared for the scan, please wait in the control room while the Technologist sets up the participant inside of the scanner. This time can be used to copy E-PRIME files to appropriate locations or perform last minute checks.

Here is a checklist for participants to help them prepare for the study.

BIRC also created a video to help a younger particpant prepare for what to expect during the entire process.

Gaining Access to Data after a Scan

Once your data is collected, it will be automatically sent to our Data Access application. 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



Scanner QC

The scanner has been extensively validated in internal tests. We have replicated multiple visual field studies as well as functional localizers across scanners from multiple other sites. We perform QA tests every week using both ACR (American College of Radiology) and fBIRN phantoms. In addition, we perform a scanner stability measurement from MGH. Results from these three weekly testsare automatically processed by routines at the BIRC and aremonitored carefully for any sudden changes in the output. The scanner is remarkably stable, which we have attributed to both our diligent efforts at managing the magnetic field as well as regular service from Siemens.

Simultaneous Systems

We have MRI compatible EEG and Eye Tracking systems. Our in-scanner EEG system is made by Electrical Geodesics and features a NetAmps 400 Amplifier with high-density 256 electrode netswith additional leads for doing physiological monitoring (ECG, Respiration, GSR). Our in-scanner Eye Tracking system is the Eye Link 1000 Plus from SR-Research.

Use of these systems in-scanner is included in the costs of the MRI.