Other Resources

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 are available to help users with their projects and provide short tutorials. See our current IBRAiN fellows page to learn more about them.

Data Management & Computing

The center houses a data analysis lab to assist members of the community with analysis of their data. Alongside Apple workstations, we offer centralized data management system for MRI data (NiDB) (campus or VPN required) and up-to-date analysis software for both MRI and EEG/ERP data as well as MATLAB, Python, and multiple language compilers (e.g. GCC, Clang). BIRC affiliates may request access (campus or VPN required) to priority scheduling on a 36-core node on the Storrs high performance computing systems.

BIRC provides a number of shared workstations for analysis, however these workstations are not backed up and may not be used for long-term storage. BIRC users may request priority access to the BIRC’s shared computing node within the UConn Storrs HPC cluster. BIRC provides general-purpose containerized processing environments suitable for use on the cluster to provide a starting point for users to implement their own cluster-based pipelines.

Experiment Scripting

Licenses for major experimental control softwares are available for use with MRI, EEG or behavioral protocols. These licenses may not be used outside of BIRC. Supported software includes:

Interfacing with MRI

For the most part, all of these software products work the same inside of the scanner as they do outside 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 program begin after it receives the first TR marker. Your programs may use subsequent TR markers to synchronize with the scanner.

We have two response boxes and a joystick available to users (made by Current Designs). Only one of these devices can be used at a time. Button boxes are available in the 2x2 button layout or straight 1x4 layout.

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 software accepts those as key presses. We recommend that you test these as much as possible before showing up for your development session. For Psychtoolbox users, the KbName of the codes are 1!, 2@, 3#, 4$ and 5% when the box is in numeric mode. The two 2-button trainer boxes (similar to the 2x2 setup) use numeric readout.

Interfacing with EEG

You will need to synchronize your event times with the EEG recording using the EGI TCP/IP experimental control interface (ECI). This is a network connection between the stimulus and recording computer. The clocks of the two computers are synchronized and timestamped events are sent from the stimulus PC to the recording computer.

This is most easily accomplished using

During your development session, BIRC staff can assist in testing the timing and synchronization of your experiment. For this purpose, it is best to replace any audio in your experiment with an audio file of the same length and sample rate containing a 20ms square wave pulse followed by silence. Visual stimuli can be replaced by a uniformly colored image that has high contrast against the background.

When using the StimTracker, configure your experiment to present a small box in the left corner of the screen to trigger the photosensor and connect the 1/8" audio cable labelled 'STIMTRACKER IN' to your desired audio source. You will need to enable the '8 DINs' option in your EEG recording workspace. By default, stimulus events will be mapped to DIN 6 (left audio) and DIN 8 (photocell).

Readings

Background readings on MR, EEG and TMS topics are available in the BIRC Zotero group.

Other Technical Resources

Additional information not found on on our Technical Guides page may be found on the BIRC Wiki (campus or VPN required) or BIRC Computing Guide.

Design Assets

If you would like to incorporate the BIRC logo or other assets into your design, you can access our graphic design elements here.