BIRC Lectures and Workshops

BIRC is offering educational sessions over the course of the 2021 Fall semester. All UConn faculty, staff, and students are invited to attend. Registration is required and is due two weeks before each event. Please send inquiries to:

Fall 2021

1. DWI Part 1: Principles and Data Acquisition - Nabin Koirala, PhD

October 22, 2021

Overview: In this two module course, Nabin will give an overview on basics of diffusion MRI including the principles of diffusion and how is it used in the (neuro) imaging. The neurobiological meaning hidden behind the magnificent images that we can obtain using this technique, and hands on analysis of the diffusion MRI data to obtain different metrics.

Topics included:

  • Understand diffusion imaging and why many people are beginning to use it
  • Analyzing data and implementing it into research 

2. DWI Part 2: Data Processing and Analyses - Dr. Nabin Koirala, PhD

November 3, 2021

Overview: This course will cover the practical aspects of Diffusion data analysis with basics of how to analyze it in your personal computer as well as in the high-performance computing (HPC) systems. The toolbox I will use to demonstrate the data analysis will be FSL. Those who are interested in testing it during the class or before, could download and install them following the instructions here: Note: For the registered users, I will provide a sample dataset to try it in the FSL.

Topics included:

  • Learning how to use FSL and learn to run a standard pipeline for dMRI data processing
  • Learning basics of shell scripting and necessary steps needed to run the data analysis in high-performance computing clusters

3. Introduction to MRI - Dr. Roeland Hancock, PhD

November 19, 2021

Overview: This workshop will introduce participants to the potential benefits of including MRI in their research and the logistics of doing so.

Topics will include:

  • Principles of magnetic resonance and common terminology
  • Survey of MRI techniques and applications
  • Logistics of planning an MRI experiment

Spring 2022

4. Introduction to fMRI - Roeland Hancock, PhD

March 10, 11-1pm ET

The topics of this workshop include:

  • How fMRI signals are measured and how this relates to neural activity
  • The principles of designing an fMRI paradigm
  • A survey of common types of fMRI experiments
  • Typical steps in analyzing fMRI data

Date: Thursday 3/10/2022

Time: 11 am - 1 pm ET

Location: BIRC Conference Room (PCSB 141)

Registration TBA

5. Freesurfer - Lihong Wang, PhD

More information TBA

Past BIRC Workshops/Lectures

Spring 2021

Workshop/Lecture Name Topics Included
Introduction to fMRI
  • How fMRI signals are measured and how this relates to neural activity
  • The principles of designing an fMRI paradigm
  • Typical steps in analyzing fMRI data
  • Logistics of planning an fMRI experiment
Introduction to fMRI Preprocessing with BIDS Apps
  • Standardizing neuroimaging file organization using the Brain Imaging Data Structure (BIDS)
  • UConn computing resources
  • Quality assurance using mriqc
  • fMRI preprocessing using fmriprep

Fall 2020

Workshop/Lecture Name Topics Included

Introduction to Neuroimaging Pipelines

  • Interpreting the components of a BIDS file name
  • Selecting a pipeline appropriate for their preprocessing objectives
  • Constructing Docker and Singularity command lines
  • Estimating the computational resources needed for preprocessing their data


Spring 2020

Workshop/Lecture Name Topics Included
Introduction to MRS
  • Describe the tradeoffs of common MRS sequences
  • Evaluate spectral quality using quantitative and qualitative measures
  • Identify potential challenges in voxel placement