The CBS Neuroimaging Core Staff offers numerous training sessions, workshops, and lectures on neuroimaging topics at introductory and advanced levels for the Harvard Neuroimaging community. A selection of these will be offered each semester. Additional sessions may be added if there is sufficient interest. If you are interested in a session but are unable to attend the scheduled time, please let us know.
We also offer tours of the Neuroimaging Facility with live demonstrations of functional MRI (with real-time data analysis) and Transcranial Magnetic Stimulation for undergraduate and graduate semester courses in related disciplines. These can be customized to suit the interests and time-constraints of the group. For more information and to schedule a tour, please contact Caroline West (wcwest@fas.harvard.edu).
These workshops and lectures are open to CBSN users and all Harvard researchers and students. Please sign up if you would like to attend so that we can ensure adequate space and snacks. Email Jenn Segawa (jsegawa@g.harvard.edu) with questions.
Spring 2024 Neuroimaging Workshop Schedule
Introduction to Functional Magnetic Resonance Imaging (description)
CBSN Core Staff
Fri 2/2, 2-4p (NW Room 453)
(for undergraduates, but all are welcome)
Register (2/2)
Optimizing Data Quality while at the Scanner (description)
Ross Mair
Fri 2/9, 2-3:30p (NW Room 453)
Register (2/9)
Accelerate Your Neuroimaging Research with the FASSE Compute Cluster (description)
Timothy O’Keefe
Fri 2/23, 2-3:30p (NW Room 453)
Register (2/23)
Overview of Non-invasive Brain Stimulation + Hands-on TMS Tutorial (description)
Mark Eldaief
Fri 3/1, 2-3:30p (NW Room 453)
Register (3/1)
Building Neuroimaging Experiments with PsychoPy (description)
Jenn Segawa
Fri 3/22, 2-3:30p (NW Room 453)
Register (3/22)
Overview of Psychiatric Disorders with Neuroimaging Considerations (description)
Mark Eldaief
Fri 4/5, 2-3:30p (NW Room 453)
Register (4/5)
Neuroimaging Workshop Descriptions
Introduction to Functional Magnetic Resonance Imaging
Functional magnetic resonance imaging (fMRI) has become one of the most important techniques for studying the human brain in action. This workshop is intended to introduce the basic principles of fMRI and to provide an opportunity for students to experience neuroimaging research first-hand. It is ideal for students considering pursuing advanced study or research assistantships within professors’ research laboratories.
Introductory MR Physics
This lecture will include MR physics basics, starting with a description of scanner hardware, why a strong magnetic field is used, how RF signals are received from the brain, and how magnetic field gradients are used to encode for spatial position and generate a three-dimensional image. MR Relaxation will be described briefly to illustrate how T1w and T2w images are acquired for anatomical scans; and the basics behind the BOLD effect for functional scanning.
Optimizing Data Quality while at the Scanner
This session will include topics on ensuring good data collection at the scanner via quality control on patient placement, coil functioning, protocol and image monitoring throughout the scan session, and the use of our online motion monitoring software FIRMM. We will also discuss whether you should acquire a fieldmap, which one to use, and how to incorporate it into your analysis pipeline, as well as which scans can be used to reduce motion at acquisition (e.g., accelerated 1-2 minute structurals, structurals with Navigator scans).
Advanced Topics in Neuroimaging Data Acquisition
This advanced course will describe the differences behind the head coils we use and the advantages of one over the other; the approaches we take with protocols for BOLD acquisition to optimize spatial or temporal resolution; and the basics behind image acceleration techniques used to get higher-quality data in less time. This includes GRAPPA for in-plane acceleration, SMS for slice acceleration, and new techniques such as compressed-sensing which are available for now for rapid T1w scanning in an investigational phase.
Overview of Neurodegenerative Disorders including Neuroimaging Considerations
This lecture will provide a brief overview of major neurodegenerative brain conditions, including Alzheimer’s disease, Frontotemporolobar degeneration and Lewy Body Dementia. A main learning objective will be how these conditions inform normal cognitive function including: episodic memory, executive function, language and social and affective functioning. For each condition, neuroimaging abnormalities will be highlighted and considerations for study design in these populations will be explored.
Overview of Psychiatric Disorders including Neuroimaging Considerations
This lecture will provide a brief overview of major diagnostic categories in psychiatry including: mood disorders, anxiety disorders and psychotic disorders. A main learning objective will be going over diagnostic criteria. In addition, we discuss dimensional, symptom-based approaches to characterizing psychiatric disease. Functional neuroimaging abnormalities in these conditions will be explored, with an emphasis on the relative absence of such findings. Considerations for study design in these populations will be explored.
Brain Network Organization as Revealed by Functional Connectivity MRI
The brain is organized into large-scale, parallel interdigitated networks. Functional connectivity MRI (fcMRI) has emerged as a tool to characterize the topography of these networks based on sampling of low-frequency BOLD fluctuations. This workshop will provide theoretical foundations of fcMRI, an overview of the brain’s major networks and their putative contributions to brain function, and practical examples showcasing some of the major issues in fcMRI.
Overview of Non-invasive Brain Stimulation + Hands-On Tutorial
The first part of this session will be a lecture providing an overview of major forms of non-invasive brain stimulation, including transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS). TMS will be particularly emphasized. Topics will include electromagnetic principles underlying TMS and tDCS, stimulation parameters and safety issues. We will also discuss TMS study design, including a discussion of combined TMS and neuroimaging protocols.
After the talk, we will go down to the Neuroimaging Facility for a hands-on workshop in which participants will view the TMS set-up: including the TMS stimulator, TMS coil and neuronavigation apparatus. We will then demonstrate how to obtain a resting motor threshold, which is commonly used to “dose” TMS. This will allow participants to learn how to hold and orient a TMS coil and gain familiarity with the stimulator and neuronavigation system.
Accelerate Your Neuroimaging Research with the FASSE Compute Cluster
In this workshop, you’ll learn everything you need to know to effectively use the FAS Secure Environment (FASSE) compute cluster. We’ll kick things off with a high-level overview of cluster resources, show you how to access the cluster through a Remote Desktop session and SSH, how to load software modules (e.g., FreeSurfer, FSL, Matlab), how to fetch data from the CBSCentral data archive, how to build and use Singularity containers, and how to submit and control jobs on the compute cluster.
Participation is more than welcome. Please bring questions and we’ll help you troubleshoot!
Neuroimaging Computing Intermediate: Scripting in Bash
In this workshop, we will provide some examples of how to write Bash scripts. This includes: how to set up your bashrc file correctly for the cluster, what queue to use, and basic scripting in Bash such as how to loop over subjects and create a slurm script.
Neuroimaging Computing Advanced: Managing your Neuroimaging Workflows – Git and Software Containers
In this hand-on workshop, we will demystify Git for source control management and demonstrate how you can run and create your own containerized images via Singularity. This includes how to run Singularity (similar to Docker, but a better match for our security requirements) or create your own containers, and how to set up a basic Git workflow, which will make it easier to replicate, share, archive, and document your software projects. We will work through an example of how to manage a software project using NCFCode, the NCF’s secure private GitLab instance.
CBSCentral Advanced: XNAT for Neuroimaging
What is XNAT? How do you use it? What are some “best practices”? What libraries/tools do we have that will help you use XNAT effectively? Find out in this hands-on workshop.
Quality control of MRI and fMRI data
This workshop will give an overview on how to perform qualitative and quantitative assessments on your data. This includes: how and what to look for when visually inspecting your data for artifacts, how to run your MRI scans through MRIQC and fMRI scans through the BOLD QC pipeline in CBSCentral, and what these metrics mean.
Introduction to Matlab for Neuroimaging
This covers the basics of coding in Matlab, including variable types, indexing using matricies, printing output, logical expressions, miscellaneous useful functions loke length and randperm, flow control (if, else, while, for loop), reading and writing files, and plotting.
Python Bootcamp for Neuroimaging Enthusiasts
In this workshop, you’ll learn the basics of Python and how to build nontrivial programs. We’ll cover everything from basic Python syntax, to building virtual environments and installing popular neuroimaging packages. At the end of the workshop, we’ll tie everything together by building a data analysis pipeline with Nipype
Participation is more than welcome. Please bring your ideas and we’ll help you get started!
Building Neuroimaging Experiments with PsychoPy
This workshop will walk you through building your very first PsychoPy experiment. We will learn to assemble and time the components of a paradigm including coordinating with the scanner. We will practice creating stimuli – including text, images, and sounds – recording responses, and logging events. No programming experience needed. This is a hands-on workshop, so bring your laptop and your PsychoPy questions about the experiments you want to build!
Introduction to fMRI Data Analysis: The How and Why
The goal of this workshop is not only to understand the steps of a classical fMRI data analysis pipeline, but also discuss why and when we use them. We’ll start with preprocessing (e.g., motion correction, slice timing correction) and continue to general linear modeling and contrasts. There is a lecture component, but also bring those burning fMRI analysis questions you’ve been waiting to ask!
Introduction to Functional Magnetic Resonance Imaging for New Researchers
In this workshop, we will discuss the basics of how and why we use fMRI as a research tool, including:
– How does MRI and fMRI work?
– What are the benefits and limitations of fMRI as a research tool?
– How do we use fMRI in research?
This workshop is intended for everyone, from summer undergrad RAs to postdocs. (Note: this is not the MRI Safety course required to earn a yellow badge.)