Neuroimaging Short Courses

These workshops and lectures are open to Harvard researchers and students. Please sign up if you would like to attend so that we can ensure adequate space for the size of the group. Email Jenn Segawa ( with questions.

Registration coming soon.


Fall 2022 Short Course Schedule  [additional sessions may be added - check back for updates]

FASSE Basics: Effectively using Computing Resources for fMRI Studies
Timothy O'Keefe
Fri 9/23, 2-3:30p (NW Room 453)

Introduction to Functional Magnetic Resonance Imaging
CBSN Core Staff
Fri 9/30, 2-4p (NW Room 453)
(for undergraduates, others may attend if space allows)

Introduction to Functional Magnetic Resonance Imaging
CBSN Core Staff
Fri 10/7, 2-4p (NW Room 453)
(for undergraduates, others may attend if space allows)

Overview of Non-invasive Brain Stimulation + Hands-on Tutorial
Mark Eldaief
Fri 10/14, 2-3:30p (NW Room 453)

Introductory MR Physics
Ross Mair
Fri 10/21, 2-3:30p (NW Room 453)

Overview of Neurodegenerative Disorders with Neuroimaging Considerations
Mark Eldaief
Fri 10/28, 2-3:30p (NW Room 425)

Advanced Topics in Neuroimaging Data Acquisition
Ross Mair
Fri 11/4, 2-3:30p (NW Room 453)


Course 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 short course is intended to introduce the basic principles of fMRI and to provide an opportunity for students to experience neuroimaging research first-hand in an informal setting. 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, and a new system for online motion monitoring. 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., 1 minute structural, Navigator scans).

Advanced Topics in Neuroimaging Data Acquisition
This advanced course will describe diffusion imaging, ASL imaging, and the basics behind image acceleration techniques used to get higher-quality data in less time, including GRAPPA for in-plane acceleration, SMS for slice acceleration, and new techniques such as wave-CAIPI and 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
This lecture will provide 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.

TMS Hands-on Tutorial
This will be a hands-on workshop in which participants will view the TMS set-up at the CBS: 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.


Neuroimaging Data Analysis Workshops:

NCF Basics: Effectively using Computing Resources for fMRI Studies
In this workshop, you will learn how to access the Harvard NCF compute cluster and get set up for data analysis. We'll begin with helping everyone gain access to the cluster (VPN), how to connect to the compute cluster (SSH, virtual desktop), how to load software modules (module commands), how to interact with the CBS central data archive (uploading and downloading data), and how to submit jobs and interact with the cluster (partitions, specifying resources, interactive jobs).

NCF 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.

NCF 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.

Introduction to Psychtoolbox for Neuroimaging
This covers the Matlab toolbox developed to create psychology experiments.  We will cover how to open a screen for presenting stimuli, how to draw stimuli, show pictures, draw text, and collect responses.  We will also cover how to control your timing for an fMRI experiment.

Introduction to Python for Neuroimaging
Topics will include using the python interpreter, data types, basic operators, importing modules, defining functions and command line arguments, reading and writing files, command line tools, regular expressions, scientific and neuroimaging specific software/commands.

Introduction to PsychoPy for Neuroimaging
We will cover the basics of creating experimental paradigms with PsychoPy. 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.