Semester Courses

Short Courses

Seminar Series

Research Opportunities

Senior Thesis in Neuroimaging

Semester Courses

PSY 1309 - Essentials of fMRI for Cognitive Neuroscientists 

Department of Psychology
Talia Konkle
Fall semester Wednesday 3:00-5:30 PM

With functional magnetic resonance imaging (fMRI), we can now see into the human brain and map activity across different regions. If you are using fMRI in your research, or think you may want to in the future, this course will cover the critical aspects of neuroimaging with the goal of making you an informed practitioner. In the first part of the course, we will cover content including signal acquisition, experimental protocol design and power, and the general linear modeling framework for data analysis. In the second part of the course, we will survey the recent advances in fMRI data analysis, e.g. multivariate analyses, voxel-wise encoding models, functional connectivity analyses. Depending on your level of experience, you will complete a project that employs one of these techniques, either on your own dataset, or from datasets available online.

Note: This course is intended for both advanced undergraduates and graduate students.


BE 128 - Introduction to Biomedical Imaging and Systems

Department of Biomedical Engineering
Linsey Moyer
Spring semester Tuesday & Thursday 3:00-4:15 PM

The course is designed as an introduction for students who want to gain both hands on training as well as an introduction to the physics and image reconstruction techniques involved in generating images. The course will introduce the fundamentals of the major imaging modalities including, but not limited to: electron microscopy, optical microscopy, x-ray, computed tomography, ultrasound, MRI, and nuclear imaging, as well as an overview of in vivo imaging and molecular imaging. This course also includes a lab section every other week.

Note: Undergraduate. Enrollment limited to 24 students.


Short Courses 

Special Topics in Functional Magnetic Resonance Imaging
Center for Brain Science
Mark Eldaief, Ross Mair, Stephanie McMains, Tammy Moran, Caroline West
Individual sessions - see calendar for full details

An alternative to the 2-day intensive short course. Many of the same topics will be covered in individual sessions. Additional lectures on advanced topics will also be offered.

Note: Priority to undergraduates. Others may attend if space permits.

Introduction to Functional Magnetic Resonance Imaging
Center for Brain Science
Enrollment: Limited to 15.
Mark Eldaief, Ross Mair, Stephanie McMains, Tammy Moran, Caroline West
2-day intensive course.

Functional magnetic resonance imaging (fMRI) has become one of the most important techniques for studying the human brain in action. This two-day workshop 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.

Note: Priority to undergraduates. Others may attend if space permits.


Computational Training Sessions for Neuroimaging

NCF Basics: Effectively using computing resources for your fMRI study
Center for Brain Science
Harris Hoke and Stephanie McMains, with Research Computing staff
Wednesday, October 10, 2018 9:00-10:45 AM, Northwest 269.10

Goal: To make everyone can access the cluster and have the basics for getting their data analyzed.

For the first 45 min, we will help everyone gain access to the cluster (VPN, VNC).  Please make sure to request your NCF account several days before you come so that it can be approved by your PI and created by RC. For the next hour we will cover how to use CBSCentral (auto-archive, metadata, automated BOLD QC, download your data), how to choose software packages (modules), and how to submit your data to the cluster (different queues, interactive sessions, choosing your memory).

NCF Intermediate: Cluster upgrade and scripting in Bash
Center for Brain Science
Harris Hoke and Stephanie McMains
Wednesday, October 10, 2018 10:45-11:45 AM, Northwest 269.10

Goal: Provide the tools to start switching over to the new Centos 7 cluster and provide some examples of how to write Bash scripts.

This includes:how to set up your .bashrc file correctly for the new cluster, which queue to use, and basic scripting in Bash such as how to loop over subjects and create a slurm script.

CBSCentral Advanced: Making XNAT work for you
Center for Brain Science
Tim O'Keefe and Harris Hoke

Goal: Expand your knowledge about what XNAT can do

How to use XNAT REST API, how to use in-house tools and APIs for querying and downloading, and common XNAT usage patterns

NCF Advanced: Managing your neuroimaging workflows: GIT and software containers
Center for Brain Science
Tim O'Keefe and Harris Hoke
Monday, October 15, 2018 11:00 AM-12:30 PM, Northwest 269.10

Goal: Demystify Git for source control management adn 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.


Additional Training Opportunities

FAS Research Computing Training Sessions

The FAS research computing team offers numerous traing sessions on general computing topics, including using the Odyssey cluster.


Continuing Education Courses at the Martinos Center for Biomedical Imaging:

Connectivity Course: Structural and Functional Brain Connectivity via MRI and fMRI: This is a five-day program on functional and structural connectivity using MRI. The next edition is October 22-26, 2018.  (Monday->Friday.) 

The CONN Toolbox: This program is devoted to teaching the use of the CONN Toolbox for analyzing resting state connectivity data. The next program will be April 29 - May 3, 2019 (Monday->Friday).

fMRI Visiting Fellowship Program: This program provides an in-depth introduction to the field of functional magnetic resonance imaging. The next programs are October 15-19, 2018 and March 25-29, 2019. (All are Monday->Friday.) 

The Multimodality Short Course: This course addresses the burgeoning collection of functional and structural brain imaging methods. It is a 7-day course; and the next edition is scheduled for 2019 (Sunday->Saturday); exact dates to be determined.

Functional Near-Infrared Spectroscopy (fNIRS) Course: This introductory course covers the fundamentals of fNIRS and offers hands-on experience in its application.

FreeSurfer Tutorial and Workshop:  The FreeSurfer Development Team hosts a three-day course for beginner and experienced users of FreeSurfer.

Seminar Series

Center for Brain Science Seminars
Center for Brain Science
Neuroscience talks by Harvard researchers and invited speakers from other institutions.
CBS Brownbag - Mondays at noon NW 243; CBS Neurolunch - Mondays at noon or Wednesdays at 1:00 NW 243; for a list of all seminars including special seminars go to

Cognition, Brain, & Behavior Research Seminar
Department of Psychology
Invited speakers from Harvard and around the country present research on relevant topics, occasionally involving neuroimaging. Thursdays at 12:00-1:30pm, William James Hall 765, 33 Kirkland St, Cambridge.

Brain Mapping
Martinos Center for Biomedical Imaging
Brain Mapping seminars are by and for researchers using neuroimaging to study human brain function, and for anyone interested in learning about neuroimaging. Presentations by Martinos Center researchers, collaborators, and outside speakers. Wednesdays at noon, MGH Building 149, room 2204, 13th St., Charlestown. Once a month the seminars are held on Wednesdays at 4pm in MIT building 46, McGovern seminar room.

Research Opportunities

Harvard Mind/Brain/Behavior Interfaculty Initiative
Research opportunities for Harvard undergraduates, some of which include neuroimaging

Martinos Center for Biomedical Imaging
Graduate and postgraduate paid and unpaid neuroimaging research opportunities.

Senior Thesis in Neuroimaging

The Center for Brain Science provides scan time at no charge for approved senior thesis projects using MRI. Every effort will be made to accomodate student thesis projects with the limited amount of scan time that is available.

To apply for a thesis award please submit the following information:

  • A copy of the approved thesis proposal in pdf format
  • Name of adviser and of any co-advisers
  • Number of subjects required
  • Estimate of the amount of time you will need in the scanner for each subject
  • Estimated timeframe for the start/end of the MRI project

Please send applications to Caroline West (wcwest [at] fas [dot] harvard [dot] edu).


List of Previous Senior Theses in Neuroimaging