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Neuroimaging Education and Training

For Credit Courses
Short Courses

Seminar Series
Online Software Tutorials, Manuals & Downloads (data analysis, stimulus presentation)
Research Opportunities
Training Programs

For Credit Courses

Courses offered at Harvard

The following courses were offered in 2006-2007 and will likely be repeated in subsequent years.

Psychology 1352. Foundations of Cognitive Neuroscience Research - Catalog Number: 9399 Enrollment: Limited to students involved in research. Randy L. Buckner Half course (fall term). Intended for undergraduates or those with no background in cognitive neuroscience. Students will attend and participate in a seminar that includes discussion of active scientific projects, recent important journal articles, and didactic lecture on technical aspects of methods central to cognitive neuroscience research. Readings will be assigned that survey basic principles of system neuroscience, cognitive science, and methods including functional MRI, MEG, and single unit physiology.

Psychology 2320. Applying fMRI to Cognitive Research - Catalog Number: 5380 Yuhong Jiang Half course (fall term). Covers basic fMRI methods in cognitive neuroscience, geared toward beginners. Topics include data collection and analysis, experimental design, and the connection between BOLD and neuronal activity. Note: Open to undergraduates with permission of instructor.

Psychology 2851r. Affective Neuroscience: Research Seminar - Catalog Number: 4937 Diego Pizzagalli Half course (fall term; repeated spring term). Provides lab experience in conducting reseasrch in the field of affective neuroscience. Students learn to design and conduct experiements and perform data analysis of behavioral, EEG, and fMRI data. Note: Open to graduate and undergraduate students working in the instructor’s laboratory. This seminar meets the laboratory methods requirement for honors undergraduates.

Courses offered at MIT

HST 582 Biomedical Signal and Image Processing
Harvard-MIT Division of Health Sciences & Technology
Fundamentals of digital signal processing with particular emphasis on problems in biomedical research and clinical medicine. Basic principles and algorithms for data acquisition, imaging, filtering and feature extraction.   Laboratory projects provide practical experience in processing data, with examples from neurophysiology, cardiology, speech processing, and medical imaging.
Course Director: Julie E Greenberg, PhD, Director of Education and Academic Affairs, HST, 617 258-6086
HST 583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis
Harvard-MIT Division of Health Sciences & Technology
Team taught, multidisciplinary course, covers the fundamentals of MRI relevant for conducting and interpretating human brain mapping studies. Provides in depth coverage of the physics of image formation, mechanisms of image contrast, and the physiological basis for image signals. Parenchymal and cerebrovascular neuroanatomy and application of structural analysis algorithms for segmentation and registration of functional data are discussed. Additional topics include fMRI experimental design and data analysis, and human subjects and safety issues. Weekly lectures are followed by laboratory and/or discussion sessions. Laboratory sessions include both fMRI data acquisition sessions and data analysis workshops.  
Course Director- Randy L Gollub, MD, PhD
HST 584 Magnetic Resonance Imaging Techniques
Harvard-MIT Division of Health Sciences & Technology
Introduction to basic NMR theory. Theory and applications of in vivo NMR spectroscopy,  and of NMR relaxation measurements. Detailed study of NMR imaging techniques including discussions of basic cross-sectional image reconstruction, image contrast, flow and real-time imaging, and hardware design considerations. Course Director: Bruce R Rosen, MD, PhD

Short Courses

fMRI Visiting Fellowship Program at the Martinos Center for Biomedical Imaging
Five day intensive course offering an introduction to the fundamentals of fMRI for those new to the field, including graduate and advanced undergraduate students, or anyone involved in fMRI research. Topics include basic MRI physics, biology and biophysics of the hemodynamic response, data analysis, stimulus presentation and response recording, and experimental design . A special emphasis of the course is the design, implementation, and execution of fMRI experiments by the participants. Offered twice annually.

Two-Week Multi-Modality Imaging Short Course at the Martinos Center for Biomedical Imaging
This two-week intensive program is an extension of the fMRI Visiting Fellowship Program, above, and will cover, in addition to fMRI, a range of techniques currently in use in Functional Brain Imaging (MRI, FMRI, DTI, DSI, MRS, PET, EEG, MEG, NIRS, DOT, TMS, and a variety of molecular and computational approaches). Includes some discussion of more invasive techniques such as implanted electrodes and direct cortical stimulation. Unifying themes including mode of activation, physiological underpinnings and others will be discussed. Activities will include design of experiments, exposure to software tools, tours and demonstrations of the techniques in action, and keynote lectures on technique application. Offered annually.

NIRS-DOT Visiting Fellowship Program at the Martinos Center for Biomedical Imaging
This two-day introductory course on Near-Infrared Spectroscopy and Diffuse Optical Tomography (NIRS-DOT) covers the fundamentals of this optical technique and offers hands-on experience in its application The course is geared toward end users in application areas such as clinical monitoring and psychology research. Offered annuall

Local Seminar Series

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.
For more schedule and to sign up for the mailing list see

Cognition, Brain, & Behavior Research Seminar, Harvard University
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. For schedule and contact information see

Mind / Brain / Behavior Graduate Student Seminars, Harvard University
An important aspect of building an interdisciplinary student community is to promote a common understanding of how different groups approach the question of mind, brain and behavior. To this end, the Mind/Brain/Behavior Initiative is holds biweekly seminars that provide a common forum for graduate students from different departments at Harvard University. Each session features a brief presentation led by a graduate student from one of the main participating programs within MBB. Thursdays, 6:15 p.m. , William James Hall, Room 1305, 33 Kirkland St., Cambridge. Dinner and refreshments are served before each presentation. All graduate students are welcome to attend.

Online Software Tutorials, Manuals, and Downloads

Data Analysis and Presentation

FreeSurfer and FSL:

  • Freesurfer Data Processing Software Tutorials - set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Use also for intersubject averaging and measuring morphometric properties of the brain including cortical thickness and regional volume.
  • FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data
  • Lecture Slides and Practical Instructions on FSL, FreeSurfer, and MRI Physics & Applications from courses offered by the Oxford group online for download


The SPM software package is designed for the analysis of brain imaging (including fMRI, PET, SPECT, EEG and MEG) data, including series of images from different cohorts or time-series from the same subject. SPM is a voxel-based approach that uses classical inference to help identify functionally specialized brain responses.

PLS Package:

Partial Least Squares analysis and the PLS Package can be used to assess functional connectivity or the correlation between neural elements. PLS analysis has been used to characterize distributed signals measured by PET, MRI, ERP and MEG. PLSgui is a MATLAB program with a graphic user interface (GUI) driven by messages from mouse and keyboard. Batch_PLSgui (see Batch Process) load messages from a batch file, and automatically send them to PLSgui program in batch.


  • Unix Tutorial for Beginners - Beginners guide to UNIX and Linux in 8 tutorials by
  • A Basic Unix Tutorial - This tutorial covers the "Introduction to UNIX" and "Intermediate UNIX" workshops offered by the Idaho State University Computer Center.

Stimulus Presentation

Psychophysics Toolbox (Psychtoolbox) - free set of Matlab functions for visual stimulus presentation. Runs on Mac OSX or Windows. Software download, users guide, Wiki.


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. See


Training Programs

Advanced Multimodal Neuroimaging Training Program (predoctoral)
One year pre-doctoral training program for advanced Harvard, HMS, and MIT grad students. Interdisciplinary training designed to integrate basic and cognitive neuroscience applications with the fundamental physical and biological bases of neuroimaging. Focus is on a jointly mentored research project (PhD thesis, or part thereof), that expands the student’s training from neuroscience to physical science, or vice versa. Mentors include the student’s primary advisor from his/her graduate program and a joint project mentor with complimentary expertise (e.g. in basic or translational neuroimaging, engineering, cognitive or basic neuroscience, etc). Students spend time in both the laboratories of the primary and joint project mentors, and engage in coursework and other educational activities. The program provides funds for a graduate stipend, travel allowance, and tuition & fees. Available to US and non-US citizens. Please address inquiries to Nichole Eusemann














revised 08/2007 jmg