Fall 2019: Principles of Human Brain Mapping with fMRI

Psych 60 Description

This course is designed to introduce students to the theoretical and practical issues involved in conducting functional magnetic resonance imaging (fMRI) experiments of cognitive and behaviorally-related brain activity. Participants will gain an understanding of the physiological principles underlying the fMRI signal change, as well as the considerations for experimental design. The course will include firsthand exposure to the scanning environment and data collection procedures. Participants will be provided conceptual and hands-on experience with image processing and statistical analysis. At the completion of this course, it is expected that participants will be prepared to critique, design and conduct fMRI studies; appreciate limitations and potentials of current fMRI methods and techniques; and better understand the broad range of expertise required in an fMRI research program. The course is designed to provide the participant with intensive, hands-on instruction. As a result, enrollment in the course will be limited to 12 people. Knowledge of MR physics, signal processing, or the UNIX/Linux operating system is not a prerequisite.

Connecting to our the class server

Initial login: jhub.dartmouth.edu

After you have logged in and selected our class, open a new tab and run the following to pull the tutorial data from github: https://dartgo.org/psych60_jhub (Links to an external site.)

Each week you will need to reload this website at the beginning of lab to pull the latest labs into your server space.

Brain anatomy resources and refreshers

Yale MNI-Talairach with Brodmann Areas

Julian Casper’s anatomy guidelines

3d Brain

Some of these resources are from here


Neurosynth - automated meta-analyses and resting-state connectivity maps

Human Brain Transcriptome - gene expression across development

Neurostars - have a problem? Someone here can probably answer it…

Links to videos to help understand concepts of fMRI

Basic concept of fMRI & history

Introduction to MRI Physics

MRI Physics by Callaghan

Explanation of k-space and image through FT

Other MRI resources



Intro to MR physics with good figures

Explanation of MRI with good figures

Online Classes

Online Brain Intensive

Dartmouth Summer MIND

Principles of fMRI with associated video here

3D Print your Anatomical MRI

Method 1: Graphical walk-through

Method 2: A docker container for 3D printing a brain As a note, Jin suggested that before printing you may want to merge the hemispheres in MeshLab. Please let me know if you would like help converting FreeSurfer output to .stl files.

Programming resources


Markdown Cheatsheet

Whilrwind Tour of Python

fMRI analysis resources






fmriprep - based on nipype



Reproducible neuroscience links and tools

Git - version control for code

Datalad - download and manage data

Docker - run applications in a reproducible manner from a container, usually locally

Singularity - containers that can be run on servers for large scale implementation

Singularity tutorial

Singularity tutorial for Dartmouth’s Discovery Cluster written by Eshin and Matteo

fmriprep singularity installation

Previous Terms

Winter 2019: Principles of Human Brain Mapping with fMRI

Fall 2018: Principles of Human Brain Mapping with fMRI

Winter 2018 Principles of Human Brain Mapping with fMRI

Fall 2017 Principles of Human Brain Mapping with fMRI