Structural MRI

Quantification of brain structures (e.g. amygdalae, hippocampi, thalami) from Structural MRI scans using the FMRIB Software Library (FSL). This module was created by Dr. William Grisham at UCLA, with the help of Dr. Nanthia Suthana. The tutorial was created by Natalie Schottler, with the help of Natalie De Shetler. It is an instructional tool for teaching molecular neurobiology that requires only a computer. Structural MRI is available for free, including student and instructor tutorials.


Enter Data (for UCLA students only)

Enter subject volume data (in mm^3) for Left Amygdala, Right Amygdala, Gray Matter, White Matter here:

  • Subject Volumes

Get Data

Download class data here:

Preparation for Structural MRI

This module requires the following items:

  • Command Line Interface: Terminal (Mac); Command Prompt (Windows)     native computer program
  • Brain Imaging Data Analysis Software Library: FSL (Mac; Windows)     requires external download
  • Image Database: CANDI Share Schizophrenia Bulletin 2008     requires external download
  • Tutorial: MDCUNE Structural MRI Tutorial

Be sure you have equipped your computer with the necessary software and files before beginning.  The subsequent sections will link you to these items if you are interested in running this module.

Accessing and Installing Files for Structural MRI

Students and Faculty can download the Structural MRI Image Database and Structural MRI Tutorials for free.

(01)  Access the Command Line Interface on your System

If you use Mac:

  • locate Terminal (application)

If you use Windows:

  • locate Command Prompt (program)

(02)  Download the Brain Imaging Data Analysis Library

The images in this module are MRI scans that can require a library of powerful tools for 3D observation.  FMRIB Software Library (FSL) was created by The Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB) at the University of Oxford.  The software library is available for download via the FSLWiki webpage.

Download the software library:

  • FSL            UPDATED on 2014-08-14 at 11:45am

(03)  Download the Image Database

The images in this module were created for the Schizophrenia Bulletin 2008 by the Child and Adolescent NeuroDevelopment Initiative (CANDI) at the University of Massachusetts Medical School (UMMS).  The original image files are available for download via the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) website.  We have simplified these files for the purpose of this module by minimizing the directories in which necessary files are found for each subject.  It is available below as a compressed/zipped file.  Be sure to extract it after downloading.

Download the zipped image database now:

(04)  Download the Tutorials

In order to access the tutorial, you must first fill out the User Consent/Download Questionnaire (after which you will be directed to the download button).  Note that you will still be allowed to download the tutorial even if you choose NOT to consent to anything.

Download the all-encompassing tutorial (for analyzing all 8 FSL-capable structures) now:

Download the structure-specific tutorials (for analyzing one of the 8 FSL-capable structures) now:

OLD structure-specific tutorials (DO NOT USE UNLESS SPECIFICALLY REQUESTED):

For Faculty

Faculty members interested in accessing faculty-related materials will need to obtain approved access. While we are still developing this website, please email or using the email listed in your institution’s faculty directory so that we can verify you as an instructor.  Please include your first and last name, and the names of the modules you wish to access.



Need Help?

  • Email or (with “Structural MRI Module Question” in the subject line).

License Information

Modular Digital Course in Undergraduate Neuroscience Education—Revised: Gel Scramble by Dr. William Grisham, Ph.D., is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.

Creative Commons License