Structural MRI – Modular Digital Course in Undergraduate Neuroscience Education

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:

Accessing and Installing Files for Structural MRI

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

This module requires the following items:

Command Line Interface: Ubuntu (Windows); Terminal (native Mac app) + XQuartz (Mac)
Brain Imaging Data Analysis Software Library: FSL (Windows; Mac)
Image Database: CANDI Share Schizophrenia Bulletin 2008
Tutorial: Structural MRI of Accumbens FSL Tutorial

The tutorial has links to all of the software and resources you will need to run this module. It includes a thorough guide for executing this module. Be sure you have equipped your computer with the necessary software and files before beginning.

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 as a compressed/zipped file that is linked in the tutorial. Be sure to extract/unzip it after downloading.

Previous (likely outdated) Tutorials

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

Structural MRI (of Various Structures) Tutorial UPDATED on 2016-01-22 at 11:45am

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

Structural MRI of Amygdala Tutorial UPDATED on 2016-01-22 at 11:45am

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

OLD Structural MRI of Amygdala Tutorial UPDATED on 2015-08-24 at 10:25am

OLD Structural MRI of Hippocampus Tutorial UPDATED on 2015-08-24 at 10:26am
OLD Structural MRI of Thalamus Tutorial UPDATED on 2015-08-24 at 10:27am

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 natalie@psych.ucla.edu or wgrisham@g.ucla.edu 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.

Extras

UNDER CONSTRUCTION

Need Help?

Email natalie@psych.ucla.edu or wgrisham@g.ucla.edu (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.