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Structural MRI

Quantification of brain structures (e.g. amygdalae, hippocampi, thalami) from Structural MRI scans downloaded from CANDI Share ( 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 basic MRI software in a way that is easily accessible to students.  All materials are available for free, including student and instructor tutorials.


Structural MRI of Amygdala Logo


Preparation for Structural MRI

Please note that this module has only been tested and executed on the Mac OS.  Windows OS compatibility is possible, but not supported through MDCUNE.

This module requires the following items:

  • (01)  Tutorial:  MDCUNE Structural MRI Tutorial     requires MDCUNE download
  • (02)  Background Study:  Frazier et al., 2008     requires external download
  • (03)  Image Database:  CANDI Share Schizophrenia Bulletin 2008 (simplified version)    requires MDCUNE download
  • (04)  Data Template:  MDCUNE Structural MRI Data Sheet (includes demographics)     requires MDCUNE download
  • (05)  X Window System Server:  X11 (Mac); Xming (Windows)     native computer program
  • (06)  Command Line Interface:  Terminal (Mac); Command Prompt (Windows)     native computer program
  • (07)  Brain Imaging Data Analysis Software Library:  FSL (Mac; Windows)     requires external download
  • (08)  Reference Atlas:  Allen Institute Brain Explorer 2 (Mac; Windows)    requires external download
  • (09)  Statistical Analysis Software:  JASP (Mac; Windows)     requires external download
  • (10)  Online Statistical Computation Tool:  VassarStats (Mac; Windows)     requires Internet access
  • 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.


    Evaluation for Structural MRI

    Take the Student Pre-Test

    If you are a student and are about to begin the Structural MRI module, please take our Pre-Test [NOTE: this will NOT affect your grade].  We are asking you to participate in a study on the efficacy of the teaching module delivered by your instructor.  This study will help us to revise this teaching module to make it more effective and to develop new modules in the future so that they are educationally effective, are easy to understand, and successfully meet student needs.  Not only will your participation help us make better teaching modules, but your participation may also help your understanding of the material (again, this will not figure into your grade).

    -->  We ask that you take a short Pre-Test BEFORE the material is presented and also take an idential Post-Test AFTER the module has ended.  These little quizzes will help us gauge your gains from this module.  The quiz can be taken over the web and should take about 10 minutes.  When you take the tests online, please use the SAME, real email address each time, as we will need them for tracking data.

    -->  Since we are going to ask you to take the quiz as well as fill out an opinion questionnaire after the unit is completed, we request that you give us your email address so that we can send you one, and ONLY one, reminder email.  We will NOT be sending you any further emails, nor will we submit your email address to any outside sources.  Note: providing you email address is voluntary, as is your participation in this study (see below).

    -->  Participation in this study is completely voluntary.  You are not required to participate to receive or use the materials included in this module.

  • Student Pre-Test     (Experimental Group)
  • Student Pre-Test     (Control Group)
  • Take the Student Post-Test

    If you are a student and have completed the Structural MRI module, please provide us with your level of scientific knowledge coming out of the module by taking the following Post-Test.  This form will also allow you to provide us with basic feedback on the materials used in this module.

  • Student Post-Test     (Experimental Group)
  • Student Post-Test     (Control Group)

    Accessing and Installing Files for Structural MRI

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


    (01)  Download the Tutorial

    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 tutorial:


    (02)  Read the Background Study

    This module intends to replicate the study done by Frazier, et al (2008), who found diagnostic and sex effects on limbic volumes (including amygdala) of early-onset bipolar and schizophrenic patients.

    Read the background study:

  • Frazier et al., 2008           UPDATED on 2016-11-30 at 08:20am

  • (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:

  • Structural MRI Image Database, Simplified (ZIP)           UPDATED on 2016-11-21 at 10:40am

  • (04)  Download the Data Template

    This is an Excel spreadsheet of subject demographics and empty columns that serves as a template for data collection.  The final four columns contain equations for calculating values needed in statistical analysis.

    Download the zipped image database:

  • Structural MRI Data Template Spreadsheet (XLSX)           UPDATED on 2017-03-21 at 10:00am

    (05)  Access the X Window System Server on your System

    This is an open, cross-platform, client/server system for managing a windowed graphical user interface (GUI) in a distributed network.

    If you use Mac:

  • locate or download X11 (application)
  • If you use Windows:

  • locate or download Xming (program)

    (06)  Access the Command Line Interface on your System

    This is a means of interacting with a computer program where the user/client issues commands to the program in the form of successive lines of text (command lines).

    If you use Mac:

  • locate Terminal (application)
  • If you use Windows:

  • locate Command Prompt (program)

    (07)  Download the Brain Imaging Data Analysis Library

    The images in this module come from actual structural MRI scans that 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 (Mac; Windows):

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

    (08)  Download the Reference Atlas

    The Brain Explorer 2 software was developed by the Allen Institute as a fully interactive version of the Allen Brain Atlas.  This desktop application allows for exploration of mouse and human brain anatomy as well as gene expression data in 3-D.

    Download the atlases:

  • Allen Institute Brain Explorer 2           UPDATED on 2016-11-23 at 10:10am

    (09)  Download the Statistical Analysis Software

    JASP is a simpler and free alternative to SPSS, and R. Bayesian statistics.

    Download the statistics software:

  • JASP            UPDATED on 2016-11-30 at 11:30am

    (10)  Access the Online Statistical Computation Tool

    VassarStats is a free online tool for statistical computation.

    Navigate to the statistics tool:

  • VassarStats            UPDATED on 2017-03-21 at 11:00am

    Lecture and Lab Slides

    Students and Faculty can download folders containing the Structural MRI instruction slides for free.


    For Faculty

    Faculty members interested in accessing faculty-related materials will need to obtain an account.  Please see the Faculty Web Page for more information:

  • Faculty Web Page - Request an Account
  • Faculty members that already have an account may log in and go directly to the Faculty Gel Scramble Web Page:

  • Structural MRI - Faculty Module
  • which includes:
    1. Instructor Notes
    2. Grading Keys

    If you are a faculty member that has individually completed or taught the Structural MRI Module, please provide us with basic feedback on the materials used in this module by filling out the multiple choice Faculty Materials Evaluation:

  • Faculty Materials Evaluation: Structural MRI


    UCLA students who have completed the module may access their Structural MRI Complete Data to use as a reference for their final papers.


    (01)  Download the Complete Data

    These data are already sorted for statistical analysis, first by Sex, then by SubjNo.


    Need Help?

  • FAQ:  Structural MRI
  • Contact:     [Please put "Structural MRI Module" in the subject line.]

    License Information

    Modular Digital Course in Undergraduate Neuroscience Education—Revised: Structural MRI 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



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    National Science Foundation            UCLA Office of Instructional Development

    Funded by the National Science Foundation and the UCLA Office of Instructional Development