From OpenWetWare

Revision as of 15:09, 19 April 2010 by Michael S Beauchamp (Talk | contribs)
Jump to: navigation, search

Brain picture
Beauchamp Lab

This is the web page for information about downloadable MRI teaching materials for the Medical Neuroscience Laboratory Course for first-year medical students at the University of Texas Medical School at Houston. This component of the laboratory requires you to download MRI datasets and a freely available viewing program to look at them.


Step 1: Download MRIcroN (software for viewing MRI datasets)

Go to Download the correct installer package for your computer (Windows, Mac and Linux are supported).

  • For Windows, double-click the installer and answer the on-screen questions
"I agree" with the license agreement
"Next >" to install all components of the software
"Install" to install the package
"Close" when finished installing

By default, MRIcron is installed in the folder C:\ProgramFiles\MRIcroN

Open a Windows Explorer window and browse to this directory. Find the MRIcroN icon (it looks like a small brain). For easier access in future, right click and drag the icon to your desktop and create a shortcut. Start the software by double-clicking the icon or file name.

detail: The first time that it is run, the software will ask if you want to associate certain file types with this program; click "No". If you want to click "Yes", Windows Vista users must right click the icon and select "Run as Administrator" the first time they open the program.

After successfully starting the program, you should see the following window. To make the images easier to see, you can enlarge the window. Go to Step 2, below.

Windows MRIcroN window
Windows MRIcroN window
  • For Macintosh, double-click the Macintosh Intel [Universal Binary] software link. Open the downloaded zip file if it does not open automatically with StuffIt Expander. A new folder called "mricronmac" will be created. Find this folder and drag it to your Applications folder. Open the folder; you should see the file next to a small brain icon.

Right click on this file or icon; select "Show Package Contents" in the pop-up menu that appears. A new window will open that contains the folder "templates". Option-Click to drag a copy of this folder into the "mricronmac" folder. (You only have to do this step once). To start the program, double click on the file or the small brain icon. For easier access in the future, drag the file or icon to the Dock. You should see the following window. To make the images easier to see, you can enlarge the window.

Macintosh MRIcroN window
Macintosh MRIcroN window

Step 2: Explore the brain

Regardless of the platform (PC or Mac), the top left of the window shows a coronal view of the brain. The top right of the window shows a sagittal view of the brain. The bottom left of the window shows an axial (horizontal) view of the brain. Click the mouse at any brain location to move the blue viewing crosshairs.

  • Find anatomical regions

To view a colored template with anatomical regions colored, perform the following steps.

  1. The dataset name is listed at the top of the MRIcroN window in Windows, at the bottom of the window for Mac. Make sure that you are looking at the appropriate template dataset, named ch2.nii.gz. If you are not viewing this dataset, open it with File/Open Templates/ch2.nii.gz
  2. Click on the Overlay menu, select Add.
  3. Find the directory in which MRIcroN lives. For PCs, the default is C:\ProgramFiles\MRIcroN. For Macs, it should be in /Applications. Select the "templates" directory. This will only be possible in Macs if you have created a copy of the folder (see above).
  4. Select the file aal.nii.gz (aal = anatomical area labels).
  5. You should see various color overlaid on the brain (picture below). To make the colors transparent, allowing you to see the brain as well, click Overlay/Transparency on Background/50%.
MRIcroN with anatomical labels
MRIcroN with anatomical labels

Surf around the brain. When clicking on a colored region, you will see the anatomical label for that colored area of the brain. The label (e.g. Putamen_L for left putamen) will appear in the bottom of the viewing window on PC, in the top of the viewing window on Mac.

Step 3: Different kinds of brain MRI

MRI is clinically very useful because it is non-invasive and safe. Because no exposure to radiation is involved, patients can receive many different kinds of MRI imaging procedures without risk. The MRI scanner can be programmed to create different kinds of images that reveal different tissue properties. The three main kinds of images are T1, T2 and Proton Density (FLAIR). The names of the image types refer to the physical priniciples used to create the images. The three links below link to three datasets, all collected from the same normal subject, that show the three different image types. Click on each link and save the file to your computer.

  1. S1T1.nii T1 dataset from a sample subject
  2. S1T2.nii T2 dataset from a sample subject
  3. S1FLAIR.nii FLAIR dataset from a sample subject

After you have downloaded the datasets, you can load and view them in MriCroN by clicking File/Open. Navigate to the directory where you saved them and select the dataset name.

 OPTIONAL: for more information on MRI imaging priniciples, see

Step 4: Different kinds of spine MRI

Because the spine is so long, it is typically imaged in three separate scans covering the cervical, thoracic, and lumbar+sacral portions of the cord. The following archive file contains T1, T2 and IR datasets for each spine portion. Download the file and unzip the 12 datasets that it contains. It is easiest if they are unzipped to the same directory as the datasets in Step 3. The datasets can then be opened in MRIcroN.

  1. Archive file containing 12 different spine MRI datasets, all from a single subject.

Step 5: Cerebral Vasculature

Here are two movies that show the results of a Magnetic Resonance Angiogram (MRA). Click to download the movies to your desktop. Then double-click on the movies to view them. They have been tested with Apple Quicktime, free software downloadable from After the movie is loaded, press the left and right arrow to scroll through the frames of the movie.

  1. MRAturn.MPG A movie that shows a maximum intensity projection of the MRA dataset, with the brain rotating from left to right.
  2. MRAtumble.MPG A movie that shows a projection of the MRA dataset, with the brain rotating from front to back (as if the subject was doing a somersault).

Coordinates of structures in labs 8 and 9

View in mricron using the "ch2" file (ch2.nii.gz)

Structure x y z

Caudate 104 136 83

Putamen 116 136 72

Globus Pallidus 109 128 72

Thalamus (anterior nucleus) 102 121 81

Midbrain (superior colliculus) 96 94 62

Crus Cerebri 109 115 61

Red Nucleus 97 108 64

Substantia Nigra 103 108 61

Cerebral Aqueduct 91 97 62

Internal Capsule, anterior limb 110 140 78

Internal Capsule, posterior limb 115 115 77

Cerebellum Dentate nucleus 104 68 43

Coordinates of structures in lab 11

Limbic System A.

Cingulate Gyrus 97 114 111

Amygdala 117 127 154

Hippocampus 117 111 48

Lateral Ventricle 134 138 67 (temporal horn)

Fornix (body) 92 123 85

Fornix (column) 92 130 70



Hypothalamus Landmarks

Lamina Terminalis 91 141 57

Anterior Commissure 92 131 67

Optic Chiasm 93 137 50

Infundibulum 93 132 47

Mamillary Body 93 121 58

Hypothalamus Proper 93 126 60

Pituitary 93 134 42

Personal tools