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 http://www.cabiatl.com/mricro/mricron/install.html Download the correct installer package for your computer (Windows, Mac and Linux are supported).
"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.
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 mricron.app 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.
Step 2: Explore the brain
To view a colored template with anatomical regions colored, perform the following steps.
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.
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 http://spinwarp.ucsd.edu/NeuroWeb/Text/br-100.htm
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.
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 www.apple.com. After the movie is loaded, press the left and right arrow to scroll through the frames of the movie.
Coordinates of structures in labs 8 and 9
View in mricron using the "ch2" file (ch2.nii.gz)
Structure x y z
Central Sulcus 56 95 129 (omega sign)
Lateral Sulcus 27 110 82
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
Coordinates of structures in lab 11
Limbic System A.
Cingulate Gyrus 97 114 111
Amygdala 117 127 154
Hippocampus 117 111 48
Lateral Ventricle 126 89 67 (temporal horn)
Fornix (body) 92 123 85
Fornix (column) 92 130 70
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 88 126 59
Pituitary 93 134 42