Beauchamp:MedNSLab
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).
- 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.
- 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 mricron.app 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 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
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.
- Click on the Overlay menu, select Add.
- 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).
- Select the file aal.nii.gz (aal = anatomical area labels).
- 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%.
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 (e.g. S1FLAIR.nii.gz) to the templates sub-directory of the MRIcroN folder created in Step 1 (above).
- FLAIR dataset from a sample subject (S1) S1FLAIR.nii
- T2 dataset from a sample subject (S1) S1T2.nii
- T1 dataset from a sample subject (S1) S1T1.nii
After you have downloaded the datasets, you can load and view them in MriCroN by clicking File/Open Templates and selecting the dataset name.
OPTIONAL: for more information on MRI imaging priniciples, see http://spinwarp.ucsd.edu/NeuroWeb/Text/br-100.htm
