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| This is a web page containing lecture notes for the neuroimaging interest group at TCH. | | This is a web page containing lecture notes for the neuroimaging interest group at TCH. |
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| #[[media:S1T1.nii.zip|S1T1.nii T1 dataset from a sample subject ]] | | #[[media:TCH_Dec09.pptx|Slides presented ]] |
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| Here is the Vul article and various replies (for teaching purposes only): | | Here is the Vul article and various replies (for teaching purposes only): |
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| <h5>Step 1: Download MRIcroN (software for viewing MRI datasets)</h5>
| | #[[media:VulAndReplies.Zip|Vul article and replies (in a single zipped file) ]] |
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| Go to
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| http://www.cabiatl.com/mricro/mricron/install.html
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| Download the correct installer package for your computer (Windows, Mac and Linux are supported).
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| * For Windows, double-click the installer and answer the on-screen questions
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| "I agree" with the license agreement
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| "Next >" to install all components of the software
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| "Install" to install the package
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| "Close" when finished installing
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| By default, MRIcron is installed in the folder C:\ProgramFiles\MRIcroN
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| 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.
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| 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.
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| 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.
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| [[Image:mricron pc.jpg|thumb|none|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 mricron.app next to a small brain icon.
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| 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).
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| 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.
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| You should see the following window. To make the images easier to see, you can enlarge the window.
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| [[Image:mricron mac.jpg|thumb|none|Macintosh MRIcroN window]]
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| <h4>Step 2: Explore the brain</h4>
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| 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.
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| *Find anatomical regions
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| To view a colored template with anatomical regions colored, perform the following steps.
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| #Click on the Overlay menu, select Add.
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| #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).
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| #Select the file aal.nii.gz (aal = anatomical area labels).
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| # 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%.
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| [[Image:mricronlabels.jpg|thumb|none|MRIcroN with anatomical labels]]
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| 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.
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| <h4>Step 3: Different kinds of brain MRI</h4>
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| 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.
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| #[[media:S1T1.nii.zip|S1T1.nii T1 dataset from a sample subject ]]
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| #[[media:S1T2.nii.zip|S1T2.nii T2 dataset from a sample subject ]]
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| #[[media:S1FLAIR.nii.zip|S1FLAIR.nii FLAIR dataset from a sample subject ]]
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| 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.
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| OPTIONAL: for more information on MRI imaging priniciples, see http://spinwarp.ucsd.edu/NeuroWeb/Text/br-100.htm
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