Beauchamp:MedNSLab: Difference between revisions
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The following instructions were tested with Mac OSX 10.8.2 running Safari. For different versions of OSX or other web browsers, the steps may be slightly different. | The following instructions were tested with Mac OSX 10.8.2 running Safari. For different versions of OSX or other web browsers, the steps may be slightly different. | ||
#Click on this link:[[ | #Click on this link:[[BeauchampMacMRIcron.zip]] | ||
#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. | #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). | #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). |
Revision as of 14:15, 18 January 2013
This is the web page for information about downloadable MRI neuroanatomy teaching materials. The instructions below describe how to download MRI datasets and a freely available viewing program to look at them. Step 1: Download MRIcroN (software for viewing MRI datasets)Download the correct installer package for your computer. Windows, Mac and Linux are supported; detailed installation instructions are provided for Windows and Mac but not Linux. For Windows: The following instructions were tested with Windows 7 running Internet Explorer 9. For different version of Windows or other web browsers, the steps may be slightly different.
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: The following instructions were tested with Mac OSX 10.8.2 running Safari. For different versions of OSX or other web browsers, the steps may be slightly different.
You should see the following window. To make the images easier to see, you can enlarge the window. For Linux: click on one of these links. Your are on your own for installation! 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 MRIMRI 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 MRIBecause 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 VasculatureHere 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 9View 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 (aka Sylvian Fissure) 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 11Limbic 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
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 88 126 59 Pituitary 93 134 42
License Information for MRIcron software. Chris Rorden's MRIcron, copyright 2012, all rights reserved. Redistribution and use in binary forms, with or without modification, are permitted provided inclusion of the copyright notice, this list of conditions and the following disclaimer is provided with the distribution: Neither the name of the copyright owner nor the name of this project (MRIcron) may be used to endorse or promote products derived from this software without specific prior written permission.This software is provided by the copyright holder "as is" and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the copyright owner be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage. |