Beauchamp:MedNSLab

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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.

REQUIRED Step 1: Download MRIcroN (free 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.

  1. Click on this link:media:Beauchamp_MRIcron_windows.zip‎
  2. Internet Explorer will ask you "What to do you want to do with the file?", click Open
  3. A Windows Explorer window should open showing the "mricron" file folder. Drag the folder to your desktop (or any other convenient location).
  4. Find the "mricron" file folder on your desktop (or wherever you have dragged it to) and double-click on it to open. Then, double click on the mricron program icon (looks like a small colored brain).
  5. The dataset name is listed at the top of the MRIcroN window in Windows. The correct brain to view is the "ch2" file (ch2.nii.gz). Load this file by selecting "File/Open/Templates/ch2.nii.gz".

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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Windows MRIcroN window

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.

  1. Click on this link:media:BeauchampMacMRIcron.zip‎
  2. The file should download and be expanded into a directory, most likely in your "Downloads" folder. A new folder called "BeauchampMacMRIcron" will be created. Open the folder; you should see the file mricron.app next to a small brain icon.
  3. To start the program, double click on the mricron.app file or the small brain icon.
  4. The dataset name is listed at the bottom of the window for Mac. The correct brain to view is the "ch2" file (ch2.nii.gz). Load this file by selecting "File/Open/Templates/ch2.nii.gz".

You should see the following window. To make the images easier to see, you can enlarge the window. To see only one plane enlarged, click View/Axial Only.

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Macintosh MRIcroN window

For Linux (or if the above instructions don't work): please go to http://www.mccauslandcenter.sc.edu/mricro/mricron/install.html You are on your own for installation!

REQUIRED Step 2: Explore the brain and learn structures found in labs 8 and 9

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. The dataset name is listed at the top of the MRIcroN window in Windows, at the bottom of the window for Mac. The correct brain to view is the "ch2" file (ch2.nii.gz). Load this file by selecting "File/Open/Templates/ch2.nii.gz". At the top of the program window are three boxes labelled "x", "y" and "z" that show the brain location. Enter each of the co-ordinates (x,y,z) listed below into MRIcron. This will take you to the structure whose name is on the first column. This material will make up part of the testing materials for these laboratories (lab exams).

Name of structure / Coordinates of structure (enter into x,y,z boxes in MriCron)

Structure Name x y z
Central Sulcus (omega sign) 56 95 129
Lateral Sulcus aka Sylvian Fissure 27 110 82
Caudate 104 136 83
Putamen 116 136 72
Globus Pallidus 109 128 72
Thalamus 102 121 81
Midbrain (inferior colliculus) 96 94 62
Crus Cerebri 109 115 61
Red Nucleus 97 108 64
Substantia Nigra 102 114 59
Cerebral Aqueduct 91 97 62
Internal Capsule, anterior limb 110 140 78
Internal Capsule, posterior limb 114 115 74
Cerebellum Dentate nucleus 103 70 43 
 this table was created with the converter at http://excel2wiki.net/index.php

Structures in lab 11

Limbic System

Structure Name x y z
Limbic System
Amygdala 117 127 54
Anterior Commissure 92 131 67
Cingulate Gyrus 94 114 113
Fornix (body) 92 123 85
Fornix (column) 92 130 70
Hippocampus 126 111 54
Hypothalamus
Hypothalamus Proper 88 126 59
Infundibulum 93 132 47
Lamina Terminalis 91 141 57
Lateral Ventricle (temporal horn) 126 89 67
Mamillary Body 94 121 58
Optic Chiasm 93 137 50
Pituitary 93 134 42


Teaching Aid: Colored Overlay to show different anatomical regions

While the above co-ordinates show examples of single locations and their label, it can also be nice to see the complete extent of an area. This can be done as follows:

  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%.
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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.

OPTIONAL 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. 

 for more information on MRI imaging priniciples, see http://spinwarp.ucsd.edu/NeuroWeb/Text/br-100.htm

OPTIONAL 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. SpineMRI.zip Archive file containing 12 different spine MRI datasets, all from a single subject.

OPTIONAL 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.

  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).


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.

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