Beauchamp:MedNSLab

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#A Windows Explorer window should open showing the "mricron" file folder. Drag the folder to your desktop (or any other convenient location).
#A Windows Explorer window should open showing the "mricron" file folder. Drag the folder to your desktop (or any other convenient location).
#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).
#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).
-
 
+
#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.
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.
[[Image:mricron pc.jpg|thumb|none|Windows MRIcroN window]]
[[Image:mricron pc.jpg|thumb|none|Windows MRIcroN window]]
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#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.  
#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.  
#To start the program, double click on the mricron.app file or the small brain icon.  
#To start the program, double click on the mricron.app file or the small brain icon.  
-
You should see the following window. To make the images easier to see, you can enlarge the window.
+
# 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.
[[Image:mricron mac.jpg|thumb|none|Macintosh MRIcroN window]]
[[Image:mricron mac.jpg|thumb|none|Macintosh MRIcroN window]]
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<b>Name of  structure    /  Coordinates of structure (enter into x,y,z boxes in MriCron) </b>
<b>Name of  structure    /  Coordinates of structure (enter into x,y,z boxes in MriCron) </b>
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+
{| {{table}}
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+
| Structure Name||x||y||z
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Central Sulcus   57  98  129 
+
|-
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(omega sign, indicating location of hand region of primary motor cortex)
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| Central Sulcus (omega sign)||56||95||129
-
 
+
|-
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Supplementary Motor Area    95 135  122
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| Lateral Sulcus aka Sylvian Fissure||27||110||82
-
 
+
|-
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Lateral Sulcus   27 110 82
+
| Caudate ||104||136||83
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(aka Sylvian Fissure)
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|-
-
 
+
| Putamen||116||136||72
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Caudate 104 136 83
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|-
-
 
+
| Globus Pallidus ||109||128||72
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Putamen 116 136 72
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|-
-
 
+
| Thalamus ||102||121||81
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Globus Pallidus 109 128 72
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|-
-
 
+
| Midbrain (inferior colliculus) ||96||94||62
-
Thalamus (anterior nucleus) 102 121 81
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|-
-
 
+
| Crus Cerebri ||109||115||61
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Midbrain (superior colliculus) 96 94 62
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|-
-
 
+
| Red Nucleus ||97||108||64
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Crus Cerebri 109 115 61
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|-
-
 
+
| Substantia Nigra ||102||114||59
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Red Nucleus 97 108 64
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|-
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+
| Cerebral Aqueduct ||91||97||62
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Substantia Nigra 103 108 61
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|-
-
 
+
| Internal Capsule, anterior limb ||110||140||78
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Cerebral Aqueduct 91 97 62
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|-
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+
| Internal Capsule, posterior limb ||114||115||74
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Internal Capsule, anterior limb 110 140 78
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|-
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| Cerebellum Dentate nucleus ||103||70||43
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Internal Capsule, posterior limb 115 115 77
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|-
-
 
+
|
-
 
+
|-
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Cerebellum
+
|
-
+
|}
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Dentate nucleus 104 68 43
+
   this table was created with the converter at http://excel2wiki.net/index.php
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+
<h4>Structures in lab 11</h4>
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Vermis                        92  86   53               
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-
<h4>OPTIONAL  Structures in lab 11</h4>
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<b>Limbic System</b>
<b>Limbic System</b>
 +
{| {{table}}
 +
| align="center" style="background:#f0f0f0;"|'''Structure Name'''
 +
| align="center" style="background:#f0f0f0;"|'''x'''
 +
| align="center" style="background:#f0f0f0;"|'''y'''
 +
| align="center" style="background:#f0f0f0;"|'''z'''
 +
|-
 +
| Limbic System ||||||
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|-
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| Amygdala ||117||127||54
 +
|-
 +
| Anterior Commissure||92||131||67
 +
|-
 +
| Cingulate Gyrus ||94||114||113
 +
|-
 +
| Fornix (body) ||92||123||85
 +
|-
 +
| Fornix (column) ||92||130||70
 +
|-
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| Hippocampus ||126||111||54
 +
|-
 +
| Hypothalamus ||||||
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|-
 +
| 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
 +
|-
 +
|
 +
|}
-
Cingulate Gyrus  97  114    111
 
-
 
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Amygdala        117  127    154
 
-
 
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Hippocampus      117  111    48
 
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Lateral Ventricle 126  89  67
 
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(temporal horn)
 
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Fornix (body)      92  123  85
 
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Fornix (column)    92  130  70
 
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<b>Hypothalamus Landmarks</b>
 
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Lamina Terminalis  91  141  57
 
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Anterior Commissure  92  131  67
 
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Optic Chiasm  93  137  50
 
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Infundibulum  93  132  47
 
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Mamillary Body  93  121  58
 
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Hypothalamus Proper  88  126  59 
 
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-
Pituitary  93  134  42
 
<h5>Teaching Aid: Colored Overlay to show different anatomical regions</h5>
<h5>Teaching Aid: Colored Overlay to show different anatomical regions</h5>

Current revision

Brain picture
Beauchamp Lab


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.

Contents

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.

Windows MRIcroN window
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.

Macintosh MRIcroN window
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 Namexyz
Central Sulcus (omega sign)5695129
Lateral Sulcus aka Sylvian Fissure2711082
Caudate 10413683
Putamen11613672
Globus Pallidus 10912872
Thalamus 10212181
Midbrain (inferior colliculus) 969462
Crus Cerebri 10911561
Red Nucleus 9710864
Substantia Nigra 10211459
Cerebral Aqueduct 919762
Internal Capsule, anterior limb 11014078
Internal Capsule, posterior limb 11411574
Cerebellum Dentate nucleus 1037043
 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 11712754
Anterior Commissure9213167
Cingulate Gyrus 94114113
Fornix (body) 9212385
Fornix (column) 9213070
Hippocampus 12611154
Hypothalamus
Hypothalamus Proper8812659
Infundibulum 9313247
Lamina Terminalis 9114157
Lateral Ventricle (temporal horn)1268967
Mamillary Body 9412158
Optic Chiasm 9313750
Pituitary 9313442


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%.
MRIcroN with anatomical labels
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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