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MRIcroGL manual
By Chris Rorden
Version 16 June 2017

1. Introduction
MRIcroGL is an intuitive viewer for medical images. This free and open source project
provides tools for 2D and 3D display of images.
MRIcroGL supports the Windows, OSX or Linux operating systems. However, it requires a
graphics card that supports volume rendering, with the appropriate driver installed.
Chris Rorden's MRIcroGL is distributed under the BSD software license. The license is as
follows: MRIcroGL, copyright 2009-2015, all rights reserved. Redistribution and use in binary forms,
with or without modification, is 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 (MRIcroGL) 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.

2. Quick start
Double-click on the MRIcroGL program to launch the application. MRIcroGL can view
NIfTI format images (these have the file extensions .hdr, .nii or .nii.gz). To view an image, simply
drag-and-drop the image onto the program. You can change between rendering and slice modes by
selecting the desired view from the “Display” menu (Figure 2.1).
Figure 2.1 An example of the mni152_2009bet image that is
distributed with MRIcroGL. On the left (back) is the 2D view,
while the right (top) panel shows the 3D rendered view.

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3. Adjusting color and transparency
Typical MRI scans and CT scans save data as a monochromatic intensity range. Crucially,
different tissue types have different image intensities. For example, bones appear bright on a CT scan
while soft tissue appears darker. Therefore, since different types of tissue have unique image
intensities, you can choose to make some tissues invisible (transparent) while revealing other types of
tissue. In addition, you can assign unique colors to specific image intensities, further helping to define
different types of material.
Figure 3.1 You can highlight different tissue using the ‘color and
transparency’ window. Both the top and bottom panels show the
abdo256 image. The top panel uses the Color/Scheme/Kidneys
command to hide the darker tissue, revealing the bones and
kidneys. In contrast, the bottom panel uses the
Color/Scheme/Muscles color mapping that shows the darker
tissue, so one cannot see beneath the muscles. Note that the top
panel has selected intensities between 114 and 302, while the lower
panel is adjusting values in the range –100..246. Within this
range the color schemes also differ in the colors used, with the top
scheme using oranges while the bottom scheme has predominantly
reds and yellows.
Note that the Color/Scheme menu allows you to select from several predefined color
schemes. For example, the top panel of Figure 3.1 shows the ‘CT_Kidneys’ color scheme, while the
lower panel shows the ‘CT_Muscles’ color scheme. However, you can also manually change the color
scheme. You can manually edit the intensity range you are interested in by adjusting the “Intensity
Minimum…Maximum” values shown in the upper left of the toolbar. For example, note that the
kidney color scheme is selecting a color range of 114..302 while the muscle color scheme includes
darker material (-100..246).
If you want to further customize the color scheme you can choose the Color/ColorEditor
menu item. A new histogram appears, as shown in Figure 3.1. Note that the color schemes are
composed of nodes. For example, the muscle color scheme has a node that makes some tissue
intensities to appear yellow. To change the color of a node, double click on the node. For example,
you could make this muscle node appear blue instead of yellow. You can also use the mouse to drag
the node to a new location. Dragging the node to the left or right will change the image intensity
selected by that node, while dragging the node up and down changes the transparency of the selected
image intensity. A sample video showing advanced usage of the colors is linked from
www.mccauslandcenter.sc.edu/mricrogl/tutorials.

4. Colorbars
An intensity colorbar is useful for recognizing the range of intensities displayed. Selecting
Color/Colorbar brings up a window that allows you to change the appearance of the colorbar. Note
that when viewing overlays, you will see one colorbar for each overlay image (e.g. see Figure 7.1).
Figure 4.1 An example of the mni152_2009 image with a colorbar visible
on the bottom. Clicking the colorbar changes its position on the screen.

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5. Clipping
As mentioned earlier, MRIcroGL can either show 3D renderings or 2D slices of an image.
However, the clipping tool allows the best of both worlds showing a 2D slice cut through a rendered
image. Further, while MRIcroGL’s 2D slices are always orthogonal planes (e.g. cut perpendicular to
the image, yielding sagittal, coronal or axial views), the clipping tool allows oblique cutting angles.
To see the clipping tool, open an image in the rendering mode (if you are in the 2D slices
mode select the Display/Render menu item). Adjust the ‘Depth’ slider to set the depth of the
clipping plane. Additional sliders allow you to specify the azimuth and elevation of the clipping plane.
Figure 5.1 An example of the mni152_2009 image with a clipping
plane applied. To see this view, drop the ‘clip.gls’ script onto
MRIcroGL.

6. Cutouts
The clipping option described in the previous section allows us to cleave off a 2D slice from
the image. The cutout option removes a 3D box from our image, allowing us to see inside. To see
the cutout tool, open an image in the rendering mode (if you are in the 2D slices mode, toggle the
View/2D menu item). There are six trackbars that adjust the position and size of the cutout. The top
two adjust the left-right position, the middle two adjust the anterior-posterior location, and the
bottom two adjust the superior-inferior dimension. A good place to start is to press the ‘nearest
sector’ button, which removes the chunk of the image facing you. This is useful, as now you can see
any changes made as you adjust the trackbars.
Figure 6.1 An example of a cutout applied to the
visible human image (from cutoutdemo2.gls).

7. Overlays
The overlay function allows you to superimpose images on top of your background image. A
common usage is to load statistical maps that show brain activity on top of anatomical scans. To add
an overlay, first open the overlay window, by choosing Overlays/AddOverlay. As shown in Figure
7.1, you can load multiple overlays and set a unique colorscheme and intensity range for each. You
can also use the Overlay/Transparency menus to control how opaque the overlays appear relative to
each other and to the background.
Figure 7.1 An example of the mni152_2009 image with the ‘motor’
statistical map loaded twice as overlays. In this example, we are showing
voxels with a brightness of more than 2 as Red and less than -3 as
Green. This is from the ‘overlay.gls’ script.

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The overlay menu has several menu commands that allow you to adjust how multiple
overlays interact with each other. You can interact with the Overlays spreadsheet in the Tool Panel to
select the color scheme and intensity. There are a couple of non-obvious commands: clicking on the
name of an overlay changes its order, so it can be either ‘above’ or ‘below’ another overlay. Shift or
right-clicking on the name makes the overlay invisible (and the name will appear in red) – shift or
right click again to show the overlay.

8. Mosaics
The mosaic function allows you to show multiple 2D slices at once. The easiest way to create
a mosaic is by using the mosaic designer form (though you can also use scripting). To see the mosaic
designer panel select the Desiplay/Mosaic menu. You can then set the number of rows and columns,
as well as the horizontal and vertical overlap. As you adjust these controls, you will see the selected
image as well as the corresponding script. You can edit the script and then press ‘Run script’ for
more control. For example, you could arbitrarily switch between axial, sagittal and coronal
orientation between rows.
Figure 8.1 A mosaic created from the
mni2009_152 image. Note that this mosaic shows
both axial and sagittal slices, and that the rows
and columns have been set to overlap a little. This
was created with the following script “A L+ H 0.300 V -0.300 0.1667 0.3333 0.5000;0.6667
0.8333 L- X S 0.5”, as described in the scripting
section.

9. GLSL Shaders
MRIcroGL uses files called shaders to generate renderings. Whenever you are in the rendering mode
(Display/Render menu item) you will see a panel named “Shader” in the tool panel. You can use the
drop-down menu in this panel to select between different shaders, and the sliders on this panel to
adjust each shader. Each shader is simply a text file in a folder called ‘shaders’ (for OSX users, you
will have to select the application and choose ‘show package contents’ to see this folder). Power users
can edit the shader text files to create unique effects. The shader minimal.txt shows how a shader can
be created with less than 50 lines of code. Here are some useful hints:
• MRIcroGL chooses the initial default shader based on alphabetically sorted filenames. So if
you prefer the ‘simple.txt’ shader to ‘default.txt’, you could simply rename it ‘basic.txt’. This
might be a good idea if you have a slow computer, as the ‘simple’ shader renders faster than
the ‘default’ one.
• Most shader text files start with a ‘pref’ section that provides the user with adjustable values.
You can easily edit these to make the default shader settings more to your liking. For
example, the default.txt shader has a preference “specular|float|0.0|0.3|1” – which means
that the user will see a slider that allows them to adjust the amount of glistening from 0 to
100%, with a starting point of 30% (the first number is the minimum, the second is the
default, the third is the maximum). If you prefer more lighting hints, you could edit the
middle number, e.g. if you prefer a matter image you would set this to
“specular|float|0.0|0.0|1”

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•
•

You can copy shader files and give each a different file name, this would allow you to set
custom preferences.
You can adjust MRIcroGL’s ini file to set default shader settings (open the ‘About
MRIcroGL’ menu item and press “Abort” to open this file): RayCastQuality1to10 allows
you to choose the quality of raycasting from 1 (fast but poor quality) to 10 (slow but
excellent quality). Changing RayCastViewCenteredLight=0 will have the lighting specified
relative to the object, not the viewer.
Figure 10.1 GLSL shaders are compact
programs that can harness the capabilities of
your graphics card. To select and tune a
shader, choose Render/Shader to view the
shader form. The drop down list at the top of
the form allows you to select from the shader
plug-ins (in this case the 'phong' shader which
provides illumination cues). Some shaders will
provide additional user adjustable settings, for
example this shader has the 'specular'
trackbar that allows the user to interactively
adjust the glint of the final image. This image
is from the shader.gls demonstration scripts.

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Individual shaders work by combining different properties of the image. The table below shows a
few popular properties.
Property Example
Notes
Volume
Brightness depends on image intensity.

Ambient
Light

Constant brightness, independent of all other factors.

Diffuse
Light

Illumination based on surface orientation with respect to light. Surfaces pointing
toward light are brighter than those facing away. (Lambertian reflection).

Specular
Light

Illumination based on reflection between light source and viewpoint. Emulates
glossy, reflective material. Includes additional adjustment ‘shininess’: mirrors have
small intense specular highlights, while duller surfaces have larger highlights

Edge
Shading

Edges parallel to viewing direction are made darker. This emphasizes edges. Only
depends on viewpoint (independent of light position).

Boundary
Opacity

Regions where image intensity is varying are made opaque, whereas regions with
consistent image intensity appear transparent. A simple way to create a ‘glass brain’
(see also edge enhancement).

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11. Overlay Shader
Recent releases of MRIcroGL include a new shaders named
‘overlay’, ‘overlay_glass’ and ‘overlay_toon’ that are specifically
designed for displaying functional or connectivity overlays on top
of anatomical scans These overlays allows you to independently set
the transparency of the background and overlay images. Note that
these shaders are much slower than the conventional shaders, and
require twice the memory on the graphics card (and typically
render half as fast). The ‘Default’ shader is also an overlay shader
(and therefore it is a lot slower than the ‘Simple’ shader). See
www.mccauslandcenter.sc.edu/mricrogl/about for more details. A
YouTube video tutorial is also available from
http://www.mccauslandcenter.sc.edu/mricrogl/tutorials

12. Atlas Templates
MRIcroGL includes several template images that show
the brain parceled into discrete regions (see section 15
for details on the provided templates). By default these
images appear in bright colors (as shown in the top
right). This can make it hard to discern overlay images.
To adjust the saturation of the template, simply adjust
the image intensity values. By default these have a range
of 100 (0..100), where the lower images on the left show
the image desaturated to 20% (0..20). If you set the
image intensity range to zero, the template will appear as
a grayscale image. Also note that clicking on any
location in the 2D slices view will reveal the region
name (in the lower left this is “PoCG_R” for ‘posterior
central gyrus of the right hemisphere’). A YouTube
video illustrating these effects is linked from
http://www.mccauslandcenter.sc.edu/mricrogl/tutorials

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13. New Features
Version 10/2011 : Thanks to Martins Upitis, David V. Smith & McKell Carter for suggestions/code
• When viewing multiple overlays, click on the overlay's filename in the overlays window to change
stacking order of overlays (Note: this feature has no influence if you have selected
Transparency/OnOtherOverlays/Additive)
• If the file /script/startup.gls exists, this script will be launched when the program starts.
• To disable this feature, edit the mricrogl.ini file and change "StartupScript=1" to read
"StartupScript=0"
• If you are having problems running MRIcroGL, launch the program with the shift key down (OSX
and Windows) or with the right mouse button depressed (Linux). You can then restore the default
settings. You will also be given the option of disabling the volume rendering (if your graphics card can
not support that feature) and enabling power-of-two upsampling (e.g. if you load an image with 192
voxels in one dimension, it will be loaded as 256 voxels, this can dramatically improve performance
on older {~2006] graphics cards, but will be slightly deleterious for newer graphics cards)
Version 7/2014 :
• Ability to display template images emulating the ‘random rainbow’ color scheme of FSLView. These
images can include text labels so that the region name is displayed when the user clicks on that
location of a 2D slice. Adjusting the ‘brightness’ of these templates influences the saturation (e.g. a
brightness range of 0..50 will have 50% of the full saturation).
• Ability to open non-NIfTI formats. Freesurfer images (MGH/MGZ format), NRRD images
(NRRD/NHDR format), AFNI (HEAD format), VTK/ITK MetaIO format (MHA/MHD). The
NRRD and MetaIO formats specify a large number of formats – this software should read most
images with at least 3 dimensions stored either uncompressed or with GZ compression.
• Overlay shader (see section 11)
• Template images (see section 12)
• Overlay window function added: File/AddOverlay(removeSmallClusters), also scripting function
overlayloadcluster (see section 15)
Version 11/2015 :
• Ability to save bitmaps to higher resolution than current display (select the ‘Preferences’ menu
command to select scaling).
• Overlay shaders improved.
• Ability to ‘Yoke’ different instances of MRIcroGL to show the same slice on different brains. Use the
‘Yoke’ command in the ‘Display’ menu. This requires running multiple instances of MRIcroGL
simultaneously (choose ‘New window’ from the ‘File’ menu).
• OSX will now show retina quality text for controls, 64-bit OSX version. Provides 3D acceleration for
modern VirtualBox installations.
• ‘Default’ shader is now an overlay shader (previous default has been renamed ‘simple’).
• ‘Occlusion’ shader.
Recent Versions
• See https://github.com/neurolabusc/MRIcroGL for recent changes

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14. Sample data
The software is distributed with sample images
• The Visible Human Project Photographed cryo-sections of a male ('visiblehuman').
• T1-weighted_MRI scan of human brain ('chris_t1' Chris Rorden).
• T2-weighted MRI scan of human brain ('chris_t2' Chris Rorden).
• Magnetic resonance angiography Time-of-flight of human head ('chris_MRA' Chris Rorden).
• Functional magnetic resonance imaging statistical maps showing regions active left versus
right hand movements (‘motor').
• X-ray computed tomography scan of human cadaver head ('ct' University of North Carolina
Volume Rendering Test Data Set).
• Average T1 scan from 152 individuals from the Montreal Neurological Institute
www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 Fonov et al. (2009)
NeuroImage 47: S102. Saved as mni152_2009bet (0.5mm isotropic). If you are working with
a large number of overlays or using a computer with a weak graphics card you may want to
reslice this to a lower resolution (e.g. use nii_reslice1mm Matlab script).
• AAL is the Automated Anatomical Labeling atlas from Tzourio-Mazoyer et al. (2002)
www.ncbi.nlm.nih.gov/pubmed/11771995
• Brodmann is Krish Singh's speculative Brodmann regions, described at
www.mccauslandcenter.sc.edu/mricro/mricro/lesion.html
• HarvardOxford-cort-maxprob is the Harvard-Oxford atlas described at
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases
• The INIA19 images are from the INIA19 Primate Brain Atlas,
www.nitrc.org/projects/inia19/ (see also PMID: 23230398)
• The natbrainlab image is a discrete version of the images from www.natbrainlab.com.

15. Scripting
New users can choose MRIcroGL’s View/Script menu item to show the scripting window,
the choose a demo script from the scripting window’s “File” menu and finally choose the Script/Run
menu item to run a script. This is a nice way to observe features. Advanced users can develop their
own macros to automate repetitive tasks or create nice demos.
Pascal is used as the scripting language. To write a script, simply select View/Scripting to
open the script engine. Type your commands into the text window and select Script/Compile to
execute your script. You can also save and open scripts using the File menu. Here is a very simple
script. It does one thing, which is to open the file named ch256.
Program Simple
Begin
LOADIMAGE('mni152_2009bet');
End.

Note that MRIcroGL is pretty intelligent. It will use files named mni152_2009bet.nii,
mni152_2009bet.nii.gz, and mni152_2009bet.hdr in the program folder and the script’s folder. If no
file is found, a dialog box allows the user to find the file. You could also be more explicit by running
“Loadimage('c:\mri\dataset.hdr')”, but this is not required.
Below is a list of all of the commands that are specific to this program, but one can also use
regular Pascal commands (like for loops, variables and constants). The included sample scripts show
some of these properties.

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SCRIPTING COMMANDS
ADDNODE(INTENSITY, R,G,B,A: byte) This command adds a new point to the color table. Consider the
default color table that has only two nodes - black is node zero and white is node one. Running
ADDNODE(192,255,0,0,64) would make images with 75% intensity (192/255) appear bright red, and be
25% opaque (64/255).
AZIMUTH (DEG: integer) This command rotates the rendering. For example, AZIMUTH(-20) rotates the
image 20 degrees counter-clockwise
AZIMUTHELEVATION (AZI, ELEV: integer). Sets the viewer location. For example,
AZIMUTHELEVATION(90,10) will show a sagittal (right side) view from a slightly inclined viewpoint.
Zero degrees azimuth refers to posterior, while 180 degress is directly anterior. Note that these values are
absolute, while the AZIMUTH and ELEVATION commands refer to relative changes in viewpoint.
BACKCOLOR (R,G,B: byte) Changes the background color, for example BACKCOLOR(255, 0, 0) will show
images on a bright red background
BMPZOOM (Z: byte) Zoom factor applied to bitmaps (Edit/Copy, File/Save and SAVEBMP). For example,
BMPZOOM = 2 will save images at twice the screen resolution.
CAMERADISTANCE (Z: single) Sets the viewing distance from the object. Values near zero will appear
inside the object (near the center of the object), values near 1 will appear at a reasonably close distance,
and larger values will make the object appear quite small.
CHANGENODE(INDEX, INTENSITY, R,G,B,A: byte) This command adjusts a point in the color table.
Consider the default color table that has only two nodes - black is node zero and white is node one.
Running CHANGENODE(1,255,255,0,0,128) would change the formerly black-to-white color table to
be black to bright red. Note that node zero can only have an intensity of zero and the final node must
have an intensity of 255.
CLIP (DEPTH: single) Creates a clip plane that hides information close to the viewer. For example, CLIP(0.5)
will hide all surfaces on the nearest half of the image.
CLIPFORMVISIBLE (VISIBLE: boolean) Shows or hides the clipping form. For example
CLIPFORMVISIBLE(TRUE) shows the form, CLIPFORMVISIBLE(FALSE) hides the form.
COLORBARCOORD (L,T,R,B: single). Sets the position of the colorbar based on the Left, Top, Right and
Bottom coordinates. The left and right coordinates are in the range 0..1 from the left to right of the
screen, while the top and bottom components range from 0 near the bottom to 1 near the top. If the
distance between L-R is greater than T-B then a horizontal colorbar will be shown, else a vertical colorbar
is displayed.
COLORBARFORMVISIBLE (VISIBLE: boolean) Shows or hides the window that allows the user to
interactively control the size and location of the colorbar. For example COLORBARFORMVISIBLE
(TRUE) shows the form, COLORBARFORMVISIBLE (FALSE) hides the form.
COLORBARTEXT (VISIBLE: boolean). If set to true, then colorbars will include text that indicates intensity
range. For example COLORBARTEXT(true).
COLORBARVISIBLE (VISIBLE: boolean). Shows a colorbar on the main images.
COLORNAME (Filename: string) Loads the requested colorscheme for the background image. For example,
running COLORNAME(CT_KIDNEY) will apply the kidney color scheme.
CONTRASTFORMVISIBLE (VISIBLE: boolean) Shows or hides the contrast and color window. For
example CONTRASTFORMVISIBLE (TRUE) shows the form, CONTRASTFORMVISIBLE (FALSE)
hides the form.
CONTRASTMINMAX (MIN,MAX: single); Sets the minumum nd maximum value for the color lookup table.
For example, consider CONTRASTMINMAX(-200,500). In this case, a voxel with the value of -200 will
be displayed with the darkest value in the color table, and voxel with a value of 500 will be shown with
the brightest value
CUTOUT (L,A,S,R,P,I: single) Selects a sector to remove from rendering view. For example
CUTOUT(0,0,0,0.5,0.5,0.5) will hide the left-anterior-superior hemiquadrant.
CUTOUTFORMVISIBLE (VISIBLE: boolean) Shows or hides the cutout window. For example
CUTOUTFORMVISIBLE (TRUE) shows the form, CUTOUTFORMVISIBLE (FALSE) hides the
form.
ELEVATION (DEG: integer) changes the render camera up or down. For example, Elevation(20) moves the
viewpoint 20-degrees above the object.
EXTRACT(LEVELS,DILATEVOX:integer; ONEOBJECT: boolean); Attempts to remove noise speckles
from dark regions (air) around object. Levels=1..5 (larger for larger surviving image), Dilate=0..12 (larger

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for larger surround). You can also specify if there is a single object or multiple objects. Default values are
5,2,true.
EXISTS(lFilename: string); Function reports whether a file exists. For example, EXISTS(‘c:\img.nii’) returns
TRUE if this file is present and false if the file is absent.
FRAMEVISIBLE (VISIBLE: boolean) Shows or hides the cube that appears around the rendered object. For
example FRAMEVISIBLE(false) will hide the frame.
LOADIMAGE (lFilename: string) Opens a NIfTI format image to view. For example,
LOADIMAGE('c:\mri\image.nii') will open the file named 'image.nii'.
MAXIMUMINTENSITY (MIP_ON: boolean) Changes the rendering mode between standard (which
highlights surfaces of objects) and Maximum Intensity Projection that shows the brightest object,
regardless of depth. For example MAXIMUMINTENSITY(false) switches to standard rendering.
MODALMESSAGE (STR: string) Displays a dialog box with a message. The script will wait until the user
responds prior to continuing.
MODELESSMESSAGE (STR: string) A text message is shown on the main window. This message requires no
response from the user, and the script does not pause for a response. The message is visible until the
script sends a MODELMESSAGE(‘’) or until the application is restarted.
MOSAIC(Str: string) Shows a series of 2D slices. For example MOSAIC(V 0.1 H 0.2 A 0.3, 0.6, 0.9; A 0.5 S 0.5
C 0.5) shows two rows of images, each with three columns - the top row shows three axial views, while
the bottom shows an axial, coronal and vertical slice. The vertical slices overlap 10% (V 0.1) and the
horizontal slices overlap 20% (H 0.2).
• A: subsequent slices in axial orientation
• C: subsequent slices in coronal orientation
• H: Horizontal overlay, e.g. H 0.5 means each slice has 50% overlap. Values can range from –1 to 1.
• L: turns on (L+) or off (L-) text labes for slices
• S: subsequent slices in sagittal orientation
• V: Vertical overlap, from –1 to 1, e.g. V 0 means no vertical overlap
• Z: mirrored sagittal slice
• Numbers are used for each slice, with semicolons denoting new rows, so 0.1 0.2 0.6; 0.8 0.9 is a
mosaic with five images, three in the first row and two in the second.
MOSAICFORMVISIBLE (VISIBLE: boolean) Shows or hides the mosaic designer window. For example
CLIPFORMVISIBLE(TRUE) shows the form, CLIPFORMVISIBLE(FALSE) hides the form.
ORTHOVIEW (X,Y,Z: single) Shows a 2D projection view of the brain, with an axial slice at the Z coordinate,
a coronal slice at the Y value, a sagittal slice at the X coordinate. For example ORTHOVIEW(0.5,0.5,0.5)
shows a slice in the middle of the volume.
ORTHOVIEWMM (X,Y,Z: single) Shows a 2D projection view of the brain, with an axial slice at the Z
coordinate, a coronal slice at the Y value, a sagittal slice at the X coordinate. For example
ORTHOVIEWMM(0, 0, 50) shows a slice 50mm superior to the anterior commissure.
OVERLAYCLOSEALL. This function has no parameters. All open overlays will be closed. The background
image (if any) will remain opened.
OVERLAYCOLORFROMZERO(FROMZERO: Boolean). If set to false, then the full color range is used to
show the overlay.If set to false, then the color range spans from zero to the most intense color. For
example, consider an overlay with a color scheme that goes from black to bright red and a
OVERLAYMINMAX(1,1,2). With colorfromzero set to false, a voxel with an intensity of 1 will appear
black (minimum in the range 1..2). On the other hand, if colorfromzero is true, then this same voxel will
appear dark red (as 1 is half way between 0 and 2). Note that in this case voxels darker than 1 will still be
invisible (as they must exceed the 1..2 threshold set by overlayminmax).
OVERLAYCOLORNAME (lOverlay: integer; lFilename: string); Set the colorscheme for the target overlay to
a specified name. For example OVERLAYCOLORNAME(1,’ CT_Kidneys’) will make the first overlay
show intermediate brightness regions as red and very bright regions as white.
OVERLAYCOLORNUMBER (lOverlay,lLUTIndex: integer) Sets the color scheme for a overlay. For
example, consider that you load a single overlay and want it to make it appear blue, you could call
OVERLAYCOLORNUMBER(1,2). The LUTindex refers to the order of the colorscheme in the overlay
menu’s drop down menu, such that 0=grayscale, 1=red, 2=blue, etc.
OVERLAYFORMVISIBLE (VISIBLE: boolean) Shows or hides the overlay window. For example
OVERLAYFORMVISIBLE (TRUE) shows the form, OVERLAYFORMVISIBLE (FALSE) hides the
form.

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OVERLAYLOAD (lFilename: string): integer; Will add the overlay named filename and return the number of
the overlay. Will return zero if unable to find the file or if there are too many overlays already loaded.
OVERLAYLOADCLUSTER (lFilename: string; lThreshold, lClusterMM3: single; lSaveToDisk: boolean):
integer; Will add the overlay named filename, only display voxels with intensity greater than threshold
with a cluster volume greater than clusterMM and return the number of the overlay.
OVERLAYLOADSMOOTH (SMOOTH: boolean) Determines whether overlays are interpolated using
trilinear interpolation (SMOOTH = true) or nearest neighbor (SMOOTH= false). Smoothed images will
not appear jagged, but a thresholded map (where values below say Z=2.3 are set to zero) may appear to
have dark edges. Note the this command does not influence currently loaded images, rather it sets how
future images will be smoothed when overlayload is called.
OVERLAYMASKEDBYBACKGROUND (MASK: BOOLEAN). If true, than a overlay will be transparent
on any voxel where the background image is transparent. If false, the overlay will always be shown,
regardless of the background image. Sometimes it is nice to mask an overlay, so for example brain activity
does not appear outside the brain. On the other hand, consider the glassbrain script, where we want to
see overlays that are inside the brain’s shell. In this case, we would want to use set this value to false.
OVERLAYMINMAX (lOverlay: integer; lMin,lMax: single) Sets the color range for the overlay. Values outside
this range but closer to zero will not be displayed, voxels with more extreme values will appear with the
maximum color from the color scheme For example OVERLAYMINMAX(1,2 9) will set the first
overlay to have an intensity range of 2..9.
OVERLAYTRANSPARENCYONBACKGROUND (lPct: integer). Controls the opacity of the overlays on
the background. For example, setting this to 50 will equally blend the overlays with the background, while
90 means that the overlays will be barely visible. Use –1 for an additive mixture (where the largest red,
green and blue components are taken from each image).
OVERLAYTRANSPARENCYONOVERLAY (lPct: integer); Controls the opacity of the overlays on other
overlays. For example, setting this to 50 will equally blend the overlays, while 90 means that the top
overlay will be barely visible against a lower overlay. Use –1 for an additive mixture (where the largest red,
green and blue components are taken from each image).
PERSPECTIVE (USEPERSPECTIVE: boolean) Toggles the usage of perspective on or off. If set on, closer
objects will appear larger than more distant objects in the rendering window. If off, an orthographic
projection is used (where size is not influenced by distance from viewer).
RESETDEFAULTS. Sets all of the user adjustable settings to their default values. Calling this at the beginning
of a script ensures that an image will always look identical, regardless of user-implemented changes.
SAVEBMP (lFilename: string) Saves the currently viewed image as a PNG format compressed bitmap image.
SCRIPTFORMVISIBLE (VISIBLE: boolean) Shows or hides the scripting window. For example
CLIPFORMVISIBLE(TRUE) shows the form, CLIPFORMVISIBLE(FALSE) hides the form.
SETCOLORTABLE (TABLENUM: integer) Changes the color scheme used to display an image. For
example, SETCOLORTABLE(0) applies the default gray-scale color scheme. To determine the color
scheme number, open the Color and Transparency Window and check the pull-down menu. For
example, the first item is the default table, so it has a value of zero, while Kidneys is the second item and
has a value of 1.
SHADERFORMVISIBLE(VISIBLE: boolean) Shows or hides the GLSL shader control window.
SHADERNAME(lFilename: string). Will load the named GLSL shader and set the shaders default variables.
For example, shadername(‘phong’) will load the ‘Phong’ shader (assuming ‘phong.txt’ is in your shader
folder).
SHADERADJUST(Property: string; Val: single). Some shaders allow the user to interactively adjust settings
(using the shader form) – this command allows you to change these settings via a script. For example,
shaderadjust('specular',1.0) would set the value specular to 1. Some shader properties are integers or floats
(both shown as trackbars), whereas others are Boolean (which are displayed as checkboxes). For Boolean
values, shaderadjust(‘name’,0) sets the value ‘name’ to false, whereas any other value
(shaderadjust(‘name’,1)) will set the property to true.
SHARPEN Applies Unsharp-mask to make background image sharper but noiser. Can be applied multiple
times for exaggerated effects.
SLICETEXT (VISIBLE: boolean) If true, the 2D slices will be displayed with text indicating which side is left
and numbers indicating slice coordinates.
VIEWAXIAL (STD: boolean) creates rendering from an axial viewpoint. VIEWAXIAL(true) shows a bird's
eye view (from directly above), while VIEWAXIAL(false) shows an image from directly below.

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VIEWCORONAL (STD: boolean) creates rendering from a coronal viewpoint. VIEWCORONAL(true)
shows a view from directly in front, while VIEWCORONAL(false) shows an image from directly behind.
VIEWSAGITTAL (STD: boolean) creates rendering from an sagittal viewpoint. VIEWAXIAL(true) shows a
profile view with the anterior dimension on the right side, while VIEWSAGITTAL(false) has the anterior
dimension on the left side.
WAIT (MSEC: integer) The program pauses for the specified duration. For example WAIT(1000) delays the
script for one second.

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mricrogl:MainPage
From NITRC Wiki

MRIcroGL user interface.

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Contents
1 Introduction
2 Requirements
3 Installation
4 Viewing images
5 Loading Overlays
6 Drawing Regions of Interest
7 Neurological versus radiological convention
8 Mosaic Views
9 Scripting
9.1 Glass Brain
9.2 Clip Plane
9.3 Cutout
9.4 Shell
9.5 Mosaic
9.6 Exploded Brain
9.7 Cluster Thresholds
9.8 Scripting from the command line and other
programs
10 Supported Formats
11 Converting Images
12 Special Images
13 New Features
14 Gallery

Introduction
MRIcroGL is medical image viewer that allows you to load overlays (e.g. statistical maps), draw
regions of interest (e.g. create lesion maps). Details can be found on the MRIcroGL home page.
MRIcroGL runs on Windows, Linux and OSX. This wiki provides some additional notes on using
MRIcroGL.

Requirements
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MRIcroGL runs on Linux, Windows, and MacOS. It requires OpenGL 2.1 (released 2006) or later. If
you have problems see the trouble shooting web page.

Installation
To install MRIcroGL download it from NITRC. If you have problems running MRIcroGL, you may
want to visit the Installation Notes and troubleshooting page. One basic hint: if you are having
trouble running MRIcroGL, try launching the program with the shift key down (or the control key if
you are using Unix). This will allow you to choose between different settings to match your
computers video card.
MRIcroGL is open source, and if you want you can download download and compile it yourself.

Viewing images

Adjusting the image contrast
and brightness can change the
appearance.

You should be able to view most medical images by dragging and
dropping the image onto MRIcroGL, or by using the File/Open
command. The software should be able to read most medical images,
including those in the following formats: NIfTI (.nii, .nii.gz, .hdr/.img),
Bio-Rad Pic (.pic), NRRD, Philips (.par/.rec), ITK MetaImage (.mhd,
.mha), AFNI (.head/.brik), Freesurfer (.mgh, .mgz), basic DICOM
(extensions vary). Since DICOM images are usually saved as 2D slices,
it is usually a good idea to convert them to NIfTI format rst, as
described in the 'Converting Images' section.

You may want to adjust the image intensity range values and the
color scheme to emphasize different tissues. For example, the image shows a high-quality CT scan
from Philips, where we can adjust the contrast to either show the scalp, the bones or the soft
tissue.
Basic tasks are shown in the basic usage and color settings videos.

Loading Overlays
After you open an image, you can add overlay images on top of the background image. To do this
you will want to choose File/Overlays which displays an overlay control window and then select
File/OpenOverlays.
For demonstrations, see the basic overlays video. For advanced usage see the overlay shaders and
the overlay glass videos.

Drawing Regions of Interest
After you open an image, you can draw regions of interest. This is useful for mapping lesions (for
analysis with vlsm or NiiStat), or for analyzing your fMRI data (for analysis with marsbar).
The basic details for drawing a region of interest are described on the MRIcroGL drawing page. In
brief you will want to do the following
1. Load an image with MRIcro

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2. Choose a 2D view of your image (use the Display menu to select sagittal, coronal, axial or
multislice views, but not the render view).
3. Choose Draw/DrawColor/Red
4. You can now drag the mouse on the image to create a lled object
5. Drag the mouse with the control key down to create an un lled object
6. Alt+click to ll a contiguous region
7. Drag with the shift key down to erase a lled region
8. Drag with the shift and control keys down to erase an un lled region
9. Alt+Shift+click to erase a contiguous region
10. Remember, you can use the arrow keys and the home/end keys to change which slice you are
viewing. This allows you to draw one slice after the other. For OSX Mac computers, the
command+left_arrow and command+right_arrow keys simulate home and end presses.
You may want to watch the drawing video.

Neurological versus radiological convention
Recent versions of MRIcroGL allow you to choose whether the 2D
axial and coronal slices are shown in neurological or radiological
convention. You can select your preference with the
Display/Radiological(FlipLR) menu item. When this is unchecked, a
left hemisphere lesion is shown on the left side of coronal and axial
slices (neurological convention). When this item is checked, a left
hemisphere lesion will appear on the right side of the screen. Note
this selection does not mirror reverse the 3D renderings. To
understand this, take a look at the gure. Neurological convention
shows coronal/axial slices with the camera posterior/superior to the
Neurolgical versus radiological
brain. Radiological view shows coronal/axial slices with the camera
convention as seen from the
anterior/inferior to the brain. Therefore, this left hemsiphere lesion
perspective of 3D rendering.
appears on the left side of the image in the neurological views, but
on the right side in the radiological views. Another way to think
about this is that neurological and radiological convention are
reversed with respect to the depth dimension (e.g. what is closer or further from the viewer). To
help you remember the convention the "L" and "R" buttons in the 2D slices panel will be either in
the order "LR" (neurological) or "RL" (radiological). Due to the brains' symmetry, left-right errors are
easy to make, so be careful with this feature. This explains why your choice of radiological versus
neurological convention does not in uence the 3D renderings. With the 3D renderings we explicitly
set the camera position with respect to the brain, and we can see the depth dimension: near
occlude more distant features.

Mosaic Views
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Choosing "Mosaic" from the "Display" menu shows the mosaic view,
where multiple slices of the same image can be seen simultaneously.
A panel named "Mosaic" appears in the tool panel, and this allows
you to interactively adjust the mosaic view with sliders, check boxes,
pulldown options and text editing. You can also create advanced
mosaics using scripting. Unlike the other views, the appearance of
mosaics may have substantially different aspect ratios when you
view them onscreen versus when you use File/Save to save an
Mosaic renderings.
image. The mosaic view is designed for generating publication
quality images, and the resolution is driven by the volume you are
viewing rather than your screen (to reduce interpolation artifacts). While you can add text labels in
this mode, for publications you probably want to generate images without labels and add labels
later using a vector-art tool that can create sharper text than is possible with bitmaps.

Scripting
Mosaic slices.

MRIcroGL can use scripts to demonstrate features and automate
laborious tasks. Scripts can be run from the graphical interface (the
View/Scripting menu item) or can be invoked from the command line (allowing other programs to
control MRIcroGL). See Github for a full listing of functions. The scripts below show the in-built
Pascal scripts, but if you prefer you can use the popular Python language.

Glass Brain
This script uses the provided example dataset from an individual
conducting a tapping task whenever they see a visual stimulus. We
expect to see the contralesional motor cortex, supplementary motor
area and visual cortices active during the task. We overlay this on a
standard brain. This script demonstrates the ‘overlay_glass’ shader
released in 2014 that allows you to independently control the
transparency of the background and overlay images. For a tutorial on
using this see the demonstration YouTube video.
A script showing glass brain
projection.

To reproduce this script choose View/Scripting and then insert the
following code. When you are done choose Script/Run.
BEGIN
LOADIMAGE('mni152_2009bet');
OVERLAYLOADSMOOTH(true);
OVERLAYLOAD('motor');
OVERLAYMINMAX(1, 2.5, 2.5);
BACKCOLOR(255, 255,255);
SHADERNAME('overlay_glass');
SHADERADJUST('edgeThresh', 0.6);
SHADERADJUST('edgeBoundMix', 0.72);
END.

Clip Plane

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This script demonstrates the ‘overlay’ shader released in 2014 that
allows you to independently control the transparency of the
background and overlay images. This shader allows you to decide
whether the clipping is only applied to the background (as shown) or
to both the background and overlay images. You can also watch the
overlay shader demonstration video on YouTube for hints on how to
use this shader.
BEGIN
LOADIMAGE('mni152_2009bet');
OVERLAYLOADSMOOTH(true);
OVERLAYLOAD('motor');
OVERLAYMINMAX(1, 2.6, 2.6);
BACKCOLOR(255, 255,255);
SHADERNAME('overlay');
CLIPAZIMUTHELEVATION(0.4, 0, 120);

A script showing a clip plane.

END.

Cutout
This script demonstrates the ability to generate cutouts. Note that I
load the statistical map ‘motor’ twice – once to show the regions
more active when the left versus right hand was active and once to
show the regions that were more active for movements of the right
versus left hand (this was a [1 -1] t-test).
BEGIN
LOADIMAGE('mni152_2009bet');
BACKCOLOR(128, 169, 255);
OVERLAYLOADSMOOTH(true);
OVERLAYLOAD('motor');
OVERLAYMINMAX(1, -4, -4);
OVERLAYLOAD('motor');
OVERLAYMINMAX(2, 4, 4);
CUTOUT(0.0, 0.45, 0.5, 0.75, 1.0, 1.0);
SHADERNAME('overlay');

A script showing a cutout.

END.

Shell
This script emphasizes the tissue surfaces (regions with strong gradient
magnitude where bright voxels are near darker voxels). This hides regions
where the image brightness is not changing, resulting in the cortex and
ventricles appearing as thin shells with a hollow interior.
BEGIN
LOADIMAGE('mni152_2009bet');
OVERLAYLOADSMOOTH(true);
OVERLAYLOAD('motor');
BACKCOLOR(255, 255, 255);
OVERLAYMINMAX(1, 2, 2);
SHADERNAME('overlay_shell');
SHADERADJUST('colorTemp', 0.0);
CLIPAZIMUTHELEVATION(0.35, 0, 140);

A script showing a shell effect.

END.

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Mosaic
This is a way to create a 3D mosaic with any shader. I prefer the ‘exploded
brain’ method as it is simpler to use interactively and you are not restricted to
orthogonal slices. See the exploded brain script for common notes. You can
show either the left or right hemisphere by setting AZIMUTHELEVATION(130,
15) or AZIMUTHELEVATION(230, 15).
A script showing merged slabs.

CONST
kSegments = 5;
VAR
i: integer;
start, thick: single;
BEGIN
thick := 1/kSegments;
RESETDEFAULTS;
COLORBARVISIBLE(false);
BACKCOLOR(255, 255, 255);
LOADIMAGE('mni152_2009bet');
OVERLAYLOAD('motor');
OVERLAYMINMAX(1, -2, -2);
AZIMUTHELEVATION(130, 15);
FOR i := 1 TO kSegments DO BEGIN
start := (i-1)*thick;
CLIPAZIMUTHELEVATION(start, 0, 180);
CUTOUT(0.0, 0.0, 0.0, 1.0, 1.0-start-thick, 1.0);
SAVEBMP('sector'+inttostr(i));
END;
END.

Exploded Brain

A script showing the exploded
brain effect.

The script generates a series of bitmaps that you can weld together to create a
nice image. Unlike the ’3D Mosaic’, this requires the ‘Overlay’ shader which has
a slider named ‘clipThick’ that allows us to adjust the thickness of the clip
plane slab. You can also press the ‘overClip’ check-box to select whether the
overlay sticks out of the slice (or for a script use ‘SHADERADJUST(‘overClip’, 1)’
and ‘SHADERADJUST(‘overClip’, 0)’). The critical value is ‘kSegments’ – here I
generate 12 slabs, you can adjust this for thinner or thicker slices. This script
will generate a series of bitmaps that you stack together using your favorite
image editor (Photoshop, Acorn, Pixelmator, etc). The trick is to feather the
edges between each image (these programs usually include a ‘magic wand’
that allows you to make regions transparent).

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CONST
kSegments = 12;
VAR
i: integer;
start, thick: single;
BEGIN
thick := 1/kSegments;
RESETDEFAULTS;
COLORBARVISIBLE(false);
BACKCOLOR(255, 255, 255);
LOADIMAGE('mni152_2009bet');
OVERLAYLOAD('motor');
OVERLAYMINMAX(1, -4, -4);
SHADERNAME('overlay');
SHADERADJUST('specular', 0.3);
SHADERADJUST('overAlpha', 0.6);
SHADERADJUST('clipThick', thick * 0.75);
AZIMUTHELEVATION(255, 25);
FOR i := 1 TO kSegments DO BEGIN
CLIPAZIMUTHELEVATION(0.001+((i-1)*thick), 0, 180);
SAVEBMP('sector'+inttostr(i));
END;
END.

Cluster Thresholds
The statistical maps generated by tools like SPM and FSL can either
be unthresholded (green top left image) or thresholded (green
bottom left). Since we typically reslice these low resolution images
A script showing a shell effect.
to map onto higher resolution images it is generally a good idea to
use the unthresholded image: the thresholded image is arti cially
surrounded by bogus values so we can not interpolate the
boundaries easily. The Overlays/Option/SmoothWhenLoading menu allows you to choose your
interpolation method. If this option is unchecked, nearest neighbor interpolation is used and you
image will appear jagged (left glass brain) – this is most appropriate if your data was previously
thresholded. However, MRIcroGL has commands to remove these small clusters (right image). If the
SmoothWhenLoading item is checked, the image will be smoothed with a trilinear lter – this looks
very nice (middle glass brain) and is typically appropriate if your raw data was not previously
thresholded. However, closer inspection of these reveals that a few tiny clusters appear. If your
original analysis used a cluster threshold, you will want to use the overlay windows’
File/AddOverlay(RemoveSmallClusters) option. This will remove any clusters smaller than the
speci ed size. You can also achieve this by calling the ‘overlayloadcluster’ function from a script.
You will supply the overlay name, the brightness threshold, and the minimum cluster size (in
mm^3), and select whether you also want this thresholded overlay saved to disk (true or false).
Note that the cluster size is speci ed in volume not voxels: if you estimated a random eld theory
familywise error corrected threshold for clusters of at least 32 voxels with data that was 3mm
isotropic (3x3x3 = 27mm^3 per voxel) then you would specify 864mm^3. In the example below we
preserve voxels that exceed a brightness of 2.0, are part of clusters of at least 1cc (1000mm^3) and
choose not to save the resliced image to disk.
BEGIN
LOADIMAGE('mni152_2009bet');
OVERLAYLOADCLUSTER('motor', 2, 1000, false);
SHADERNAME('overlay_glass');
END.
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Scripting from the command line and other programs
You can also call scripts from the command line or other programs, including those you create in
Python and Matlab. MRIcroGL's scripting is similar to that of Surf Ice, so you may want to look at the
Surf Ice wiki. Here is a simple example:
/Users/rorden/Documents/osx/MRIcroGL.app/Contents/MacOS/MRIcroGL -S "begin LOADIMAGE('ct.nii.gz'); end."

Supported Formats
MRIcroGL's native format is NIfTI. However, it can also read images stored in other formats. Not all
features of these formats may be supported, so use with caution:
AFNI format (.head/.brik)
Analyze format (predecessor to NIfTI, .hdr/.img les)
BioRad PIC format (.pic)
Blender voxel format (.bvox)
BrainVoyager (.vmr/.v16)
DeltaVision (.dv)
DICOM - simple drag and drop display or conversion to NIfTI (see below).
ECAT (.v)
Guys Image Processing Lab (.gipl)
ITK format (.mha, .mhd)
MGH format (.mgh, .mgz)
MRtrix format n.b. currently only saves images saved as axial slices (.mif, .mih)
NRRD format (.nrrd, .nhdr)
Some tagged image le format variations (.tif, .tiff, .lsm)
VTK legacy format (.vtk)

Converting Images
Use the Import menu item to start dcm2nii. A new window appears, and you can set up your
preferences by adjusting the values in the dcm2nii window toolbar. You then drag-and-drop the
folder containing you DICOM images onto the dcm2nii window (note: if you drag the DICOM images
onto the main MRIcroGL window you will view rather than convert the image). For more details see
the dcm2nii wiki.

Special Images
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MRIcroGL includes a few NIfTI format images to illustrate the software. Here are some additional
images that are available for download.
Philips CT scan (60mb). MRIcroGL comes with a low resolution version of this image
(198x231x256 voxels) to support a wider range of graphics cards. The version linked here is
at native resolution and is 384x448x539 voxels. This image provided by Philips Medical and
distributed with permission. The DICOM images for this scan are also available.
mni152_2009ns (34mb). MRIcroGL includes copies of of the mni152_2009 atlas. While this
atlas was based on non-linear deformations, it retains the overall size and shape of the
original MNI/ICBM 152 template. That template is used for normalization by many tools.
However, the MNI template is actually larger than the average brain. In contrast, SPM12's
segmentation/normalization generates brains that are roughly aligned but are more typically
sized. Therefore, the SPM New Segment ('ns') image here is more appropriate if you use SPM's
normalization (though the differences are subtle).

New Features
If you have used MRIcroGL before, but have updated to the latest version you may want to brie y
nd out what new functions have been added.
1. The MRIcroGL download includes a PDF le named "manual.pdf" - section 13 of the manual is
named "New Features" and it describes changes and improvements to the software.
2. The latest/upcoming features are described on the beta page.

Gallery

Photographs

CT

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primate atlas

mouse

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Gift

Stag beetle

Daisy pollen

Jet

Overlays

[1]

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MNI Template

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