3D Slicer
Data Loading and
Visualization Tutorial
Tutorial dataset
Please download the following two datasets:
https://github.com/Slicer/SlicerDataLoadingAndVisualizationTut
orial/raw/main/VisualizationTutorial_HeadScene.mrb
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Main user interface
3D view
Slice
views
Module
panel
Data probe
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Load sample MRI data
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Load sample MRI data
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Load sample MRI data
The axial, sagittal, and
coronal views automatically
show the loaded volume
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Adjust window/level
Switch to window/level
mouse mode
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Adjust window/level
Adjust window/level
(brightness/contrast)
using the left mouse
button on a slice view
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Switch back to view/transform mode
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Maximize view
Click on the
maximize view
button
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Slice view options
Position your mouse cursor over
the pin icon to display the slice
view toolbar
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Slice view options
Once the slice
viewer toolbar is
shown, click on the
“>>”
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Show ruler
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Rotate to volume plane
Often, MRI volumes are not
axis-aligned. To show the true
axial view, click the ‘Rotate to
volume plane’ button.
Note: This image will not be
affected, but many DICOM MR
images need to be aligned.
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Switch to conventional layout
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Link views
After linking views, if any
setting is changed in a 2D
view, all others follow.
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Show slices in 3D
Now the slice views are
linked. If you click the
‘Toggle slice visibility in
3D view’ button, then all
slices will show up.
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Show slices in 3D
All three anatomical slices
are shown in the 3D view
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Navigating the 3D view
Use the left mouse button to
rotate, and the right mouse
button to zoom in and out
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Close the scene
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Part 2:
3D visualization of surface models
of the brain
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Load tutorial scene
Drag and drop the file
VisualizationTutorial_HeadScene.mrb
into Slicer, then click OK
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Center view
Click on the small box
icon to center the
view, in 3D or in 2D
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Explore loaded data
You can use the
module list, or the
favorite module
toolbar to switch to
the Data module
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Explore loaded data
The Data module shows all the data in the scene.
The data items (“nodes”) can be shown/hidden,
renamed, deleted, cloned, etc.
Hide the ‘skin’ model by clicking the eye icon.
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Foreground image
Images can be overlaid (“fused”)
by setting the foreground image.
• Select ‘T2 MRI’ as foreground
• Adjust foreground opacity
using the slider
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Create folder
Right-click the scene (or the
empty area on the bottom), then
choose ‘Create new folder’.
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Context menu actions
For list of “subject hierarchy” options for a
certain node, right-click it in the list. Note that
the options are different for each node type.
Right-click the just created folder ‘NewFolder’.
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Rename folder
Choose the Rename option and
rename the volume to ‘White matter
models’
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Select multiple nodes
Click ‘left cerebral white matter’,
hold down Shift, and click ‘left
cerebellar white matter’.
Note: You can use Control/Cmd
button to select individually.
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Move nodes to folder
Drag&drop models into the folder
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Hide all nodes in folder
Click the eye icon of the ‘Models’
folder to hide all non-brain
structures.
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Volume rendering
Click&drag volume to the 3D view.
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Display options
Right-click the eye icon to
see display options.
Choose ‘Volume rendering
options…’.
(It switches to the Volume
Rendering module)
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Adjust volume rendering
Click on ‘Select a
Preset’ and choose
MR-Default.
Adjust the Shift
slider to optimize
visualization.
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Show models again
Turn off volume rendering
using the eye icon.
Switch back to the Data
module using the
Modules history.
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Show models again
Show the folder again
by clicking the closed
eye icon in its row.
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Change skull model opacity
Right-click the eye
icon of the skull
model, select Opacity,
and adjust the slicer
to around 0.30
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Show axial slice in 3D
Hover the push-pin icon and
then the eye icon to show a
slice view in 3D view.
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Show coronal slice in 3D
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Model clipping
Right-click a model node in
the data tree and choose
‘Edit properties…’ to go to
the Models module.
(It can be accessed from the
toolbar or the module list as
well)
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Model clipping
Select all brain models using
Shift, then scroll down to the
3D Display section.
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Model clipping
Turn on Clipping.
Click Configure.
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Model clipping
Turn off Red Slice Clipping
and turn on Green Slice
Clipping.
The optic chiasm becomes
visible in the 3D view
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3D display options
Hide the coronal (green)
plane.
Position your cursor over
the pin icon in the 3D view
to display the 3D display
options. Select the A
(Anterior) view.
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Save the scene
Click the ‘Save data’ button.
Note: Also accessible from
the File menu
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Save the scene
The Save Scene and
Unsaved Data window lists
all elements of the scene.
You can save as MRB
bundle or as list of files.
Double-click the scene and
rename it to
myNewScene.mrb
Click Save.
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Close the scene
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Load your recently saved scene
Load the new scene using
the Recent data list.
(You can load the scene
using drag&drop or Add
data as well)
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Thanks for participating!
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