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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