Slicer Training 1
Loading and Viewing Data
Sonia Pujol, Ph.D.
Randy Gollub, M.D., Ph.D.
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Acknowledgments
National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218
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Disclaimer
It is the responsibility of the user of 3DSlicer
to comply with both the terms of the license
and with the applicable laws, regulations
and rules.
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Welcome to 3D Slicer
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Goal of the tutorial
Guiding you step
by step through
the process of
Loading and
Viewing Data
within Slicer
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Material
• Slicer 2.6
http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started
• Sample Tutorial Data: tutorial-with-dicom.zip
http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
Exercises
Questions
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Answers
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Goal of the tutorial
Final result
of the series
of exercises
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Overview
• Part 1: Slicer Interface
• Part 2: Loading Data
• Part 3: Interacting with Data
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Slicer Interface
Menu
Viewer
Tk
window
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Slicer Menu
Select the Volumes
Module
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Panels and Tabs
The Panel of the
Volumes Module
appears
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Slicer Menu
Panels
Sliders
Buttons
Control
Window
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Main Menu
Observe the different options of the Main Menu
•File
–Opening files
–Saving files
–Closing files
–Exit
•View
Selecting view mode
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•Modules
Slicer Modules
•Help
Links to Slicer
Modules information
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Viewer window
Observe the Viewer Window
• Upper part is
3D Viewer
• Lower part is 2D Viewer
3 separate views
Independent controls
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Slicer Modules
The architecture of
Slicer is modular
Select Modules in
the SubMenu
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Slicer Modules
Settings
IO
Application
Filtering
Segmentation
Registration
Measurement
The list of Slicer
Modules categories
appears
Visualization
Examples
Unfiled
Alpha
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Slicer Modules: tutorials
Settings
IO
•fMRIEngine ………. SlicerTraining 5
Application
•vtkFreeSurferReaders ... SlicerTraining 6
Filtering
Segmentation
•Editor …………….. SlicerTraining 2
Registration
•Level-Sets ……….. SlicerTraining 3
Measurement
Visualization
•DTMRI ……………. SlicerTraining 4
Examples
Unfiled
Alpha
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Exercise 1: Slicer GUI
• Launch Slicer.
– Observe Main window and Viewer window.
• Click File, View, Help, and Modules
– Examine submenus
• Click Main Menu buttons: Data, Volumes,
Models, Alignments, Editor, and
ModelMaker
– Click tabs
– Examine panels
• Click More
– Click modules: click tabs, examine panels
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Overview
• Part 1: Slicer Interface
• Part 2: Loading Data
• Part 3: Interacting with Data
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Loading Data
Slicer can load
• Volumes …………………..
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Loading Data
Slicer can load
• Volumes …………………..
• Models …………………….
A model is a 3D reconstruction of the anatomy
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Loading Data
Slicer can load
• Volumes …………………..
• Models …………………….
A model is a 3D reconstruction of the anatomy
• Scenes …………………….
Scene = Volume + Model
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Loading Data
Slicer Advantage
Putting together
Images and Surface
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Data representation
Header
Header
Header
Header
Raw Data
Raw Data
Raw Data
Raw Data
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• Volume = collection of image files
• Image file = header + raw data
The header contains the parameters of the image.
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Data representation
Header
Header
Header
Header
Raw Data
Raw Data
Raw Data
Raw Data
a
The header contains the parameters of the image.
Pixel (a,b)
b
Intensity
I (a,b)
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• Volume = collection of image files
• Image file = header + raw data
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• Representation of an image:
2D Array of pixels containing the
intensity values
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Loading DICOM Volumes
Click on Add Volume in
the Slicer Menu
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Loading DICOM Volumes
The Panel Props
appears by default.
Left-click on the Menu
Properties and change Basic
to DICOM
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Loading DICOM Volumes
The DICOM panel appears
Click on Select DICOM Volume
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Loading DICOM Volumes
Select the directory dicom in
the Tutorial-with-dicom dataset
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Loading DICOM Volumes
The list of DICOM
studies appears.
Click OK
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Loading DICOM Volumes
Slicer loads the dicom study
Name : The name that the
volume will have within Slicer
Change to something
descriptive: Cortex and
click on Header
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Loading DICOM Volumes
The DICOM Header
information panel appears
Click Apply
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Loading DICOM Volumes
Slicer loads the
DICOM volume of
the brain
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Visualization Support
• Control Window: displays a zoomed view of
the position of the mouse on the selected image
Move the mouse inside
an anatomical view
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Visualization Support
The value of the gray
level of the pixel
under the cursor
appears in the
corresponding slice
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Viewing Volumes
V toggle button controls
whether slice is
visible in 3D Viewer
Click on the three V
buttons to display the
Axial, Sagittal and
Coronal images
inside the Viewer
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Viewing Volumes
The Axial, Sagittal
and Coronal Images
appear in the Viewer
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Manipulating the images
• Rotation
Position the mouse
on the images inside
the Viewer
Left-click and move
the mouse to the left
The images move
to the left
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Manipulating the images
• Zoom
Position the mouse
on the images inside
the Viewer
Right-click and move
the mouse down
The viewer gets
closer to the model
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Manipulating the images
• Zoom
Position the mouse
on the images inside
the Viewer
Right-click and move
the mouse up
The viewer moves
away from the model
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Viewing Volumes
The View Menu contains
different options to visualize
the data
Select the 3D View
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Viewing Volumes
3D View
focuses on 3D
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Viewing Volumes
The View Menu contains
different options to visualize
the data
Select 4x512
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Viewing Volumes
4x512 view:
larger image
views to see
details
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Viewing Volumes
The View Menu contains
different options to visualize
the data
Select 1x512
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Viewing Volumes
1x512:
one large TRANSVERSE
view and three small
images
1x512 COR:
one large CORONAL view
and three small images
1x512 SAG:
one large SAGITTAL view
and three small images
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Viewing Volumes
The View Menu contains
different options to visualize
the data
Select 4x256
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Viewing Volumes
4x256 view:
smaller equalsized images
Come back to
Normal View
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2D Viewer
2
3
1
1• Three 2D windows (red, yellow, and green)
2• Slider selects which slice of volume to display
3• Field shows the slice number
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2D Viewer
4
5
4• Bg (Background): displays volume in background layer
5• Fg (Foreground): displays volume in foreground layer
Superimposed over the background layer
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Volumes without Header
Motivations:
• The DICOM file format incorporates all
the parameters that Slicer requires to
render the data
• Other images files types may not
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Volumes without Header
Motivations:
• The DICOM file format incorporates all
the parameters that Slicer requires to
render the data
• Other images files types may not
Slicer has a simple protocol for
loading volumes without header
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Volumes without Header
1. Main  Data
2. Add Volume
3. Browse to find the
first image of the
Volume spgr in the
directory tutorial
4. Select first image I.001
of volume to load, and
click Open
5. Click on Manual
6. Click on Apply
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Volumes without Header
The Header section of
the Props tab appears.
1 File Pattern: Pattern
of file names, in C syntax.
Example: a file named
skin.001 has a pattern of
%s.%03d.
2 Image Size: Number of
pixels of image in x and y
directions.
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Volumes without Header
3
4
6
3
5
7
Pixel Size in the x and y
directions.
4 Slice Thickness z dimension
of the voxel.
5 Scan Order:
• LR = left to right
• IS = inferior to superior
• PA = posterior to anterior
6 Scalar Type:
Data format of the pixel.
Generally, it is Short (16 bit integer).
7 Slice Tilt:
The tilt of the gantry during an MRI.
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Volumes without Header
8 Num Scalars:
Number of scalar components for
each voxel. Gray-scale data: 1.
Color data: 3.
9 Little Endian:
8
9
10
Click Apply to load
the volume.
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In little-endian architectures, the
rightmost bytes are most
significant. In big-endian
architectures (Slicer default), the
leftmost bytes (those with a lower
address) are most significant.
10 DTI data, Swap, No Swap:
Placeholders for future.
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Volumes without Header
The spgr volume
appears in the
Viewer
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Loading Data
Slicer can load
• Volumes …………………..
• Models …………………….
A model is a 3D reconstruction of the anatomy
• Scenes …………………….
Scene = Volume + Model
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Loading Models
In the main Menu select the
module Data and Click on
Add Model.
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Loading Models
The Props tab of the module
Models appears
Select the model named
Vessels in the directory
tutorial/models
Click on Apply
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Loading Models
The model of the
vessels appears in
the Viewer.
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Loading Data
Slicer can load
• Volumes …………………..
• Models …………………….
A model is a 3D reconstruction of the anatomy
• Scenes …………………….
Scene = Volume + Model
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Loading a Scene
A Scene is represented as an Xml file.
•Select File  Open Scene
in the Main Menu
•Select the file tutorial.xml in the directory
Tutorial-with-dicom/tutorial.
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Loading a Scene
The viewer
displays the
tutorial Scene
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Loading a Scene
The elements of the Scene are
listed in the Menu Window
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Overview
• Part 1: Slicer Interface
• Part 2: Loading Data
• Part 3: Interacting with Data
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Manipulating a Model
The model appears in the
3D Viewer.
•Rotate the model: with left
mouse button
•Zoom the model: with right
mouse button
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Manipulating a Model
Put the mouse on
the 3D Slicer icon
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Manipulating a Model
The Control Window
appears
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Manipulating a Model
Position the mouse
on the R letter
(Right) inside the
window
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Manipulating a Model
The View Panel
shows the model
from the right side of
the patient
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Manipulating a Model
Click on the Spin
button
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Manipulating a Model
The model starts
spinning inside the
Viewer Panel.
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Manipulating a Model
Click on the Rock
button
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Manipulating a Model
The model starts
rocking inside the
Viewer Panel.
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Manipulating a Model
Come back to initial
orientation of the
Viewer Panel by
clicking on the A letter
(Anterior) inside the
window.
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Models representation
A model is a 3D representation
of the anatomy.
Type W (Wireframe) in
the Main Window
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Models representation
The triangles of the Model
become visible in the Viewer.
Type S (Surface) to come back
to Surface Mode rendering
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Model Opacity
1. Click on Models in the
Main Menu
2. Select the Display Tab
The properties Panel of
the model appears
3. Opacity
Set the opacity of the
Skin model to 0.5
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Model Opacity
Skin model
Opacity = 0.5
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Model Visibility
Visibility on and off by
left clicking on the name of
model in the list
Left Click on the Vessels
button in the list of models
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Model Visibility
Vessels model
Visibility 0ff
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Global Visibility
Show All to display all
models in the 3D Viewer.
Click Show None to display
none of the models in the 3D
Viewer
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Viewing 3D Models
Show None:
the models have
disappeared
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2D Viewer
Lb: displays label map
Displays results of a segmentation
Left click on Lb in the Axial View and select
the Label Map named None
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2D Viewer
Lb: displays label map
Displays results of a segmentation
The segmented volume named all disappears
from the 2D Viewer.
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2D Viewer
Lb: displays label map
Displays results of a segmentation
Left click on Lb in the Axial View and select
the Label Map named all.
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2D Viewer
Lb: displays label map
Displays results of a segmentation
The segmented volume named all appears in the
2D Viewer.
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2D Viewer
Images in the label map layer appear as
outlines around the structures that were
segmented.
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2D Viewer
Left Click on Fg in the Axial View and select
the Volume named all in the Axial,
Sagittal and Coronal slices.
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Image Fusion
•Fade slider:
fades between foreground
and background.
Set the Fade slider to 0.5
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2D Viewer
The volume all is
superimposed on the
images
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Clipping Models
• Clipping: cutting away sections of a
model at one or more selected slices.
• The model is removed from one side of
each selected slice, revealing the image
of each selected slice and the rest of
the visible model.
Select the Models  Display tab
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Clipping Models
1. Click on Show all to make
all the models visible
2. Right-click the Skin model
in the list
A drop-down menu appears.
3. Check that the Clipping
option is selected.
4. Set the opacity of the Skin
model to 1.0.
5. Select the Clip tab of the
Models panel.
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Clipping Models
Click + or - to select which side of
each slice to clip on.
Set the sides to:
Red Slice +
Yellow Slice Green Slice -
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Clipping Models
Clipping
Model
Result
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Conclusion
• Intuitive Interface for Loading and
Visualizing Data
• Slicer Outcome = fusion of Volumes
and Surface
• Open-source tool for developing
your own module
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