Download - Data Loading and Visualization-3735
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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 ComputingNIH 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
Questions Answers
Exercises
• Slicer 2.6http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started
• Sample Tutorial Data: tutorial-with-dicom.ziphttp://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
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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
Tk window
Viewer
Menu
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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 MenuObserve the different options of the Main Menu
•ViewSelecting view mode
•ModulesSlicer Modules
•File–Opening files–Saving files–Closing files–Exit
•HelpLinks to Slicer Modules information
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Viewer window
• Upper part is
3D Viewer
• Lower part is 2D Viewer3 separate views
Independent controls
Observe the Viewer Window
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Slicer Modules
The architecture of Slicer is modular
Select Modules in the SubMenu
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Slicer Modules
The list of Slicer Modules categories appears
Settings
IO
Application
Filtering
Segmentation
Registration
Measurement
Visualization
Examples
Unfiled
Alpha
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Slicer Modules: tutorialsSettings
IO
Application
Filtering
Segmentation
Registration
Measurement
Visualization
Examples
Unfiled
Alpha
•Editor …………….. SlicerTraining 2
•Level-Sets ……….. SlicerTraining 3
•fMRIEngine ………. SlicerTraining 5
•vtkFreeSurferReaders ... SlicerTraining 6
•DTMRI ……………. SlicerTraining 4
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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
• Volume = collection of image files• Image file = header + raw dataThe header contains the parameters of the image.
Header
Raw Data
Header
Raw Data
Header
Raw Data
Header
Raw Data
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Data representation
• Volume = collection of image files• Image file = header + raw dataThe header contains the parameters of the image.
• Representation of an image:
2D Array of pixels containing the intensity values
Header
Raw Data
Header
Raw Data
Header
Raw Data
Header
Raw Data
Pixel (a,b)
Intensity
I (a,b)
a
b
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Loading DICOM Volumes
Click on Add Volume in the Slicer Menu
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Left-click on the Menu
Properties and change Basicto DICOM
Loading DICOM Volumes
The Panel Propsappears by default.
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Click on Select DICOM Volume
Loading DICOM Volumes
The DICOM panel appears
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Select the directory dicom in
the Tutorial-with-dicom dataset
Loading DICOM Volumes
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Loading DICOM Volumes
The list of DICOM studies appears.
Click OK
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Loading DICOM Volumes
Name : The name that the
volume will have within Slicer
Change to something descriptive: Cortex and click on Header
Slicer loads the dicom study
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Loading DICOM Volumes
The DICOM Headerinformation panel appears
Click Apply
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Loading DICOM Volumes
Slicer loads theDICOM volume ofthe 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 VolumesV 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
Position the mouse on the images inside the Viewer
Left-click and move the mouse to the left
• Rotation
The images move to the left
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Manipulating the images
Position the mouse on the images inside the Viewer
Right-click and move the mouse down
The viewer gets closer to the model
• Zoom
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Manipulating the images
Position the mouse on the images inside the Viewer
Right-click and move the mouse up
The viewer moves away from the model
• Zoom
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Viewing Volumes
Select the 3D View
The View Menu contains
different options to visualize the data
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Viewing Volumes
3D Viewfocuses on 3D
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Viewing Volumes
Select 4x512
The View Menu contains
different options to visualize the data
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Viewing Volumes
4x512 view: larger image views to see details
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Viewing Volumes
Select 1x512
The View Menu contains
different options to visualize the data
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Viewing Volumes
1x512: one large TRANSVERSEview and three smallimages
1x512 COR: one large CORONAL viewand three small images1x512 SAG: one large SAGITTAL viewand three small images
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Viewing Volumes
The View Menu containsdifferent options to visualizethe data
Select 4x256
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Viewing Volumes
4x256 view: smaller equal-sized images
Come back to Normal View
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2D Viewer
• Three 2D windows (red, yellow, and green)• Slider selects which slice of volume to display • Field shows the slice number
1
2
1
2
3
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2D Viewer
• Bg (Background): displays volume in background layer • 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 Header1. 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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File Pattern: Pattern of file names, in C syntax.
Example: a file named skin.001 has a pattern of %s.%03d.
Image Size: Number of
pixels of image in x and y
directions.
Volumes without Header
2
1
The Header section of the Props tab appears.
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Volumes without Header
Pixel Size in the x and y directions. Slice Thickness z dimension of the voxel. Scan Order:
• LR = left to right • IS = inferior to superior • PA = posterior to anterior
Scalar Type: Data format of the pixel. Generally, it is Short (16 bit integer). Slice Tilt: The tilt of the gantry during an MRI.
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56
7
3
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Num Scalars:
Number of scalar components for each voxel. Gray-scale data: 1. Color data: 3.
Little Endian:
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.
DTI data, Swap, No Swap: Placeholders for future.
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Click Apply to load the volume.
Volumes without Header
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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
•Select File Open Scene
in the Main Menu•Select the file tutorial.xml in the directory Tutorial-with-dicom/tutorial.
A Scene is represented as an Xml file.
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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 Opacity1. Click on Models in the
Main Menu
2. Select the Display Tab
The properties Panel of the model appears
3. OpacitySet 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 VisibilityVisibility 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
The segmented volume named all disappears from the 2D Viewer.
Lb: displays label map
Displays results of a segmentation
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2D Viewer
Left click on Lb in the Axial View and select the Label Map named all.
Lb: displays label map
Displays results of a segmentation
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2D Viewer
The segmented volume named all appears in the 2D Viewer.
Lb: displays label map
Displays results of a segmentation
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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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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.
Clipping Models
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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