data loading & 3d visualization - slicer · data loading & 3d visualization sonia pujol,...
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![Page 1: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/1.jpg)
Data Loading &
3D Visualization
Sonia Pujol, Ph.D.
Surgical Planning Laboratory
Harvard Medical School
National Alliance for Medical Image ComputingNeuroimage Analysis Center
Leonardo da Vinci (1452-1519), Virgin and Child Alte
Pinakothek, München
![Page 2: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/2.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Slicer3
• An end-user applicationfor image analysis
• An open-source environment for software development
• A software platform that is both easy to use for clinical researchers and easy to extend for programmers
![Page 3: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/3.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Slicer3
• Slicer3 is a multi-platform software that is
developed and maintained on:
– Windows XP
– Linux x86_64
– Linux x86
– Mac OSX – Darwin x86-Intel
![Page 4: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/4.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization dataset
• This course is built upon three datasets of a single
healthy subject brain:
MR DICOM
GRASS
MR Nrrd
SPGR
Pre-computed
Label Map
![Page 5: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/5.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Learning objective
Following this tutorial,
you’ll be able to load
and visualize volumes
within Slicer3, and to
interact in 3D with
structural images and
models.
![Page 6: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/6.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Start Slicer3
Linux/Mac users
Launch the Slicer3
executable located in
the Slicer3.6 directory
Windows users
Select
Start All Programs
Slicer3-3.6-2010-08-23Slicer3
![Page 7: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/7.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Slicer Welcome
The SlicerWelcome module is the module
displayed by default.
This module gives an overview of the GUI
of Slicer3, and data loading & saving
functionalities.
![Page 8: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/8.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Slicer3 GUIThe Graphical User
Interface (GUI) of
Slicer3.6 integrates
8 main
components:
•the File Menu
•the Menu Toolbar
•the Module GUI
Panel
•the 3D Viewer
•the Slice Viewer
•the Slice
Controller
•the 3D View
Controller
Slice Viewer
3DViewerModule GUI
Panel
Slice Controller
File Menu Menu Toolbar
Progress and Error Log3DView
Controller
![Page 9: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/9.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Overview
Part 4. The
lightbox viewer
Part 2. Loading and
visualizing segmented
structures overlaid on
grayscale images
Part 1. Loading
and visualizing
multiple volumes
simultaneously
Part 3. Visualizing 3D
reconstructions of
anatomical surfaces
Part 5. Saving data
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Data Representation
•The result of a volumetric acquisition is a 3D volume of datarelated to the patient.
•The 3D raster dataset is sampled on a discrete grid with elements called voxels which contain the signal intensity.
j
ik
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
![Page 11: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/11.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Part 1: Loading
and visualizing
multiple volumes
simultaneously
![Page 12: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/12.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Select FileAdd Volume
from the file menu.
Loading Volumes
![Page 13: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/13.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Browse to the location of the
Slicer3VisualizationDataset directory
![Page 14: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/14.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Select the file 001.dcm in the /dicom directory
![Page 15: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/15.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Slicer displays the Dicom header information of the
images. Browse through the Dicom information panel to
display the dimensions of the images.
![Page 16: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/16.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Image dimensions: Rows = 256, Columns = 256
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Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Click on Apply to load the Dicom volume in Slicer.
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Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
The Dicom images appear in
the Background display of
the 2DViewer.
![Page 19: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/19.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Left click on the menu Modules and
select All Modules to display the list
of 95 modules available for image
analysis and 3D visualization.
Select the module Volumes
![Page 20: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/20.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
The panel of the module Volumes
appears in the interface.
Click on the panel Display
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Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Use the Window/Level slider to
adjust the display of the MR images.
![Page 22: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/22.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Select FileAdd Volume
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Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Browse to find the header file of the spgr volume
spgr.nhdr located in the directory
Slicer3VisualizationDataset/nrrd and click on Open.
![Page 24: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/24.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Select Image Origin Centered and click on Apply to
load the volume spgr.nhdr
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Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
The spgr volume appears in the Background
display of the 2D Viewer.
![Page 26: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/26.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Click on the
choose view
icon
Exploring the data
![Page 27: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/27.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Select the red
slice only layout
from the menu
Exploring the data
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Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Exploring the data
The axial slices of
the spgr volume
appear in the 3D
viewer.
Click on the icon slices fit
to window to adjust
the dimensions of the
image to the size of the
window.
![Page 29: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/29.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Exploring the data
To simultaneously view the
dicom and the nrrd volumes, left
click on the drop-down menu to the right of the Foreground icon
and select the image 001.dcm
![Page 30: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/30.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Exploring the data
Click on the Background icon or the
Foreground icon to display the spgr or
the DICOM volumes in the Viewer
![Page 31: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/31.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Exploring the data
Browse the
images using the
slider to display
the ventricles
(~slice 38)
![Page 32: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/32.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Exploring the data
Click on the
conventional layout
icon to come back to
the standard view
![Page 33: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/33.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading Volumes
Click on the icon slices fit
to window to adjust
the dimensions of the
image to the size of the
window.
![Page 34: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/34.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Part 2: Loading and
visualizing segmented
structures overlaid on
grayscale images
![Page 35: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/35.jpg)
Label map
Image segmentation is the extraction of
structural information of particular
interest from surrounding image.
Each pixel is assigned a specific label
value which corresponds to the
anatomical structure that it belongs to.
The three-dimensional result of the
segmentation is a binary array called a
label map.
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
![Page 36: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/36.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading a label map
Click on Select Volume File
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Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading a label map
Browse to find the header file all.nhdr of the
label map dataset located in the directory
Slicer3VisualizationDataset/nrrd and click
on Open
![Page 38: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/38.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a label map
Set Image Origin to Centered Check
the Label Map box and click on
Apply
![Page 39: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/39.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a label mapSlicer displays the label
map all in the Label layer
Click on the
links
icon.
![Page 40: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/40.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing Multiple Volumes
Label Viewer
Left click the drop-
down menu to the right of the L icon and
select None
![Page 41: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/41.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing Multiple VolumesForeground Viewer
Left click on the drop-
down menu to the right of the F icon and select
the volume all
![Page 42: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/42.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing Multiple VolumesSelect Manipulate
Slice Views
Use the slider to fade between the
labelmap all (Foreground) and the
spgr volume (Background).
![Page 43: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/43.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
Select the module Data in
the module menu
![Page 44: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/44.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
The Data module displays the
volumes loaded in the current
Slicer Scene.
![Page 45: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/45.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
The Load & Add Scene tab
displays the different data types
that can be added to the scene.
![Page 46: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/46.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
Slicer displays 2D
anatomical slices in the
3D viewer
Click on the Slice
Visibility icon to
display the slices in the
3D Viewer
Click on the
links
icon.
![Page 47: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/47.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
Slicer displays 2D
anatomical slices in the
3D viewer
![Page 48: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/48.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
Position the mouse in
the 3D Viewer, hold
down the left mouse
button and drag to rotate
the volumes
![Page 49: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/49.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Part 3: Loading and
visualizing 3D models
of the anatomy
![Page 50: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/50.jpg)
3D modelsA 3D model is a surface
reconstruction of an anatomical
structure.
The model is a triangular mesh
that approximates a surface from a
3D label map.
The scalar values for surface
models are integers which
correspond to the label that had
been assigned in the segmentation
process.Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
![Page 51: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/51.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
Click on the left icon in Add data or
data directory
![Page 52: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/52.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
A small window displays information
on how to use the function Add data
or data directory
Click on the icon
![Page 53: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/53.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
3D Visualization
Click on Add Directory to select the directory
Slicer3VisualizationDataset
![Page 54: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/54.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading 3D models
Select the directory Slicer3VisualizationDataset/models
and click on OK
![Page 55: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/55.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading 3D models
The list of elements present in the models
directory appears in the Add Data window.
Click on Apply to load all the 3D models.
![Page 56: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/56.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading 3D models
Slicer loads the 3D models in the 3D Viewer. The
models have been added to the MRML scene.
![Page 57: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/57.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading a 3D model
Click on the panel Hierarchy &
Display to access the module’s
display components
Select the module Models
![Page 58: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/58.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D modelSelect the model Skin.vtk
Click on the icon Set Color
and choose a new color for
the 3D model of the head.
![Page 59: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/59.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Change the opacity of the
skin model from 1.0 to 0.5
using the opacity slider:
![Page 60: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/60.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
The 3D models of the brain
and vessels appear through
the skin
![Page 61: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/61.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Turn off the visibility of the
skin model
![Page 62: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/62.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Select the model Brain and
change its color to white
![Page 63: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/63.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Select Green Slice Only
Layout from the Viewer menu
![Page 64: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/64.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Click on the icon to adjust
the size of the image to the
size of the window.
![Page 65: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/65.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Select Slice Intersection Visible
to display the model
intersection on the slice plane.
![Page 66: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/66.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
The intersection of the 3D model
of the brain with the 2D image
plane appears in the viewer.
Go back to the conventional layout
![Page 67: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/67.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Select the model Vessels and
change its color to red
![Page 68: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/68.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Select the model Brain and
select the option Clipping
![Page 69: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/69.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Set Yellow Slice Clipping to
Positive Space
![Page 70: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/70.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Click on the letter S in the Control
Window to display a superior view
of the 3D models
![Page 71: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/71.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Use the yellow slice slider to
expose the 3D model of the
vasculature
![Page 72: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/72.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Turn off the option clipping for the model Brain
and set the Yellow Slice Clipping to Off
Turn on the visibility of the model Skin
![Page 73: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/73.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Slicer displays the 3D models of the
Skin, Vessels and Brain.
![Page 74: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/74.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Part 4: Lightbox viewer
![Page 75: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/75.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Select the option Compare Layout in
the Viewer menu
![Page 76: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/76.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Visualizing a 3D model
Set the Number of compare Viewers
to 1 and the number of lightbox rows
and columns to 2
Click on Apply
![Page 77: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/77.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Lightbox viewer
Slicer displays a lightbox view of the
Background dataset.
![Page 78: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/78.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Lightbox viewer
Browse through the spgr volume
using the lightbox slider
![Page 79: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/79.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Lightbox viewer
Slicer displays 4 adjacent axial slices of
the spgr volume simultaneously
![Page 80: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/80.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Lightbox viewer
Left click on the Slice Viewer menu of
the Compare Layout viewer
![Page 81: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/81.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Lightbox viewer
Select the lightbox view option
![Page 82: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/82.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Lightbox viewer
Set the configuration of the light
box view to 6x6
![Page 83: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/83.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Lightbox viewer
Slicer displays a matrix of 36 adjacent axial slices of
the spgr volume.
![Page 84: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/84.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Lightbox viewer
Select the option Conventional Layout
in the Viewer menu
![Page 85: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/85.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Part 5: Loading and
saving a Scene
![Page 86: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/86.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving Data
Click on File and
Select Save
![Page 87: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/87.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving Data
The list of elements currently
loaded into Slicer3 appears.
Make sure only the first check box is selected
![Page 88: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/88.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving DataClick on Change Destination for All
Selected and browse to the location
where the scene will be saved
![Page 89: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/89.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving Data
Browse to the directory
where you would like to
save your scene and
click OK
![Page 90: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/90.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving DataDouble click on the file name SlicerScene1 and
change it to Slicer3DScene
![Page 91: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/91.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving DataClick on Save Selected
![Page 92: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/92.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Creating Scene Snapshots
Choose a 3D view of the
scene and click on the
capture snapshot icon
![Page 93: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/93.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Creating Scene Snapshots
Enter the Snapshot name
MySceneSnapshot1 and
click on OK
![Page 94: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/94.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Creating Scene Snapshots
Select a Superior view of the
dataset, and click on the
capture snapshot icon
![Page 95: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/95.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Creating Scene Snapshots
Enter the name
MySceneSnapshot2
and click on OK
![Page 96: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/96.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Creating Scene SnapshotsSelect FileSave and click on
Save Selected to include the two
scene snapshots in the saved
scene
![Page 97: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/97.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Creating Scene Snapshots
Click Yes to
overwrite the file
with a new file that
contains the scene
snapshots
![Page 98: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/98.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving Data
Select FileClose Scene in
the main menu and click on OK
![Page 99: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/99.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving Data
The elements of the previous scene
disappear from the Viewer.
![Page 100: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/100.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving Data
Select FileLoad Scene
from the main menu
![Page 101: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/101.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Saving Data
Browse to find the file
Slicer3DScene.mrml and click
on Open
![Page 102: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/102.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading a Scene
Slicer loads the elements from the scene
Slicer3DScene.mrml
![Page 103: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/103.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading a Scene
Left-click on the restore
snapshot icon.
Select MySceneSnapshot2
and click on restore
![Page 104: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/104.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Loading a Scene
Slicer restores the
scene snapshot
MySceneSnapshot2
![Page 105: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/105.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Conclusion
• 3D visualization of
anatomical surface
reconstructions
• 3D interaction with
volumes and models
• Open-source platform
![Page 106: Data Loading & 3D Visualization - Slicer · Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image](https://reader031.vdocuments.mx/reader031/viewer/2022021913/5c69614d09d3f2d4158cee9c/html5/thumbnails/106.jpg)
Sonia Pujol, PhD National Alliance for Medical Image Computing
http://na-mic.org © 2010, ARR
Acknowledgments
National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218