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Transcript 
Slicer3 Training Compendium
Slicer3 Training Tutorial
Manual segmentation of orbit
structures from isotropic MRI data
within 3D Slicer for windows
Dr Raphael Olszewski
Surgical Planning Laboratory
Brigham and Women’s Hospital
Harvard Medical School
Massachussets General Hospital
National Alliance for Medical Image Computing
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Learning Objective
Guiding you step by step
through the process of manual
segmentation of human orbit
structures from isotropic MRI
data within 3D Slicer
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Prerequisites
This tutorial assumes that you have already completed
the tutorial Data Loading and Visualization. Tutorials
for Slicer3 are available at the following location:
• Slicer3 tutorials
http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training
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Materials
This tutorial requires the installation of the Slicer3
software and the tutorial dataset. They are available at
the following locations:
• Slicer3 download page (Slicer 3.2)
http://www.slicer.org/pages/Downloads/
• Tutorial dataset (<name of dataset>)
http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training
Disclaimer: It is the responsibility of the user of Slicer to comply with both the terms
of the license and with the applicable laws, regulations, and rules.
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Overview
Loading data and visualization
Volumes module
Editor module
Basic tools
Save data
Re-loading data
Example: choice of colors
3D reconstruction
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slides 14-25
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slides 39-54
slides 55-64
slides 65-70
slides: 71-73
slides 74-89
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Loading data and visualization
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Volumes module
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Editor module
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Basic tools
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Save data
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Re -loading data
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Example: Choice of colors
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1 (dark blue) : not used
2 (pink) : fat tissue
3 (white) : not used
4(blue) : inferior extraocular muscle
5(red) : medial extraocular muscle
6 (green) : superior extraocular muscle
7 (azure blue) : superior oblique extraocular muscle
8 (olive green) : lateral extraocular muscle
9 (violet) : inferior extraocular muscle
10 (olive green) : non used
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3D reconstruction
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Conclusion
• Anatomical knowledge
• Intuitive graphical user interface to interact with the data
• Open-source environment
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Acknowledgements
National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218
Morphometry Biomedical Informatics Research Network
NIH U24RRO21382
Surgical Planning Laboratory (BWH)
<specific thanks>
National Center for Image Guided Therapy
NIH U41RR019703
Fondation Saint Luc, Brussels, Belgium http://www.fondationsaintluc.be
Cliniques Universitaires saint Luc, Brussels, Belgium
http://www.saintluc.be
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