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Surgical Planning Laboratoryhttp://www.slicer.org-1-
Brigham and Women’s Hospital
Slicer 3 TutorialThe SPL Abdominal Atlas
Ion-Florin Talos, M.D.
Surgical Planning Laboratoryhttp://www.slicer.org-2-
Brigham and Women’s Hospital
Acknowledgments
NIH P41RR013218 (Neuroimage Analysis Center)
NIH U54EB005149 (NA-MIC)
Surgical Planning Laboratoryhttp://www.slicer.org-3-
Brigham and Women’s Hospital
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.
Surgical Planning Laboratoryhttp://www.slicer.org-4-
Brigham and Women’s Hospital
Material
• Slicer 3http://www.slicer.org/pages/Special:Slicer_Downloads/Release
Atlas data sethttp://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
• CT• Labels• 3D-models
Surgical Planning Laboratoryhttp://www.slicer.org-5-
Brigham and Women’s Hospital
Learning Objectives
• Loading the atlas data
• Creating and displaying customized 3D-views of anatomy
Surgical Planning Laboratoryhttp://www.slicer.org-6-
Brigham and Women’s Hospital
Prerequisites
• Slicer Training Slicer 3 Training 1: Loading and Viewing
Data
http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
Surgical Planning Laboratoryhttp://www.slicer.org-7-
Brigham and Women’s Hospital
Overview
• Part 1: Loading the Abdominal Atlas Data• Part 2: Creating and Displaying
Customized 3D anatomical Views
Surgical Planning Laboratoryhttp://www.slicer.org-8-
Brigham and Women’s Hospital
Loading the Abdominal Atlas Data
Slicer can load:
• Anatomic grayscale data (CT, MRI) ………………………………………….
• Label maps……………………………
• 3D-Models………………………………
• MRML Scenes ……………………….
Surgical Planning Laboratoryhttp://www.slicer.org-9-
Brigham and Women’s Hospital
Loading the Atlas Data
Select “File” -> “Load Scene”
In the pop-up window, select the file named Abdominal_Atlas2008.mrml,
then click “Open”
Surgical Planning Laboratoryhttp://www.slicer.org-10-
Brigham and Women’s Hospital
3D-models
Loading the Atlas Data
CT with overlaidlabel maps
Surgical Planning Laboratoryhttp://www.slicer.org-11-
Brigham and Women’s Hospital
Overview
• Part 1: Loading the Brain Atlas Data• Part 2: Creating and displaying
customized 3D anatomical views
Surgical Planning Laboratoryhttp://www.slicer.org-12-
Brigham and Women’s Hospital
Creating customized 3D-Views
By taking advantage of the ability to selectively display 3D-models, customized 3D-views of anatomy can be created
Surgical Planning Laboratoryhttp://www.slicer.org-13-
Brigham and Women’s Hospital
Customized 3D-Views
Surgical Planning Laboratoryhttp://www.slicer.org-14-
Brigham and Women’s Hospital
Creating customized 3D-Views (1)
Select the “Models” module
Select the “Display” tab
From the pull-down menu, select the models of interest, then click the checkbox, in order to make them visible in the 3D-view; to remove models from the 3D-view, uncheck the box
Surgical Planning Laboratoryhttp://www.slicer.org-15-
Brigham and Women’s Hospital
Creating customized 3D-Views (2)
Select the “Data” module
Click “Create Scene Snapshot”; when prompted, select a name for your customized 3D-view (e.g. Portal Circulation)
Surgical Planning Laboratoryhttp://www.slicer.org-16-
Brigham and Women’s Hospital
Creating customized 3D-Views (3)
To switch between different customized 3D-views select the view you wish to display from the pull-down menu, then click “Restore”