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Slicer 3 TutorialThe SPL Abdominal Atlas

Ion-Florin Talos, M.D.

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Acknowledgments

NIH P41RR013218 (Neuroimage Analysis Center)

NIH U54EB005149 (NA-MIC)

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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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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

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Learning Objectives

• Loading the atlas data

• Creating and displaying customized 3D-views of anatomy

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Prerequisites

• Slicer Training Slicer 3 Training 1: Loading and Viewing

Data

http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

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Overview

• Part 1: Loading the Abdominal Atlas Data• Part 2: Creating and Displaying

Customized 3D anatomical Views

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Loading the Abdominal Atlas Data

Slicer can load:

• Anatomic grayscale data (CT, MRI) ………………………………………….

• Label maps……………………………

• 3D-Models………………………………

• MRML Scenes ……………………….

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Loading the Atlas Data

Select “File” -> “Load Scene”

In the pop-up window, select the file named Abdominal_Atlas2008.mrml,

then click “Open”

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3D-models

Loading the Atlas Data

CT with overlaidlabel maps

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Overview

• Part 1: Loading the Brain Atlas Data• Part 2: Creating and displaying

customized 3D anatomical views

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Creating customized 3D-Views

By taking advantage of the ability to selectively display 3D-models, customized 3D-views of anatomy can be created

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Customized 3D-Views

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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

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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)

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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”