1. The SPL Abdominal Atlas
Slicer3 Tutorial
The SPL Abdominal Atlas
Florin Talos, MD
Marianna Jakab, MS
© 2011, All Rights Reserved
Surgical Planning Laboratory
Harvard Medical School

2. Acknowledgements NIH P41RR013218 (NAC) NIH U54EB005149 (NA-MIC)
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

3. Disclaimer Disclaimer 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 Laboratory
Harvard Medical School
© 2011, All Rights Reserved

4. Materials Slicer 3 Atlas data set CT Labels 3D-models
Atlas data set CT
Labels
3D-models
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

5. Learning Objectives Loading the atlas data
Creating and displaying customized 3D-views of anatomy
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

6. Prerequisites Slicer Training Loading and Viewing Data
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

7. Overview Part 1: Loading the Abdominal Atlas Data
Part 2: Creating and Displaying Customized 3D Anatomical Views
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

8. Loading the Abdominal Atlas Data
Slicer can load:
Anatomic grayscale data (CT, MRI)...
Label maps…………………………….
3D-Models……………………………..
MRML Scenes ………………………..
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

9. Loading the Atlas Data Loading the Abdominal Atlas Data
Select File Load Scene...
In the Select File window, select the Abdominal_Atlas_2011v1.0.mrml file and click Open
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

10. Loading the Abdominal Atlas Data
3D-models
CT with overlaid
label maps
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

11. Overview Part 1: Loading the Brain Atlas Data
Part 2: Creating and displaying customized 3D anatomical views
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

12. 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 Laboratory
Harvard Medical School
© 2011, All Rights Reserved

13. Customized 3D Views Capture and name a scene snapshot
Restore or delete saved scene snapshots
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

14. Creating Customized 3D Views
Select the Models module
Expand the
Hierarchy & Display tab
From the pull-down menu, select the model of interest, then check the Visibility box, in order to make them visible in the 3D viewer; to make the models invisible uncheck the box.
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved

15. Creating Customized 3D Views
Click on the Capture a screenshot of the 3D view in the Manipulate 3D View Panel
Select a directory and a name for your customized 3D-view (e.g. Portal Circulation)
Surgical Planning Laboratory
Harvard Medical School
© 2011, All Rights Reserved