1. Surgical Planning Laboratory http://www.slicer.org -1- Brigham and Womens Hospital Slicer 3 Tutorial The SPL Abdominal Atlas Ion-Florin Talos, M.D.

2. Surgical Planning Laboratory http://www.slicer.org -2- Brigham and Womens Hospital Acknowledgments NIH P41RR013218 (Neuroimage Analysis Center) NIH U54EB005149 (NA-MIC)

3. Surgical Planning Laboratory http://www.slicer.org -3- Brigham and Womens 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.

4. Surgical Planning Laboratory http://www.slicer.org -4- Brigham and Womens Hospital Material Slicer 3 http://www.slicer.org/pages/Special:Slicer_Downloads/Release Atlas data set http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 CT Labels 3D-models

5. Surgical Planning Laboratory http://www.slicer.org -5- Brigham and Womens Hospital Learning Objectives Loading the atlas data Creating and displaying customized 3D-views of anatomy

6. Surgical Planning Laboratory http://www.slicer.org -6- Brigham and Womens 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

7. Surgical Planning Laboratory http://www.slicer.org -7- Brigham and Womens Hospital Overview Part 1: Loading the Abdominal Atlas Data Part 2: Creating and Displaying Customized 3D anatomical Views

8. Surgical Planning Laboratory http://www.slicer.org -8- Brigham and Womens Hospital Loading the Abdominal Atlas Data Slicer can load: Anatomic grayscale data (CT, MRI) …………………………………………. Label maps…………………………… 3D-Models……………………………… MRML Scenes ……………………….

9. Surgical Planning Laboratory http://www.slicer.org -9- Brigham and Womens Hospital Loading the Atlas Data Select File -> Load Scene In the pop-up window, select the file named Abdominal_Atlas2008.mrml, then click Open

10. Surgical Planning Laboratory http://www.slicer.org -10- Brigham and Womens Hospital 3D-models Loading the Atlas Data CT with overlaid label maps

11. Surgical Planning Laboratory http://www.slicer.org -11- Brigham and Womens Hospital Overview Part 1: Loading the Brain Atlas Data Part 2: Creating and displaying customized 3D anatomical views

12. Surgical Planning Laboratory http://www.slicer.org -12- Brigham and Womens Hospital Creating customized 3D-Views By taking advantage of the ability to selectively display 3D-models, customized 3D-views of anatomy can be created

13. Surgical Planning Laboratory http://www.slicer.org -13- Brigham and Womens Hospital Customized 3D-Views

14. Surgical Planning Laboratory http://www.slicer.org -14- Brigham and Womens 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

15. Surgical Planning Laboratory http://www.slicer.org -15- Brigham and Womens 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)

16. Surgical Planning Laboratory http://www.slicer.org -16- Brigham and Womens 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 clickRestore