Slicer3 Training Tutorial Manual segmentation of orbit structures from isotropic MRI data within 3D Slicer for windows

Transcription

1 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 -1-

2 Learning Objective Guiding you step by step through the process of manual segmentation of human orbit structures from isotropic MRI data within 3D Slicer National Alliance for Medical Image Computing -2-

3 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 National Alliance for Medical Image Computing -3-

4 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) Tutorial dataset (<name of dataset>) 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. National Alliance for Medical Image Computing -4-

5 Overview Loading data and visualization slides 6-13 Volumes module slides Editor module slides Basic tools slides Save data slides Re-loading data slides Example: choice of colors slides: D reconstruction slides National Alliance for Medical Image Computing -5-

6 Loading data and visualization National Alliance for Medical Image Computing -6-

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71 Example: Choice of colors 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 National Alliance for Medical Image Computing -71-

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73 3D reconstruction National Alliance for Medical Image Computing -74-

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89 Conclusion Anatomical knowledge Intuitive graphical user interface to interact with the data Open-source environment National Alliance for Medical Image Computing -90-

90 Acknowledgements National Alliance for Medical Image Computing NIH U54EB Neuroimage Analysis Center NIH P41RR Morphometry Biomedical Informatics Research Network NIH U24RRO21382 Surgical Planning Laboratory (BWH) <specific thanks> National Center for Image Guided Therapy NIH U41RR Fondation Saint Luc, Brussels, Belgium Cliniques Universitaires saint Luc, Brussels, Belgium National Alliance for Medical Image Computing -91-