Slicer Welcome Tutorial

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Presentation transcript:

Slicer Welcome Tutorial Sonia Pujol, Ph.D. Brigham and Women’s Hospital Harvard Medical School Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Goal This tutorial is a short introduction to the Welcome module of the 3D Slicer open-source software. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Slicer4 Basics Slicer is an open-source software for segmentation, registration and visualization of medical imaging data The platform is developed through a multi-institution effort of several NIH funded large-scale consortia Slicer is for medical research only, and is not FDA approved Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Slicer4 Basics Slicer4 contains 92 modules for image segmentation, registration and 3D visualization of medical imaging data. Images courtesy of Ron Kikinis, MD Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Supported Platforms Slicer is a multi-platform software developed and maintained on Mac OSX, Linux 64 & 32, and Windows 64 & 32. Slicer requires a minimum of 2 GB of RAM and a dedicated graphic accelerator with 64 MB of on-board graphic memory. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. 3DSlicer version 4.0 The Welcome module is the default start-up module. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Welcome to Slicer Each module of Slicer includes a series of tabs, which give access to different functionalities. Click on the arrow symbol to display the content of each tab. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. The Main Window tab contains information on the basic organization of Slicer’s user interface. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer User Interface Main Menu Toolbar 3D viewer User Interface (UI) panel of the Slicer Welcome Module Data Probe 2D anatomical viewers Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Welcome Module The Tutorials & Information tab contains links to the Slicer4 training compendium and documentation. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer4.0 Documentation &Training http://www.slicer.org/slicerWiki/index.php/Documentation/4.0 http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Welcome Module The Welcome module panel contains shortcuts for loading different types of data. A series of sample data are also available. Click on Download Sample Data to access the Sample Data Module Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Sample Data The Sample Data module contains links to six different sample datasets that can be downloaded into Slicer. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Sample Data Brain MRI Chest CT Cardiac CT Diffusion Tensor Imaging (DTI) Dataset Brain MRI (tumor patient) Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Sample Data Click on Download MRHead to download the dataset in Slicer. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Welcome Module The MR scan of the brain appears in the 2D viewers. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

MR Brain Sample Dataset Click on the pin icon at the top left corner of the red viewer to display the viewer menu Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

MR Brain Sample Dataset Click on the link icon to link all three 2D viewers, and on the eye icon next to it to display the slices in the 3D viewer. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

MR Brain Sample Dataset The axial, coronal and sagittal slices appear in the 3D viewer. Go back to the Welcome module using the green arrow in the toolbar. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

MR Brain Sample Dataset Click on the tab Mouse & Keyboard to learn the different mouse actions to rotate the images and zoom in and out. Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D., Going Further To learn more about Slicer and its different functionalities, visit the Slicer4.0 training compendium. http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training Slicer Welcome - Sonia Pujol, Ph.D., NA-MIC ARR 2011-2012

Slicer Welcome - Sonia Pujol, Ph.D. Acknowledgments National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218 Slicer Welcome - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012