Slicer4Minute Tutorial Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR 2011-2012 1.

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Presentation transcript:

Slicer4Minute Tutorial Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

Slicer4 minute tutorial This tutorial is a 4-minute introduction to the 3D visualization capabilities of the Slicer4 software for medical image analysis. Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

Slicer4 software The Slicer4 software is available for download: Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

Slicer4 minute dataset Download the slicer4minute-data.zip training dataset Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

3DSlicer version 4.0 Start Slicer on your computer: the Welcome module is the default start-up module. Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

3D Slicer Scene  A Slicer scene is a MRML file which, contains the list of elements loaded into Slicer (volumes, models, fiducials…)  The following example uses a 3D Scene, which contains images and 3D surface models of the head. Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

3DSlicer version 4.0 Select File  Load Scene from the main menu, and load slicer4minute.mrml Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

Slicer4 minute Scene Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Slicer displays the elements of the slicer4minute scene, which contains the MR volume of the brain and a series of 3D surface models. 8

Slice4 minute scene Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Select Conventional Widescreen from the viewing mode menu 9

Slicer4minute Scene Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Select Models from the Modules menu 10

3D Visualization Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR The Models module GUI displays the list of models loaded in the slicer4minute scene, their color and the value of their opacity (between 0.0 an 1.0) 11

3D Visualization Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Click on the pin icon on the top left corner of the red slice to display the slice viewer menu then click on the eye icon to display the axial slice in the 3D Viewer 12

3D Visualization Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Use the slider of the red viewer to browse through the axial MR slices. Slicer simultaneously displays the slices in the 3D viewer. 13

3D Visualization The skull_bone.vtk model appears through the skin. Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Lower the opacity of the Skin.vtk model in the Display tab 14

3D Visualization Position the mouse in the 3D viewer. Click the left-mouse button to drag and rotate the model. Click the right-mouse button to zoom in and out. Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

Anatomical Views Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Click on the pin icons in the top left corners of the red and green viewers to display the viewers’ menu, and click on the eye icon to display the axial and coronal slice in the 3D viewer. 16

3D Visualization Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Turn off the visibility of the skull bone to display the hemispheric white matter model 17

3D Visualization The white matter surface, as well as the left and right optic nerves appear in the viewer Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

3D Visualization Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Select the hemispheric_white_ matter.vtk model, and check Clip in the Display tab. 19

3D Visualization Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Use the slider of the coronal view (green) to expose the optic chiasm. 20

3D Visualization Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Increase the opacity of the skin model, and select the viewing mode 3D only 21

Visualization 3D Visualization Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR Click on the Pin icon at the top left corner of the 3D viewer, and click on the Spin icon. 22

3D Visualization The 3D models and 2D anatomical slices start spinning in the 3D viewer. Click a second time on the spin icon to stop the models from spinning. Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

Slicer4 minute tutorial This tutorial was a short introduction to the 3D visualization capabilities of Slicer. Visit the Slicer4 training compendium for more information on the software. Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

Acknowledgments Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR National Alliance for Medical Image Computing NIH U54EB Neuroimage Analysis Center NIH P41RR013218