Surgical Planning Laboratory
`Brigham and Women’s Hospital
`Boston, Massachusetts USA
`
`a teaching affiliate of
`Harvard Medical School
`
`3D VISUALIZATION OF DICOM IMAGES
`RADIOLOGICAL APPLICATIONS
`
`FOR
`
`Sonia Pujol, PhD, Harvard Medical School
`Surgical Planning Laboratory, Brigham and Women’s Hospital
`
`Kitt Shaffer, MD, PhD, Boston University
`Vice-Chairman for Education, Boston University School of Medicine
`
`1
`
`Ron Kikinis, MD, Harvard Medical School
`Surgical Planning Laboratory, Brigham and Women’s Hospital
`
`Medivis Exhibit 1007
`
`
`Brigham and Women’s Hospital
`Boston, Massachusetts USA
`
`a teaching affiliate of
`Harvard Medical School
`
`3D VISUALIZATION OF DICOM IMAGES
`RADIOLOGICAL APPLICATIONS
`
`FOR
`
`Sonia Pujol, PhD, Harvard Medical School
`Surgical Planning Laboratory, Brigham and Women’s Hospital
`
`Kitt Shaffer, MD, PhD, Boston University
`Vice-Chairman for Education, Boston University School of Medicine
`
`1
`
`Ron Kikinis, MD, Harvard Medical School
`Surgical Planning Laboratory, Brigham and Women’s Hospital
`
`Medivis Exhibit 1007
`
`
`
`3D Visualization of DICOM images for Radiological applications
`
`Following this tutorial, you
`will be able to load and
`visualize DICOM volumes
`with 3D Slicer, and to
`interact in 3D with structural
`images and models of the
`anatomy.
`
`2
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 2
`
`
`
`Overview
`
`Part I: Introduction to the 3DSlicer software
`
`Part II: 3D Data Loading and visualization of DICOM
`images
`- Volume Rendering of thoraco-abdominal CT data
`
`- Surface Rendering of MR head data
`
`Part III: 3D interactive exploration of the anatomy
`- Exploration of the Segments of the liver
`
`- Exploration of the Segments of the lung
`
`3
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 3
`
`
`
`Tutorial Datasets
`
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`
`4
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 3
`
`
`
`Overview
`
`Part I: Introduction to the 3DSlicer software
`
`Part II: 3D Data Loading and visualization of DICOM images
`
`
`- Volume Rendering of thoraco-abdominal CT data
`
`- Surface Rendering of MR head data
`
`Part III: 3D interactive exploration of the anatomy
`- Exploration of the Segments of the liver
`
`- Exploration of the Segments of the lung
`
`5
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 4
`
`
`
`Introduction to the
`3DSlicer software
`
`6
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 5
`
`
`
`3DSlicer
`
`3D Slicer is a freely available
`open-source platform for
`segmentation, registration and
`3D visualization of medical
`imaging data.
`
`3D Slicer is a multi-institutional
`effort supported by the National
`Institute of Health.
`
`7
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 6
`
`
`
`3DSlicer
`
`• 3DSlicer version 4.3 is a multi-
`platform software running on
`Windows, Linux, and Mac OSX
`
`• Slicer is distributed under a
`BSD license with no restriction
`on use
`
`•
`
`Slicer is a tool for research,
`and is not FDA approved
`
`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.
`
`8
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 7
`
`
`
`An interdisciplinary platform
`
`An open-source environment for
`software developers
`
`An end-user application for
`clinical investigators and scientists
`
`A software platform that is both easy to use
`for clinical researchers and easy to
`extend for programmers
`
`9
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 8
`
`
`
`3DSlicer History
`
`• 1997: Slicer started as a
`research project between
`the Surgical Planning Lab
`
`(Harvard) and the CSAIL
`(MIT)
`
`Image Courtesy of the CSAIL, MIT
`
`10
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 9
`
`
`
`3DSlicer History
`
`• 1997: Slicer started as a
`research project between
`the Surgical Planning Lab
`(Harvard) and the CSAIL
`(MIT)
`
`•
`
`2014: Multi-institution effort
`to share the latest advances
`in image analysis with the
`clinical and scientific
`community
`
`11
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 10
`
`
`
`A multi-institution: NA-MIC, NAC, NCIGT
`
`PI: Ron Kikinis, M.D.
`
`PIs: Ferenc Jolesz, M.D.,
`Clare Tempany, M.D.
`
`12
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 11
`
`
`
`Slicer: Behind the scenes
`
`$
`
`Slicer is built every
`night on Windows,
`Mac and Linux
`platforms
`
`13
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 12
`
`
`
`Slicer Training events
`
`• Hands-on training
`workshops at national
`and international venues
`
`•
`
`More than 2,700
`clinicians, clinical
`researchers and
`scientists trained since
`2005
`
`14
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 13
`
`
`
`Slicer Training events
`
`
`Major international conferences
`–
`RSNA 2008, 2009, 2010,
`2011, 2012, 2013, 2014
`MICCAI 2008, 2009, 2011,
`2012, 2013, 2014
`
`–
`
`–
`–
`
`SfN 2009, 2011
`
`SPIE 2012, 2013, 2014
`
`–
`
`CAOS 2010
`
`–
`
`CARS 2010, 2012, 2013
`
`15
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`RSNA 2011
`
`Slide 14
`
`
`
`RSNA Activities
`
`Hands-on refresher courses
`
`•
`•
`
`3D Visualization of DICOM images for Radiology Applications
`Quantitative Imaging for Clinical Research and Practice
`
`Quantitative Imaging Reading Room Exhibit
`
`• 3DSlicer: An Open Source Platform for Segmentation,
`Registration, Quantitative Imaging, and 3D Visualization
`Multi-Modal Image Data.
`
`of
`
`16
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 15
`
`
`
`Overview
`
`Part I: Introduction to the 3DSlicer software
`
`Part II: 3D Data Loading and visualization of DICOM
`images
`- Volume Rendering of thoraco-abdominal CT data
`
`- Surface Rendering of MR head data
`
`Part III: 3D interactive exploration of the anatomy
`- Exploration of the Segments of the liver
`
`- Exploration of the Segments of the lung
`
`17
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 16
`
`
`
`Welcome to Slicer4
`
`The Welcome module
`is the default start-up
`module
`
`18
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 17
`
`
`
`Navigating the Application GUI
`
`19
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 18
`
`
`
`Welcome to Slicer4.3.1.1
`
`$
`
`Click on Welcome to Slicer to display the list
`of modules of Slicer in the Modules menu
`
`20
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 19
`
`
`
`Welcome to Slicer4
`
`Slicer4.3.1 contains
`more than 100
`modules for image
`segmentation,
`registration and 3D
`visualization of
`medical imaging data
`
`21
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 20
`
`
`
`Part 1:
`
`Loading a DICOM Volume
`
`22
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 21
`
`
`
`Loading a DICOM volume
`
`Drag and drop the
`“dataset1_Thorax_Abdomen”
`file into slicer
`
`23
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 22
`
`
`
`Loading a DICOM volume
`
`A pop-up window appears:
`Select Load directory into DICOM
`database and click on OK
`
`24
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 23
`
`
`
`Loading a DICOM volume
`
`Slicer starts loading the DICOM images
`
`25
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 24
`
`
`
`Loading a DICOM volume
`
`Click on OK once
`the directory import
`is completed
`
`26
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 25
`
`
`
`Loading a DICOM volume
`
`The patient1 DICOM dataset appears in the DICOM browser.
`Click on ‘patient1’ to display the file hierarchy, select the
`DICOM volume CT_Thorax_Abdomen_CT
`©2012-2014 Surgical Planning Laboratory, ARR
`
`27
`
`Slide 26
`
`
`
`Loading a DICOM volume
`
`Click on Load Selection to Slicer to
`load the DICOM volume into Slicer
`(note: this may take a few minutes)
`©2012-2014 Surgical Planning Laboratory, ARR
`
`28
`
`Slide 27
`
`
`
`Loading a DICOM volume
`
`Slicer displays the axial, coronal and
`sagittal slices of the DICOM dataset
`
`
`$
`
`29
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 28
`
`
`
`Loading a DICOM volume
`
`Select the Volumes
`module in the
`modules menu
`
`
`
`30
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 29
`
`
`
`Loading a DICOM volume
`Select the Active Volume
`6:CT_Thorax_Abdomen
`
`Slicer has a series of window/
`level presets available.
`
`Click on the Window Level Preset CT-
`abdomen, or adjust manually the Window
`and Level using the Manual W/L slider
`
`31
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 30
`
`
`
`Loading a DICOM volume
`
`Position the mouse cursor over the red banner in the Red Viewer to
`display the slice menu. Click on the Links icon to link the slice
`controls across all Slice Viewers. Click on the Eye icon to display the
`three anatomical slices in the 3D Viewer
`
`32
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 31
`
`
`
`Loading a DICOM volume
`
`The three anatomical slices appear in the
`3D viewer. Use the right- mouse button in
`the 3D Viewer to zoom in and out
`
`33
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 32
`
`
`
`Loading a DICOM volume
`
`Use the left-mouse button in the 3D
`Viewer to rotate the 3D volume
`
`34
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 33
`
`
`
`Loading a DICOM volume
`
`
`Click the icon next to the
`number ‘1’ in the blue banner to
`center the 3D view on the scene.
`
`35
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 34
`
`
`
`Loading a DICOM volume
`
`Click on the Slicer layout menu
`icon, and select the Conventional
`Widescreen layout.
`
`36
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 35
`
`
`
`Loading a DICOM volume
`
`Use the red slice, yellow
`slice and green slice
`sliders to slice through
`the volume in all three
`anatomical directions
`
`37
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 36
`
`
`
`3D Interactive exploration of
`thoraco-abdominal CT data
`using Volume Rendering
`
`38
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 37
`
`
`
`Volume Rendering
`
`Select the module
`Volume Rendering in
`the modules menu
`
`39
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 38
`
`
`
`Volume Rendering
`
`Select the volume
`6:CT_Thorax_Abdomen
`
`40
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 39
`
`
`
`Volume Rendering
`
`Click on Preset in the Display
`tab to display the list of available
`presets for the transfer function
`Select the Preset CT-Cardiac3
`
`41
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 40
`
`
`
`Volume Rendering
`
`Select the Rendering VTK CPU Ray Casting, and click
`on the eye icon in the Volume tab to display the
`Volume rendered volume in the 3D viewer.
`
`Note: VTK CPU Ray Casting is the default rendering in
`3D Slicer. If your computer has a good graphics card, we
`recommend the VTK GPU Ray Casting
`
`42
`
`Slide 41
`
`
`
`Volume Rendering
`
`Slicer displays the 3D rendered
`volume of the
`CT_Thorax_Abdomen dataset
`
`43
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 42
`
`
`
`Volume Rendering
`
`Move the Shift slider toward the
`right, to shift the transfer function
`and display the aorta
`
`44
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 43
`
`
`
`Volume Rendering
`
`The volume rendered image of
`the aorta and rib cage appears
`in the 3D viewer
`
`45
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 44
`
`
`
`Volume Rendering
`
`Click on the eye icon in the red
`viewer to turn off the visibility of the
`anatomical slices in the 3D viewer
`
`46
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 45
`
`
`
`Volume Rendering
`
`Use the mouse in the 3D window to
`rotate the volume rendered image
`
`47
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 46
`
`
`
`Volume Rendering
`
`Click on the eye icon in the volume
`rendering panel to remove the volume
`rendered image from the 3D viewer
`
`48
`
`, ARR
`©2012-2014 Surgical Planning Laboratory
`
`Slide 47
`
`
`
`Volume Rendering
`
`Click on Display ROI to display a region of
`interest that we will use for cropping the
`dataset, and check the option Enabled
`
`49
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 48
`
`
`
`Volume Rendering
`
`The region of interest appears
`in the 3DViewer
`
`50
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 49
`
`
`
`Volume Rendering
`
`Turn on the visibility of the grayscale
`images in to the 3D Viewer, and position
`the ROI around the left and right kidneys
`using the ROI controls in the 2D
`anatomical views and in the 3D viewer
`
`51
`
`Slide 50
`
`
`
`Volume Rendering
`
`Click on the eye
`icon to display the
`volume rendered
`image of the kidney
`
`52
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 51
`
`
`
`Volume Rendering
`
`Slicer displays the
`volume rendered image
`of the left kidney
`
`53
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 52
`
`
`
`Volume Rendering
`
`Extend the ROI to
`the right kidney and
`then click the eye
`icon to remove the
`2D slice views
`
`54
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 53
`
`
`
`Volume Rendering
`
`Slicer displays the
`cropped volume rendered
`images showing the left
`and right kidney
`
`55
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 54
`
`
`
`Volume Rendering
`
`Click on File and then Close Scene
`
`Then click on Exit to quit Slicer
`
`56
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 55
`
`
`
`Volume Rendering
`
`8+).G$!"
`
`57
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 56
`
`
`
`3D visualization of surface
`models of the brain
`
`58
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 57
`
`
`
`3D Data Loading and Visualization
`
`• This tutorial is a short introduction to the
`advanced 3D visualization capabilities
`Slicer
`
`• The Slicer4 Minute dataset is composed of an
`MR scan of the brain and 3D surface
`reconstructions of anatomical structures.
`
`• The data are part of the SPL Multi-modality MRI-
`based atlas of the brain by Halle et al. The atlas is
`available at:
`
`http://www.spl.harvard.edu/publications/item/view/2037
`
`59
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 58
`
`
`
`Welcome to Slicer4
`
`9=#-$&=$23$H+).#($
`9=#-$&=$23$H+).#($
`
`60
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 59
`
`
`
`Slicer4 Minute Tutorial: Viewing the Scene
`
`$
`
`Open the directory dataset2_Head located in
`C:/3DSlicerData_RSNA2014/3DVisualizationDICOM_Tuesday_Dec3
`Drag and drop the file Head_Scene.mrb into Slicer
`61
`©2012-2014 Surgical Planning Laboratory, ARR Slide 60
`
`
`
`Slicer4 Minute Tutorial: Viewing the Scene
`
`$
`
`62
`
`Click on OK to load the file MRHead_Scene.mrb into Slicer
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 61
`
`
`
`Slicer4 Minute Tutorial: Viewing the Scene
`
`3D Viewer
`
`When the scene is finished
`loading, Slicer displays:
`• a 3D model of the head in
`the 3D Viewer, and
`• anatomical MR slices of
`the brain in the 2D Slice
`Viewers.
`
`63
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 62
`
`
`
`Slicer4 Minute Tutorial:
`
`Exploring Slicer(cid:1)s
`
`functionality
`
`To access the Models
`module click on
`Welcome to Slicer.
`
`64
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 63
`
`
`
`Slicer4 Minute Tutorial: Switching to the Models Module
`
`Slicer displays the GUI of
`the Models Module
`
`65
`
`©2012-2014 Surgical Planning Laboratory, ARR Slide 64
`
`
`
`Slicer4 Minute Tutorial: Basic 3D Interaction
`
`Left-click & drag
`
`Position the mouse in
`the 3D Viewer.
`
`Hold down the left
`mouse button and drag
`to rotate the model.
`
`66
`
`©2012-2014 Surgical Planning Laboratory, ARR Slide 65
`
`
`
`Slicer4 Minute Tutorial: Viewing Slices in the 3D Viewer
`
`Click on the Slice Visibility
`Icon to display the Axial Slice in
`the 3D Viewer
`
`67
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 66
`
`
`
`$#
`
`licer4 Minute Tutorial: 3D Visualizationlicer4 Minute Tutorial: 3D Visualization
`
`Slicer adds a view of
`the Axial slice in the
`3D View.
`
`68
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 67
`
`
`
`Slicer4 Minute Tutorial: Viewing Slices in the 3D Viewer
`
`Click on the layout menu in the
`toolbar, and select the
`Conventional layout
`
`69
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 68
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization
`
`Select the Skin.vtk
`Change the opacity of the model
`from 1.0 to 0.0.
`
`70
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 69
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization
`
`The model of the skin becomes
`invisible in the 3D viewer and the
`model of the skull bone and
`eyeballs become visible.
`
`71
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 70
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization
`
`Click on the Slice Visibility icon
`"
`in the Green Slice Viewer to display
`the Coronal Slice in the 3D Viewer.
`
`72
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 71
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization
`
`Select the 3D model skull_bone.vtk
`in the Model Hierarchy and turn on
`the Clipping option.
`
`73
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 72
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization
`
`Browse through the coronal
`slices to expose the 3D model
`of the white matter, and the
`left and right optic nerves.
`
`74
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 73
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization
`
`Now make the skull invisible
`
`75
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 74
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization
`
`Scroll the Coronal Slices to
`display the hemispheric white
`matter model in the context of
`the image data in the 3D.
`
`76
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 75
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization
`
`Select the hemispheric white matter
`model called
`hemispheric_white_matter.vtk
`
`Turn off its visibility.
`77
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 76
`
`
`
`
`
`Slicer4 Minute Tutorial: 3D VisualizationSlicer4 Minute Tutorial: 3D Visualization
`
`Slicer displays the optic nerve,
`optic chiasm and optic tracts
`overlaid on the MR images of
`the brain.
`
`78
`
`©2012-2014 Surgical Planning Laboratory, ARR Slide 80Slide 80
`
`
`©2012-2014 Surgical Planning Laboratory, ARR RR
`Slide 77
`
`
`
`Slicer4 Minute Tutorial: 3D Visualization: Zoom the view
`
`Windows/Linux users: Position the
`mouse in the 3D Viewer, hold down
`the right mouse button and move
`the mouse down to zoom in.
`
`Mac users: Position the mouse in
`the 3D Viewer, hold down the apple
`button and the mouse button and
`move the mouse down to zoom in
`(or use two fingers on the touch
`pad).
`
`79
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 78
`
`
`
`Close the existing scene and all its data
`
`Select File->Close Scene
`This removes any dataset
`previously loaded into slicer.
`
`Click on Exit to exit Slicer
`
`80
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 79
`
`
`
`Overview
`
`Part I: Introduction to the 3DSlicer software
`
`Part II: 3D Data Loading and visualization of DICOM images
`
`
`- Volume Rendering of thoraco-abdominal CT data
`
`- Surface Rendering of MR head data
`
`Part III: 3D interactive exploration of the anatomy
`- Exploration of the Segments of the liver
`
`- Exploration of the Segments of the lung
`
`81
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 80
`
`
`
`Part II:
`
`Interactive 3D Visualization
`of the segments of the liver
`
`82
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 81
`
`
`
`(cid:3)(cid:22)(cid:12)(cid:27)(cid:23)(cid:21)(cid:31)(cid:1)(cid:23)(cid:16)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:20)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)
`
`83
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 82
`
`
`
`Liver dataset
`
`The liver dataset is
`a contrast-enhanced CT
`
`abdominal scan of a
`
`healthy 36 year-old male.
`
`84
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 83
`
`
`
`
`3D segments of the liver
`
`Segment VII
`
`$
`
`Segment IVa
`
`$
`
`Segment II
`
`Segment VI
`
`$
`
`Segment V
`
`$
`
`Segment III
`
`$
`
`Segment IVb
`
`85
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 84
`
`
`
`3D segments of the liver
`
`Segment II
`
`$
`
`Segment I
`
`$
`
`Segment VII
`
`$
`
`$
`
`Segment III
`
`$
`
`86
`
`Segment IVb
`
`$
`
`IVC
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`$
`
`Segment V
`
`$
`
`Segment VI
`
`Slide 85
`
`
`
`$
`
`Liver vasculature
`Middle
`hepatic vein
`
`$
`
`Left portal
`vein
`
`Right portal
`vein
`
`$
`
`$
`
`Right hepatic
`vein
`
`$
`
`Left hepatic
`vein
`
`$
`
`Caudate vein
`
`$
`
`Main portal
`vein
`
`$
`
`IVC
`
`87
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 86
`
`
`
`(cid:8)(cid:23)(cid:12)(cid:14)(cid:19)(cid:22)(cid:17)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:13)(cid:15)(cid:22)(cid:15)(cid:1)
`
`Browse to the directory
`C:\3DSlicerData_RSNA2014\3DVisualizationDICOM_Monday_Dec1
`Select the directory dataset3_Liver
`Drag and drop the file LiverSegments_Scene.mrb into Slicer
`
`88
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 87
`
`
`
`(cid:8)(cid:23)(cid:12)(cid:14)(cid:19)(cid:22)(cid:17)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:13)(cid:15)(cid:22)(cid:15)(cid:1)
`
`Click on OK to load the scene into Slicer
`
`89
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 88
`
`
`
`(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:1)(cid:10)(cid:13)(cid:15)(cid:22)(cid:15)(cid:1)
`
`$
`
`The elements of the scene appear in the Viewer
`
`90
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 89
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:21)(cid:23)(cid:14)(cid:15)(cid:20)(cid:26)(cid:1)(cid:23)(cid:16)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:20)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)
`
`$
`
`Segment IVa
`
`$
`
`Segment II
`
`$
`
`Segment VIII
`
`Segment VII
`
`Segment VI
`
`$
`
`Segment V
`
`$
`
`Segment III
`
`$
`
`Segment IVb
`
`91
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 90
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:21)(cid:23)(cid:14)(cid:15)(cid:20)(cid:26)(cid:1)(cid:23)(cid:16)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:20)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)
`
`Segment II
`
`$
`
`Segment I
`
`$
`
`Segment VII
`
`$
`
`$
`
`Segment III
`
`$
`
`92
`
`Segment IVb
`
`$
`
`IVC
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`$
`
`Segment V
`
`$
`
`Segment VI
`
`Slide 91
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:21)(cid:23)(cid:14)(cid:15)(cid:20)(cid:26)(cid:1)(cid:23)(cid:16)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:20)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)
`
`$
`
`$
`
`Middle
`hepatic vein
`
`Left portal
`vein
`
`$
`
`Left hepatic
`vein
`
`$
`
`Caudate vein
`
`$
`
`Main portal
`vein
`
`$
`
`IVC
`
`Right portal
`vein
`
`$
`
`$
`
`Right hepatic
`vein
`
`93
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 92
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:32)
`(cid:1)
`
`$
`
`Example:
`What organ abuts the
`
`left-most margin of
`
`segment II in this
`
`patient ?
`
`94
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 93
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:32)
`
`Select the module Models
`
`Click on the Liver Structures Models Hierarchy
`
`95
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 94
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:32)
`
`Select the model Liver_Segment II
`Turn on/off its visibility to locate it in the 3D
`viewer.
`
`96
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 95
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:32)
`
`Click the eye icon on the Red Slicer
`
`Position the mouse in the 3D Viewer, hold
`down the left mouse button and drag to
`orient the 3D model to a superior view.
`
`97
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 96
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:32)
`
`Seg II
`
`Question 1:
`
`Slide 101
`
`What organ abuts the left- most
`margin of segment II in Patient 1?
`
`98
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 97
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:32)
`
`Question 1:
`
`What organ abuts the left-
`most margin of segment II in
`this patient?
`
`Answer 1: Stomach
`
`stomach
`
`Seg II
`
`99
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 98
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:1)
`
`Question 2:
`
`Which segment would most likely
`
`be affected by an aggressive
`
`tumor invading locally from the
`
`right adrenal gland?
`
`100
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 99
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:32)
`
`Segment VII
`
`Question 2:
`
`Which segment would most likely
`
`be affected by an aggressive
`
`tumor invading locally from the
`
`right adrenal gland?
`
`Answer 2: Segment VII
`
`101
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 100
`
`
`
`(cid:2)(cid:5)(cid:1)(cid:6)(cid:30)(cid:24)(cid:20)(cid:23)(cid:25)(cid:12)(cid:27)(cid:19)(cid:23)(cid:22)(cid:1)(cid:23)(cid:16)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:15)(cid:17)(cid:21)(cid:15)(cid:22)(cid:27)(cid:26)(cid:32)
`(cid:1)
`Question 3:
`Which vessel separates
`Segment IVb and
`Segment V?
`
`$
`
`102
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 101
`
`
`
`(cid:9)(cid:19)(cid:14)(cid:14)(cid:20)(cid:15)(cid:1)(cid:7)(cid:15)(cid:24)(cid:12)(cid:27)(cid:19)(cid:13)(cid:1)(cid:11)(cid:15)(cid:19)(cid:22)(cid:1)
`
`Segment IVb
`
`Middle
`hepatic vein
`
`Segment V
`
`Question 3:
`
`Which vessel separates Segment IVb and Segment V?
`
`Answer 3: The middle hepatic vein
`
`103
`
`©2012-2014 Surgical Planning Laboratory, ARR Slide 102
`
`
`
`(cid:4)(cid:20)(cid:23)(cid:26)(cid:19)(cid:22)(cid:17)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:8)(cid:19)(cid:29)(cid:15)(cid:25)(cid:1)(cid:10)(cid:13)(cid:15)(cid:22)(cid:15)(cid:1)
`
`Select Exit and then click on
`Exit (discard modifications)
`
`104
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 103
`
`
`
`Interactive 3D Visualization
`of the segments of the lungs
`
`105
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 104
`
`
`
`Segments of the lung
`
`Segmentation and 3D surface
`reconstruction of the lung and
`pulmonary vessels
`
`Acknowledgment:
`Segmentation of the lung surface and vasculature: Raul
`San Jose Estepar, Ph.D., George Washko, M.D., Ed
`Silverman, M.D. and James Ross, MSc. Brigham and
`Women’s Hospital (K25 HL104085) and COPDGene (01
`HL089897 and U01 HL089856)
`
`106
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 105
`
`
`
`Segments of the lung
`
`$
`
`3D parcellation of arteries and veins from
`original model of pulmonary vessels
`(Kitt Shaffer, M.D., Ph.D. - Sonia Pujol, Ph.D.)
`
`- Right Upper Lobe (RUL)
`-
`RUL Pulmonary Vein
`RUL Anterior Segment
`-
`RUL Apical Segment
`-
`RUL Posterior Segment
`-
`- Right Middle Lobe (RML)
`-
`RML Pulmonary Vein 1 & 2
`-
`RML Lateral Segment
`-
`RML Medial Segment
`- Right Lower Lobe (RLL)
`-
`RLL Pulmonary Vein 1,2,3
`-
`RLL Anterior Basal Segment
`RLL Medial Basal Segment
`-
`RLL Lateral Basal Segment
`-
`RLL Posterior Basal Segment
`-
`
`Slide 110
`
`107
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`
`
`Loading the Chest Data Scene
`
`Open the directory C:\3DSlicerData_RSNA2014\3DVisualizationDICOM_Monday_Dec1
`Select the subdirectory dataset4_Chest
`Drag and drop the file LungSegments_Scene.mrb into Slicer
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 111
`
`108
`
`
`
`(cid:8)(cid:23)(cid:12)(cid:14)(cid:19)(cid:22)(cid:17)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:8)(cid:28)(cid:22)(cid:17)(cid:1)(cid:10)(cid:13)(cid:15)(cid:22)(cid:15)(cid:1)
`
`$
`
`Click on OK to load the file into Slicer
`
`109
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 108
`
`
`
`(cid:8)(cid:23)(cid:12)(cid:14)(cid:19)(cid:22)(cid:17)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:8)(cid:28)(cid:22)(cid:17)(cid:1)(cid:10)(cid:13)(cid:15)(cid:22)(cid:15)(cid:1)
`
`
`Click on the icon to e
`center the 3D view
`
`110
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 109
`
`
`
`(cid:8)(cid:23)(cid:12)(cid:14)(cid:19)(cid:22)(cid:17)(cid:1)(cid:27)(cid:18)(cid:15)(cid:1)(cid:8)(cid:28)(cid:22)(cid:17)(cid:1)(cid:10)(cid:13)(cid:15)(cid:22)(cid:15)(cid:1)
`
`Select the module Models
`from the modules Menu.
`
`111
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 110
`
`
`
`Lung Segments
`
`Slicer displays the list of 15 surface
`models of pulmonary structures.
`
`112
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 111
`
`
`
`Lung Segments – Question 1
`
`113
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 112
`
`Q1: Why is there
`a gap in the
`vessels at the
`arrows?
`
`
`
`Lung Segments – Question 2
`
`114
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 113
`
`Q2: Which
`segment’s vascular
`supply is shown at
`the arrow?
`
`
`
`Lung Segments – Question 2
`
`Q2: Which segment’s
`vascular supply is shown
`at the arrow?
`Answer 2: Right Upper
`Lobe Apical Segment
`
`115
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 114
`
`
`
`Lung Segments – Question 3
`
`Q3: Which
`segment’s vascular
`supply is shown at
`the arrow?
`
`116
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 115
`
`
`
`Lung Segments – Question 3
`
`Q3: Which segment’s
`vascular supply is shown
`at the arrow?
`Answer 2: Right Lower
`Lobe Pulmonary Vein 1
`
`117
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 116
`
`
`
`Lung Segments – Question 4
`
`Q4: Classify the
`segments of the
`lower lobe by size.
`
`118
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 117
`
`
`
`Lung Segments – Question 4
`
`$
`
`Smallest: Medial Basal
`
`$ ©
`
`2012-2014 Surgical Planning Laboratory, ARR Slide 118
`
`119
`
`
`
`Lung Segments – Question 4
`
`$
`
`Largest: Anterior / Posterior Basal
`
`$
`
`120
`
`©2012-2014 Surgical Planning Laboratory, ARR Slide 119
`
`
`
`
`
`3D Visualization of DICOM images
`
`•
`
`•
`
`•
`
`to
`
`Interactive user-interface
`load and manipulate
`greyscale volumes,
`labelmaps and 3D models.
`User-defined 3D view of the
`anatomy
`
`3D Open-source platform for
`Linux, Mac and Windows
`
`121
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 120
`
`
`
`3DSlicer website
`
`122
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 121
`
`
`
`Acknowledgments
`
`National Alliance for Medical
`(NIH Grant U54EB005149)
`
`Image Computing (NA-MIC)
`
`Neuroimage Analysis Center
`(NIH Grant P41 EB015902)
`
`(NAC)
`
`123
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 125
`
`
`
`www.slicer.org
`www.na-mic.org
`
`Questions and comments: spujol@bwh.harvard.edu
`
`124
`
`©2012-2014 Surgical Planning Laboratory, ARR
`
`Slide 126
`
`
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