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Data Loading and Visualization-3735
 

Data Loading and Visualization-3735

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http://hdl.handle.net/1926/521

http://hdl.handle.net/1926/521

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Data Loading and Visualization-3735 Data Loading and Visualization-3735 Presentation Transcript

  • Slicer Training 1 Loading and Viewing Data Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
  • Acknowledgments
    • National Alliance for Medical Image Computing
    • NIH U54EB005149
    • Neuroimage Analysis Center
    • NIH P41RR013218
  • 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.
  • Welcome to 3D Slicer
  • Goal of the tutorial Guiding you step by step through the process of Loading and Viewing Data within Slicer
  • Material
    • Slicer 2.6
    • http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started
    • Sample Tutorial Data: tutorial-with-dicom.zip
    • http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
    Questions Answers Exercises
  • Goal of the tutorial Final result of the series of exercises
  • Overview
    • Part 1: Slicer Interface
    • Part 2: Loading Data
    • Part 3: Interacting with Data
  • Slicer Interface Tk window Viewer Menu
  • Slicer Menu Select the Volumes Module
  • Panels and Tabs The Panel of the Volumes Module appears
  • Slicer Menu Panels Sliders Buttons Control Window
  • Main Menu Observe the different options of the Main Menu
    • View
    • Selecting view mode
    • Modules
    • Slicer Modules
    • File
      • Opening files
      • Saving files
      • Closing files
      • Exit
    • Help
    • Links to Slicer Modules information
  • Viewer window
    • Upper part is
    • 3D Viewer
    • Lower part is 2D Viewer
      • 3 separate views
      • Independent controls
    Observe the Viewer Window
  • Slicer Modules The architecture of Slicer is modular Select Modules in the SubMenu
  • Slicer Modules The list of Slicer Modules categories appears Settings IO Application Filtering Segmentation Registration Measurement Visualization Examples Unfiled Alpha
  • Slicer Modules: tutorials Settings IO Application Filtering Segmentation Registration Measurement Visualization Examples Unfiled Alpha
    • Editor …………….. SlicerTraining 2
    • Level-Sets ……….. SlicerTraining 3
    • fMRIEngine ………. SlicerTraining 5
    • vtkFreeSurferReaders ... SlicerTraining 6
    • DTMRI ……………. SlicerTraining 4
  • Exercise 1: Slicer GUI
    • Launch Slicer.
      • Observe Main window and Viewer window.
    • Click File , View , Help , and Modules
      • Examine submenus
    • Click Main Menu buttons: Data , Volumes , Models , Alignments , Editor , and ModelMaker
      • Click tabs
      • Examine panels
    • Click More
      • Click modules: click tabs, examine panels
  • Overview
    • Part 1: Slicer Interface
    • Part 2: Loading Data
    • Part 3: Interacting with Data
  • Loading Data
    • Slicer can load
    • Volumes …………………..
  • Loading Data
    • Slicer can load
    • Volumes …………………..
    • Models …………………….
    • A model is a 3D reconstruction of the anatomy
  • Loading Data
    • Slicer can load
    • Volumes …………………..
    • Models …………………….
    • A model is a 3D reconstruction of the anatomy
    • Scenes …………………….
    • Scene = Volume + Model
  • Loading Data Slicer Advantage Putting together Images and Surface
  • Data representation
    • Volume = collection of image files
    • Image file = header + raw data
    • The header contains the parameters of the image.
    Header Raw Data Header Raw Data Header Raw Data Header Raw Data
  • Data representation
    • Volume = collection of image files
    • Image file = header + raw data
    • The header contains the parameters of the image.
    • Representation of an image:
    • 2D Array of pixels containing the intensity values
    Pixel (a,b) Intensity I (a,b) a b Header Raw Data Header Raw Data Header Raw Data Header Raw Data
  • Loading DICOM Volumes Click on Add Volume in the Slicer Menu
  • Loading DICOM Volumes Left-click on the Menu Properties and change Basic to DICOM The Panel Props appears by default.
  • Loading DICOM Volumes Click on Select DICOM Volume The DICOM panel appears
  • Loading DICOM Volumes Select the directory dicom in the Tutorial-with-dicom dataset
  • Loading DICOM Volumes The list of DICOM studies appears. Click OK
  • Loading DICOM Volumes
    • Name : The name that the
    • volume will have within Slicer
    Change to something descriptive: Cortex and click on Header Slicer loads the dicom study
  • Loading DICOM Volumes
    • The DICOM Header
    • information panel appears
    Click Apply
  • Loading DICOM Volumes
    • Slicer loads the
    • DICOM volume of
    • the brain
  • Visualization Support
    • Control Window : displays a zoomed view of the position of the mouse on the selected image
    Move the mouse inside an anatomical view
  • Visualization Support The value of the gray level of the pixel under the cursor appears in the corresponding slice
  • Viewing Volumes
    • V toggle button controls whether slice is visible in 3D Viewer
    Click on the three V buttons to display the Axial, Sagittal and Coronal images inside the Viewer
  • Viewing Volumes The Axial, Sagittal and Coronal Images appear in the Viewer
  • Manipulating the images Position the mouse on the images inside the Viewer Left-click and move the mouse to the left
    • Rotation
    The images move to the left
  • Manipulating the images Position the mouse on the images inside the Viewer Right-click and move the mouse down The viewer gets closer to the model
    • Zoom
  • Manipulating the images Position the mouse on the images inside the Viewer Right-click and move the mouse up The viewer moves away from the model
    • Zoom
  • Viewing Volumes Select the 3D View The View Menu contains different options to visualize the data
  • Viewing Volumes 3D View focuses on 3D
  • Viewing Volumes Select 4x512 The View Menu contains different options to visualize the data
  • Viewing Volumes 4x512 view: larger image views to see details
  • Viewing Volumes Select 1x512 The View Menu contains different options to visualize the data
  • Viewing Volumes
    • 1x512:
    • one large TRANSVERSE
    • view and three small
    • images
    1x512 COR: one large CORONAL view and three small images 1x512 SAG: one large SAGITTAL view and three small images
  • Viewing Volumes
    • The View Menu contains
    • different options to visualize
    • the data
    Select 4x256
  • Viewing Volumes 4x256 view: smaller equal-sized images Come back to Normal View
  • 2D Viewer
    • Three 2D windows (red, yellow, and green)
    • Slider selects which slice of volume to display
    • Field shows the slice number
    1 2 1 2 3 3
  • 2D Viewer
    • Bg (Background): displays volume in background layer
    • Fg (Foreground): displays volume in foreground layer
    • Superimposed over the background layer
    4 5 4 5
  • Volumes without Header
    • Motivations:
    • The DICOM file format incorporates all the parameters that Slicer requires to render the data
    • Other images files types may not
  • Volumes without Header
    • Motivations:
    • The DICOM file format incorporates all the parameters that Slicer requires to render the data
    • Other images files types may not
    Slicer has a simple protocol for loading volumes without header
  • Volumes without Header 1. Main  Data 2. Add Volume 3. Browse to find the first image of the Volume spgr in the directory tutorial 4. Select first image I.001 of volume to load, and click Open 5. Click on Manual 6. Click on Apply
      • File Pattern : Pattern
      • of file names, in C syntax. Example: a file named skin.001 has a pattern of %s.%03d.
      • Image Size : Number of
      • pixels of image in x and y
      • directions.
    Volumes without Header 2 1 The Header section of the Props tab appears.
  • Volumes without Header
      • Pixel Size in the x and y
      • directions.
      • Slice Thickness z dimension
      • of the voxel.
      • Scan Order :
        • LR = left to right
        • IS = inferior to superior
        • PA = posterior to anterior
      • Scalar Type :
      • Data format of the pixel.
      • Generally, it is Short (16 bit integer).
      • Slice Tilt :
      • The tilt of the gantry during an MRI.
    3 4 5 6 7 3 4 5 6 7
  • Volumes without Header
      • Num Scalars :
      • Number of scalar components for each voxel. Gray-scale data: 1. Color data: 3.
      • Little Endian :
      • In little-endian architectures, the rightmost bytes are most significant. In big-endian architectures (Slicer default), the leftmost bytes (those with a lower address) are most significant.
      • DTI data , Swap , No Swap : Placeholders for future.
    8 9 10 Click Apply to load the volume. 8 9 10
  • Volumes without Header The spgr volume appears in the Viewer
  • Loading Data
    • Slicer can load
    • Volumes …………………..
    • Models …………………….
    • A model is a 3D reconstruction of the anatomy
    • Scenes …………………….
    • Scene = Volume + Model
  • Loading Models
    • In the main Menu select the
    • module Data and Click on
    • Add Model.
  • Loading Models
    • The Props tab of the module
    • Models appears
    Select the model named Vessels in the directory tutorial/models Click on Apply
  • Loading Models The model of the vessels appears in the Viewer.
  • Loading Data
    • Slicer can load
    • Volumes …………………..
    • Models …………………….
    • A model is a 3D reconstruction of the anatomy
    • Scenes …………………….
    • Scene = Volume + Model
  • Loading a Scene
    • Select File  Open Scene
    • in the Main Menu
    • Select the file tutorial.xml in the directory Tutorial-with-dicom/tutorial.
    A Scene is represented as an Xml file.
  • Loading a Scene The viewer displays the tutorial Scene
  • Loading a Scene The elements of the Scene are listed in the Menu Window
  • Overview
    • Part 1: Slicer Interface
    • Part 2: Loading Data
    • Part 3: Interacting with Data
  • Manipulating a Model
    • The model appears in the
    • 3D Viewer .
    • Rotate the model: with left mouse button
    • Zoom the model: with right mouse button
  • Manipulating a Model Put the mouse on the 3D Slicer icon
  • Manipulating a Model The Control Window appears
  • Manipulating a Model Position the mouse on the R letter (Right) inside the window
  • Manipulating a Model The View Panel shows the model from the right side of the patient
  • Manipulating a Model Click on the Spin button
  • Manipulating a Model The model starts spinning inside the Viewer Panel.
  • Manipulating a Model Click on the Rock button
  • Manipulating a Model The model starts rocking inside the Viewer Panel.
  • Manipulating a Model Come back to initial orientation of the Viewer Panel by clicking on the A letter (Anterior) inside the window.
  • Models representation
    • A model is a 3D representation
    • of the anatomy.
    Type W (Wireframe) in the Main Window
  • Models representation
    • The triangles of the Model become visible in the Viewer.
    Type S (Surface) to come back to Surface Mode rendering
  • Model Opacity
    • Click on Models in the Main Menu
    • Select the Display Tab
    • The properties Panel of the model appears
    • 3. Opacity
    • Set the opacity of the Skin model to 0.5
  • Model Opacity Skin model Opacity = 0.5
  • Model Visibility
    • Visibility on and off by
    • left clicking on the name of model in the list
    Left Click on the Vessels button in the list of models
  • Model Visibility Vessels model Visibility 0ff
  • Global Visibility
    • Show All to display all
    • models in the 3D Viewer.
    Click Show None to display none of the models in the 3D Viewer
  • Viewing 3D Models Show None: the models have disappeared
  • 2D Viewer
    • Lb : displays label map
    • Displays results of a segmentation
    Left click on Lb in the Axial View and select the Label Map named None
  • 2D Viewer
    • Lb : displays label map
    • Displays results of a segmentation
    The segmented volume named all disappears from the 2D Viewer.
  • 2D Viewer
    • Lb : displays label map
    • Displays results of a segmentation
    Left click on Lb in the Axial View and select the Label Map named all.
  • 2D Viewer
    • Lb : displays label map
    • Displays results of a segmentation
    The segmented volume named all appears in the 2D Viewer.
  • 2D Viewer Images in the label map layer appear as outlines around the structures that were segmented.
  • 2D Viewer Left Click on Fg in the Axial View and select the Volume named all in the Axial, Sagittal and Coronal slices.
  • Image Fusion
    • Fade slider:
    • fades between foreground
    • and background .
    Set the Fade slider to 0.5
  • 2D Viewer The volume all is superimposed on the images
  • Clipping Models
    • Clipping: cutting away sections of a model at one or more selected slices.
    • The model is removed from one side of each selected slice, revealing the image of each selected slice and the rest of the visible model.
    Select the Models  Display tab
  • Clipping Models
    • 1. Click on Show all to make all the models visible
    • 2. Right-click the Skin model in the list
      • A drop-down menu appears.
    • 3. Check that the Clipping option is selected.
    • 4. Set the opacity of the Skin model to 1.0 .
    • 5. Select the Clip tab of the Models panel.
  • Clipping Models Click + or - to select which side of each slice to clip on. Set the sides to: Red Slice + Yellow Slice - Green Slice -
  • Clipping Models Clipping Model Result
  • Conclusion
    • Intuitive Interface for Loading and Visualizing Data
    • Slicer Outcome = fusion of Volumes and Surface
    • Open-source tool for developing your own module