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Slicer Training 1: Loading and Viewing Data. Welcome to 3D Slicer . Goal of this tutorial. Guiding you step by step through the process of Loading and Viewing Data within Slicer. Material.

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Slicer training 1 loading and viewing data l.jpg

Slicer Training 1: Loading and Viewing Data



Goal of this tutorial l.jpg
Goal of this tutorial

Guiding you step by step through the process of Loading and Viewing Data within Slicer


Material l.jpg
Material

  • Slicer2.5: https://share.spl.harvard.edu/share/birn/public/software/slicer2.5/slicer2.5-opt-win32-2005-05-23.zip

  • Tutorial Data: tutorial-with-dicom.zip

20 Exercises

Questions

Answers


Goal of the tutorial l.jpg
Goal of the tutorial

Final Result of the series of exercises


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Overview of Training 1

  • Part 1: Slicer Interface

  • Part 2: Loading Data

  • Part 3: Viewing Data


Slicer interface l.jpg
Slicer Interface

Menu

Viewer

Tk window


Slicer menu l.jpg
Slicer Menu

Main Menu

Panels

Sliders

Select the Volumes Module

Buttons


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Panels and Tabs

The Panel of the Volumes Module appears

  • Each panel has tabs along the top.

  • Leftmost tab is Help.

  • Panel may contain controls and displays.


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Slicer Modules

Click on More

The list of Modules appears.


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Submenus

  • File

    • Opening files

    • Saving files

    • Close

    • Exit

  • View

    • Selecting view mode

  • Help

    • Links to Slicer information


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Viewer window

  • Upper part is 3D Viewer

  • Lower part is 2D Viewer

    • 3 separate views

    • Independent controls


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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 of training 114 l.jpg
    Overview of Training 1

    • Part 1: Slicer Interface

    • Part 2: Loading Data

    • Part 3: Viewing Data


    Loading data l.jpg
    Loading Data

    Slicer can load

    • Volumes

    • Models

    • Scenes = Volumes + Models


    Loading volumes overview l.jpg
    Loading Volumes: Overview

    1. Main  Data

    2. Add Volume

    Props tab of Volumes

    panel appears

    3. Browse to find the first image

    4. Select first image of volume to load, and click Open

    The number of the last image automatically appears

    5. Apply


    Dicom volumes l.jpg
    DICOM Volumes

    • Main  Data  Add Volume  Props

    • 2. From Properties Change Basic DICOM


    Dicom volumes18 l.jpg
    DICOM Volumes

    DICOM panel appears

    3. Select DICOM Volume

    A dialog box appears

    4. Select directory and click OK

    Slicer searches for every DICOM file.


    Dicom volumes19 l.jpg
    DICOM Volumes

    • Select or Deselect

      images to load:

      Selected images are green,

      Deselected images are red.

    • Increasing or Decreasing

      Loads images in either order.


    Dicom volumes20 l.jpg
    DICOM Volumes

    • Preview:

      small icon-size images

      in bottom panel (default size is

      32x32 pixels)

    • List Headers

      displays header information

    • Check

      displays information about

      how to group the data.

      Helps to show when slices are missing.

      Also useful when several DICOM acquisitions are lumped together.


    Dicom volumes21 l.jpg
    DICOM Volumes

    • Name

      the name that volume will have within Slicer

    • Optional Description

      You may enter a description.

    Change to something descriptive: “Cortex“

    Click Header


    Loading dicom volumes l.jpg
    Loading DICOM Volumes

    The DICOM Header information panel appears

    …Slicer loads the data

    Click Apply


    Loading dicom volumes23 l.jpg
    Loading DICOM Volumes

    The Viewer contains the DICOM volume


    Loading volumes without header l.jpg
    Loading Volumes without Header

    1. Main  Data

    2. Add Volume

    3. Browse to find the first image of the Volume spgr

    4. Select first image I.001 of volume to load, and click Open

    5.Click on Manual

    6. Click on Apply


    Loading volumes without header25 l.jpg
    Loading Volumes without Header

    The Header section of the Props tab appears.


    Loading volumes without header26 l.jpg
    Loading Volumes without Header

    The Header section of the Props tab appears.

    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.

    1

    2


    Loading volumes without header27 l.jpg

    3

    4

    5

    3

    4

    6

    5

    6

    7

    7

    Loading 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.


  • Loading volumes without header28 l.jpg

    8

    9

    10

    Loading Volumes without Header

    8

    • 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.

    9

    10

    Click Apply to read in the volume.


    Loading volumes without header29 l.jpg
    Loading Volumes without Header

    The spgr volume appears in the Viewer


    Loading data30 l.jpg
    Loading Data

    Slicer can load

    • Volumes

    • Models

    • Scenes = Volumes + Models


    Loading models l.jpg
    Loading Models

    • A model is a 3D surface.

      1. MainData Add Model

      Props tab appears.

      2. Browse

      3. Name field

      Give a name within Slicer.

      4. Color pull-down menu

      select color for the 3D Viewer

      5. Click Apply to read in the model.

    In dialog box, select the model named Vessels and click Open.

    Make descriptive: “Vessels“.


    Loading models32 l.jpg
    Loading Models

    The model of the vessels appears in the Viewer.


    Loading data33 l.jpg
    Loading Data

    Slicer can load

    • Volumes

    • Models

    • Scenes = Volumes + Models


    Loading a scene l.jpg
    Loading a Scene

    File Open Scene.

    Find the scene tutorial.xml file,

    Double-click it,

    …Wait for the volumes and models to load.


    Loading a scene35 l.jpg
    Loading a Scene

    tutorial Scene


    Overview of training 136 l.jpg
    Overview of Training 1

    • Part 1: Slicer Interface

    • Part 2: Loading Data

    • Part 3: Viewing Data


    Manipulating model l.jpg
    Manipulating Model

    The model appears in the

    3D Viewer:

    Rotate the model: with left mouse button.

    Zoom the model: with right mouse button.


    Model opacity l.jpg
    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 opacity39 l.jpg
    Model Opacity

    Skin model Opacity

    = 0.5


    Model visibility l.jpg
    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 the models


    Model visibility41 l.jpg
    Model Visibility

    Vessels model Visibility 0ff


    Global visibility l.jpg
    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 l.jpg
    Viewing 3D Models

    Show None Models have disappeared


    Viewing volumes 1 of 5 l.jpg
    Viewing Volumes (1 of 5)

    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 in the Viewer


    Viewing volumes 1 of 545 l.jpg
    Viewing Volumes (1 of 5)

    The Axial, Sagittal and Coronal Images appear in the Viewer


    Viewing volumes 1 of 546 l.jpg
    Viewing Volumes (1 of 5)

    • View Menu contains different options to visualize the data

    Select the 3D View


    Viewing volumes l.jpg
    Viewing Volumes

    3D view: focuses on 3D.


    Viewing volumes 1 of 548 l.jpg
    Viewing Volumes (1 of 5)

    • View Menu contains different options to visualize the data

    Select 4x512


    Viewing volumes49 l.jpg
    Viewing Volumes

    4x512 view: larger image views to see details


    Viewing volumes 1 of 550 l.jpg
    Viewing Volumes (1 of 5)

    • View Menu contains different options to visualize the data

    Select 1x512


    Viewing volumes51 l.jpg
    Viewing Volumes

    1x512 view: one large, three small images.


    Viewing volumes 1 of 552 l.jpg
    Viewing Volumes (1 of 5)

    • View Menu contains different options to visualize the data

    Select 4x256


    Viewing volumes53 l.jpg
    Viewing Volumes

    4x256 view: smaller equal-sized images.

    Come back to Normal View


    2d viewer l.jpg
    2D Viewer

    2

    • Three 2D windows (red, yellow, and green).

      Both grayscale and label map images in windows.

    • Slider selects which slice of volume to display.

      Field shows the slice number.

    3

    1

    1

    2

    3


    Superimpose l.jpg
    Superimpose

    4

    • Bg (background): displays volume in background layer.

    • Fg (foreground): displays volume in foreground layer.

      • Superimposed over the background layer.

    5

    4

    5


    2d viewer56 l.jpg
    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 viewer57 l.jpg
    2D Viewer

    Images in the label map layer appear as outlines around the structures that were segmented.


    2d viewer58 l.jpg
    2D Viewer

    Left Click on Fg in the Axial View and select the Volume named all


    2d viewer59 l.jpg
    2D Viewer

    The volume is superimposed to the images


    Image fusion l.jpg
    Image Fusion

    Fade slider: fades between foreground and background.

    Set the Fade slider to 0.5


    2d viewer61 l.jpg
    2D Viewer

    Fade slider effect


    Clipping models l.jpg
    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.

    • Models  Display tab


    Clipping models63 l.jpg
    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. Select Clipping.

    • 4. Select the Clip tab of the Models panel


    Clipping models64 l.jpg
    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 models65 l.jpg
    Clipping Models

    Clipping Model Result


    Conclusion l.jpg
    Conclusion

    • Intuitive Interface for Loading/Visualizing Data

    • Each Slicer module contains tools for

      • Visualizing

      • Registering

      • Segmenting

      • Modeling

      • Quantifying

    • Open-source tool for developing your own module


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