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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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goal of this tutorial
Goal of this tutorial

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

material
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
Goal of the tutorial

Final Result of the series of exercises

overview of training 1
Overview of Training 1
  • Part 1: Slicer Interface
  • Part 2: Loading Data
  • Part 3: Viewing Data
slicer interface
Slicer Interface

Menu

Viewer

Tk window

slicer menu
Slicer Menu

Main Menu

Panels

Sliders

Select the Volumes Module

Buttons

panels and tabs
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.
slicer modules
Slicer Modules

Click on More

The list of Modules appears.

submenus
Submenus
  • File
    • Opening files
    • Saving files
    • Close
    • Exit
  • View
    • Selecting view mode
  • Help
    • Links to Slicer information
viewer window
Viewer window
  • Upper part is 3D Viewer
  • Lower part is 2D Viewer
    • 3 separate views
    • Independent controls
exercise 1 slicer gui
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
Overview of Training 1
  • Part 1: Slicer Interface
  • Part 2: Loading Data
  • Part 3: Viewing Data
loading data
Loading Data

Slicer can load

  • Volumes
  • Models
  • Scenes = Volumes + Models
loading volumes overview
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
DICOM Volumes
  • Main  Data  Add Volume  Props
  • 2. From Properties Change Basic DICOM
dicom volumes18
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
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
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
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
Loading DICOM Volumes

The DICOM Header information panel appears

…Slicer loads the data

Click Apply

loading dicom volumes23
Loading DICOM Volumes

The Viewer contains the DICOM volume

loading volumes without header
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
Loading Volumes without Header

The Header section of the Props tab appears.

loading volumes without header26
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

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

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
Loading Volumes without Header

The spgr volume appears in the Viewer

loading data30
Loading Data

Slicer can load

  • Volumes
  • Models
  • Scenes = Volumes + Models
loading models
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
Loading Models

The model of the vessels appears in the Viewer.

loading data33
Loading Data

Slicer can load

  • Volumes
  • Models
  • Scenes = Volumes + Models
loading a scene
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
Loading a Scene

tutorial Scene

overview of training 136
Overview of Training 1
  • Part 1: Slicer Interface
  • Part 2: Loading Data
  • Part 3: Viewing Data
manipulating model
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
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
Model Opacity

Skin model Opacity

= 0.5

model visibility
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
Model Visibility

Vessels model Visibility 0ff

global visibility
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
Viewing 3D Models

Show None Models have disappeared

viewing volumes 1 of 5
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
Viewing Volumes (1 of 5)

The Axial, Sagittal and Coronal Images appear in the Viewer

viewing volumes 1 of 546
Viewing Volumes (1 of 5)
  • View Menu contains different options to visualize the data

Select the 3D View

viewing volumes
Viewing Volumes

3D view: focuses on 3D.

viewing volumes 1 of 548
Viewing Volumes (1 of 5)
  • View Menu contains different options to visualize the data

Select 4x512

viewing volumes49
Viewing Volumes

4x512 view: larger image views to see details

viewing volumes 1 of 550
Viewing Volumes (1 of 5)
  • View Menu contains different options to visualize the data

Select 1x512

viewing volumes51
Viewing Volumes

1x512 view: one large, three small images.

viewing volumes 1 of 552
Viewing Volumes (1 of 5)
  • View Menu contains different options to visualize the data

Select 4x256

viewing volumes53
Viewing Volumes

4x256 view: smaller equal-sized images.

Come back to Normal View

2d viewer
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
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
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
2D Viewer

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

2d viewer58
2D Viewer

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

2d viewer59
2D Viewer

The volume is superimposed to the images

image fusion
Image Fusion

Fade slider: fades between foreground and background.

Set the Fade slider to 0.5

2d viewer61
2D Viewer

Fade slider effect

clipping models
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
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
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
Clipping Models

Clipping Model Result

conclusion
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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