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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

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slicer training 1 loading and viewing data

Slicer Training 1 Loading and Viewing Data

Sonia Pujol, Ph.D.

Randy Gollub, M.D., Ph.D.

acknowledgments
Acknowledgments

National Alliance for Medical Image Computing

NIH U54EB005149

Neuroimage Analysis Center

NIH P41RR013218

disclaimer
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.

goal of the tutorial
Goal of the tutorial

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

material
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

Exercises

Questions

Answers

goal of the tutorial7
Goal of the tutorial

Final result of the series of exercises

overview
Overview
  • Part 1: Slicer Interface
  • Part 2: Loading Data
  • Part 3: Interacting with Data
slicer interface

Menu

Viewer

Tk window

Slicer Interface
slicer menu
Slicer Menu

Select the Volumes Module

panels and tabs
Panels and Tabs

The Panel of the Volumes Module appears

slicer menu12

Panels

Sliders

Buttons

Control Window

Slicer Menu
main menu

File

    • Opening files
    • Saving files
    • Closing files
    • Exit
  • Modules
  • Slicer Modules
  • View
  • Selecting view mode
  • Help
  • Links to Slicer Modules information
Main Menu

Observe the different options of the Main Menu

viewer window
Viewer window

Observe the Viewer Window

  • Upper part is

3D Viewer

  • Lower part is 2D Viewer

3 separate views

Independent controls

slicer modules
Slicer Modules

The architecture of Slicer is modular

Select Modules in the SubMenu

slicer modules16
Slicer Modules

Settings

IO

Application

Filtering

Segmentation

Registration

Measurement

Visualization

Examples

Unfiled

Alpha

The list of Slicer Modules categories appears

slicer modules tutorials

fMRIEngine ………. SlicerTraining 5

  • vtkFreeSurferReaders ... SlicerTraining 6
  • Editor …………….. SlicerTraining 2
  • Level-Sets ……….. SlicerTraining 3
  • DTMRI ……………. SlicerTraining 4
Slicer Modules: tutorials

Settings

IO

Application

Filtering

Segmentation

Registration

Measurement

Visualization

Examples

Unfiled

Alpha

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
overview19
Overview
  • Part 1: Slicer Interface
  • Part 2: Loading Data
  • Part 3: Interacting with Data
loading data
Loading Data

Slicer can load

  • Volumes …………………..
loading data21
Loading Data

Slicer can load

  • Volumes …………………..
  • Models …………………….

A model is a 3D reconstruction of the anatomy

loading data22
Loading Data

Slicer can load

  • Volumes …………………..
  • Models …………………….

A model is a 3D reconstruction of the anatomy

  • Scenes …………………….

Scene = Volume + Model

loading data23
Loading Data

Slicer Advantage

Putting together Images and Surface

data representation

Header

Header

Header

Header

Raw Data

Raw Data

Raw Data

Raw Data

Data representation
  • Volume = collection of image files
  • Image file = header + raw data

The header contains the parameters of the image.

data representation25

Header

Header

Header

Header

Raw Data

Raw Data

Raw Data

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

a

Pixel (a,b)

b

Intensity

I (a,b)

loading dicom volumes
Loading DICOM Volumes

Click on Add Volume in the Slicer Menu

loading dicom volumes27
Loading DICOM Volumes

The Panel Props

appears by default.

Left-click on the Menu

Properties and change Basic

to DICOM

loading dicom volumes28
Loading DICOM Volumes

The DICOM panel appears

Click on Select DICOM Volume

loading dicom volumes29
Loading DICOM Volumes

Select the directory dicom in

the Tutorial-with-dicom dataset

loading dicom volumes30
Loading DICOM Volumes

The list of DICOM studies appears.

Click OK

loading dicom volumes31
Loading DICOM Volumes

Name : The name that the

volume will have within Slicer

Slicer loads the dicom study

Change to something descriptive: Cortex and click on Header

loading dicom volumes32
Loading DICOM Volumes

The DICOM Header

information panel appears

Click Apply

loading dicom volumes33
Loading DICOM Volumes

Slicer loads the

DICOM volume of

the brain

visualization support
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 support35
Visualization Support

The value of the gray level of the pixel under the cursor appears in the corresponding slice

viewing volumes
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 volumes37
Viewing Volumes

The Axial, Sagittal and Coronal Images appear in the Viewer

manipulating the images
Manipulating the images
  • Rotation

Position the mouse on the images inside the Viewer

Left-click and move the mouse to the left

The images move to the left

manipulating the images39
Manipulating the images
  • Zoom

Position the mouse on the images inside the Viewer

Right-click and move the mouse down

The viewer gets closer to the model

manipulating the images40
Manipulating the images
  • Zoom

Position the mouse on the images inside the Viewer

Right-click and move the mouse up

The viewer moves away from the model

viewing volumes41
Viewing Volumes

The View Menu contains

different options to visualize the data

Select the 3D View

viewing volumes42
Viewing Volumes

3D View

focuses on 3D

viewing volumes43
Viewing Volumes

The View Menu contains

different options to visualize the data

Select 4x512

viewing volumes44
Viewing Volumes

4x512 view: larger image views to see details

viewing volumes45
Viewing Volumes

The View Menu contains

different options to visualize the data

Select 1x512

viewing volumes46
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 volumes47
Viewing Volumes

The View Menu contains

different options to visualize

the data

Select 4x256

viewing volumes48
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)
  • Slider selects which slice of volume to display
  • Field shows the slice number

3

1

1

2

3

2d viewer50
2D Viewer

4

  • Bg (Background): displays volume in background layer
  • Fg (Foreground): displays volume in foreground layer

Superimposed over the background layer

5

4

5

volumes without header
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 header52
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 header53
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

volumes without header54
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

volumes without header55

3

4

5

3

4

6

5

6

7

7

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.

volumes without header56

8

9

10

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 load the volume.

volumes without header57
Volumes without Header

The spgr volume appears in the Viewer

loading data58
Loading Data

Slicer can load

  • Volumes …………………..
  • Models …………………….

A model is a 3D reconstruction of the anatomy

  • Scenes …………………….

Scene = Volume + Model

loading models
Loading Models

In the main Menu select the

module Data and Click on

Add Model.

loading models60
Loading Models

The Props tab of the module

Models appears

Select the model named Vessels in the directory tutorial/models

Click on Apply

loading models61
Loading Models

The model of the vessels appears in the Viewer.

loading data62
Loading Data

Slicer can load

  • Volumes …………………..
  • Models …………………….

A model is a 3D reconstruction of the anatomy

  • Scenes …………………….

Scene = Volume + Model

loading a scene
Loading a Scene

A Scene is represented as an Xml file.

  • Select File Open Scene
  • in the Main Menu
  • Select the file tutorial.xml in the directory Tutorial-with-dicom/tutorial.
loading a scene64
Loading a Scene

The viewer displays thetutorial Scene

loading a scene65
Loading a Scene

The elements of the Scene are listed in the Menu Window

overview66
Overview
  • Part 1: Slicer Interface
  • Part 2: Loading Data
  • Part 3: Interacting with Data
manipulating a model
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 model68
Manipulating a Model

Put the mouse on the 3D Slicer icon

manipulating a model69
Manipulating a Model

The Control Window appears

manipulating a model70
Manipulating a Model

Position the mouse on the R letter (Right) inside the window

manipulating a model71
Manipulating a Model

The View Panel shows the model from the right side of the patient

manipulating a model72
Manipulating a Model

Click on the Spin button

manipulating a model73
Manipulating a Model

The model starts spinning inside the Viewer Panel.

manipulating a model74
Manipulating a Model

Click on the Rock button

manipulating a model75
Manipulating a Model

The model starts rocking inside the Viewer Panel.

manipulating a model76
Manipulating a Model

Come back to initial orientation of the Viewer Panel by clicking on the A letter (Anterior) inside the window.

models representation
Models representation

A model is a 3D representation

of the anatomy.

Type W (Wireframe) in the Main Window

models representation78
Models representation

The triangles of the Model become visible in the Viewer.

Type S (Surface) to come back to Surface Mode rendering

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 opacity80
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 models

model visibility82
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:the models have disappeared

2d viewer85
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 viewer86
2D Viewer

Lb: displays label map

Displays results of a segmentation

The segmented volume named all disappears from the 2D Viewer.

2d viewer87
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 viewer88
2D Viewer

Lb: displays label map

Displays results of a segmentation

The segmented volume named all appears in the 2D Viewer.

2d viewer89
2D Viewer

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

2d viewer90
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
Image Fusion
  • Fade slider:
  • fades between foreground
  • and background.

Set the Fade slider to 0.5

2d viewer92
2D Viewer

The volume all is superimposed on the images

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.

Select the Models  Display tab

clipping models94
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 models95
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 models96
Clipping Models

Clipping Model Result

conclusion
Conclusion
  • Intuitive Interface for Loading and Visualizing Data
  • Slicer Outcome = fusion of Volumes and Surface
  • Open-source tool for developing your own module
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