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Slicer Training 1 Loading and Viewing Data PowerPoint PPT Presentation


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

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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

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

Exercises

Questions

Answers


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


Menu

Viewer

Tk window

Slicer Interface


Slicer Menu

Select the Volumes Module


Panels and Tabs

The Panel of the Volumes Module appears


Panels

Sliders

Buttons

Control Window

Slicer 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

Observe the Viewer Window

  • Upper part is

    3D Viewer

  • Lower part is 2D Viewer

    3 separate views

    Independent controls


Slicer Modules

The architecture of Slicer is modular

Select Modules in the SubMenu


Slicer Modules

Settings

IO

Application

Filtering

Segmentation

Registration

Measurement

Visualization

Examples

Unfiled

Alpha

The list of Slicer Modules categories appears


  • 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

  • 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


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.


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

Click on Add Volume in the Slicer Menu


Loading DICOM Volumes

The Panel Props

appears by default.

Left-click on the Menu

Properties and change Basic

to DICOM


Loading DICOM Volumes

The DICOM panel appears

Click on Select DICOM Volume


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

Slicer loads the dicom study

Change to something descriptive: Cortex and click on Header


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

  • 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 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 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 Volumes

The View Menu contains

different options to visualize the data

Select the 3D View


Viewing Volumes

3D View

focuses on 3D


Viewing Volumes

The View Menu contains

different options to visualize the data

Select 4x512


Viewing Volumes

4x512 view: larger image views to see details


Viewing Volumes

The View Menu contains

different options to visualize the data

Select 1x512


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

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 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

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


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


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.


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 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

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 Scene

The viewer displays thetutorial 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


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