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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

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Slicer training 1 loading and viewing data l.jpg

Slicer Training 1 Loading and Viewing Data

Sonia Pujol, Ph.D.

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


Acknowledgments l.jpg

Acknowledgments

National Alliance for Medical Image Computing

NIH U54EB005149

Neuroimage Analysis Center

NIH P41RR013218


Disclaimer l.jpg

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 l.jpg

Welcome to 3D Slicer


Goal of the tutorial l.jpg

Goal of the tutorial

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


Material l.jpg

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 l.jpg

Goal of the tutorial

Final result of the series of exercises


Overview l.jpg

Overview

  • Part 1: Slicer Interface

  • Part 2: Loading Data

  • Part 3: Interacting with Data


Slicer interface l.jpg

Menu

Viewer

Tk window

Slicer Interface


Slicer menu l.jpg

Slicer Menu

Select the Volumes Module


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Panels and Tabs

The Panel of the Volumes Module appears


Slicer menu12 l.jpg

Panels

Sliders

Buttons

Control Window

Slicer Menu


Main menu l.jpg

  • 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 l.jpg

Viewer window

Observe the Viewer Window

  • Upper part is

    3D Viewer

  • Lower part is 2D Viewer

    3 separate views

    Independent controls


Slicer modules l.jpg

Slicer Modules

The architecture of Slicer is modular

Select Modules in the SubMenu


Slicer modules16 l.jpg

Slicer Modules

Settings

IO

Application

Filtering

Segmentation

Registration

Measurement

Visualization

Examples

Unfiled

Alpha

The list of Slicer Modules categories appears


Slicer modules tutorials l.jpg

  • 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 l.jpg

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 l.jpg

Overview

  • Part 1: Slicer Interface

  • Part 2: Loading Data

  • Part 3: Interacting with Data


Loading data l.jpg

Loading Data

Slicer can load

  • Volumes …………………..


Loading data21 l.jpg

Loading Data

Slicer can load

  • Volumes …………………..

  • Models …………………….

    A model is a 3D reconstruction of the anatomy


Loading data22 l.jpg

Loading Data

Slicer can load

  • Volumes …………………..

  • Models …………………….

    A model is a 3D reconstruction of the anatomy

  • Scenes …………………….

    Scene = Volume + Model


Loading data23 l.jpg

Loading Data

Slicer Advantage

Putting together Images and Surface


Data representation l.jpg

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 l.jpg

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 l.jpg

Loading DICOM Volumes

Click on Add Volume in the Slicer Menu


Loading dicom volumes27 l.jpg

Loading DICOM Volumes

The Panel Props

appears by default.

Left-click on the Menu

Properties and change Basic

to DICOM


Loading dicom volumes28 l.jpg

Loading DICOM Volumes

The DICOM panel appears

Click on Select DICOM Volume


Loading dicom volumes29 l.jpg

Loading DICOM Volumes

Select the directory dicom in

the Tutorial-with-dicom dataset


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Loading DICOM Volumes

The list of DICOM studies appears.

Click OK


Loading dicom volumes31 l.jpg

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 l.jpg

Loading DICOM Volumes

The DICOM Header

information panel appears

Click Apply


Loading dicom volumes33 l.jpg

Loading DICOM Volumes

Slicer loads the

DICOM volume of

the brain


Visualization support l.jpg

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 l.jpg

Visualization Support

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


Viewing volumes l.jpg

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 l.jpg

Viewing Volumes

The Axial, Sagittal and Coronal Images appear in the Viewer


Manipulating the images l.jpg

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 l.jpg

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 l.jpg

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 l.jpg

Viewing Volumes

The View Menu contains

different options to visualize the data

Select the 3D View


Viewing volumes42 l.jpg

Viewing Volumes

3D View

focuses on 3D


Viewing volumes43 l.jpg

Viewing Volumes

The View Menu contains

different options to visualize the data

Select 4x512


Viewing volumes44 l.jpg

Viewing Volumes

4x512 view: larger image views to see details


Viewing volumes45 l.jpg

Viewing Volumes

The View Menu contains

different options to visualize the data

Select 1x512


Viewing volumes46 l.jpg

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 l.jpg

Viewing Volumes

The View Menu contains

different options to visualize

the data

Select 4x256


Viewing volumes48 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)

  • Slider selects which slice of volume to display

  • Field shows the slice number

3

1

1

2

3


2d viewer50 l.jpg

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 l.jpg

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 l.jpg

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 l.jpg

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 l.jpg

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 l.jpg

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 l.jpg

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 l.jpg

Volumes without Header

The spgr volume appears in the Viewer


Loading data58 l.jpg

Loading Data

Slicer can load

  • Volumes …………………..

  • Models …………………….

    A model is a 3D reconstruction of the anatomy

  • Scenes …………………….

    Scene = Volume + Model


Loading models l.jpg

Loading Models

In the main Menu select the

module Data and Click on

Add Model.


Loading models60 l.jpg

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 l.jpg

Loading Models

The model of the vessels appears in the Viewer.


Loading data62 l.jpg

Loading Data

Slicer can load

  • Volumes …………………..

  • Models …………………….

    A model is a 3D reconstruction of the anatomy

  • Scenes …………………….

    Scene = Volume + Model


Loading a scene l.jpg

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 l.jpg

Loading a Scene

The viewer displays thetutorial Scene


Loading a scene65 l.jpg

Loading a Scene

The elements of the Scene are listed in the Menu Window


Overview66 l.jpg

Overview

  • Part 1: Slicer Interface

  • Part 2: Loading Data

  • Part 3: Interacting with Data


Manipulating a model l.jpg

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 l.jpg

Manipulating a Model

Put the mouse on the 3D Slicer icon


Manipulating a model69 l.jpg

Manipulating a Model

The Control Window appears


Manipulating a model70 l.jpg

Manipulating a Model

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


Manipulating a model71 l.jpg

Manipulating a Model

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


Manipulating a model72 l.jpg

Manipulating a Model

Click on the Spin button


Manipulating a model73 l.jpg

Manipulating a Model

The model starts spinning inside the Viewer Panel.


Manipulating a model74 l.jpg

Manipulating a Model

Click on the Rock button


Manipulating a model75 l.jpg

Manipulating a Model

The model starts rocking inside the Viewer Panel.


Manipulating a model76 l.jpg

Manipulating a Model

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


Models representation l.jpg

Models representation

A model is a 3D representation

of the anatomy.

Type W (Wireframe) in the Main Window


Models representation78 l.jpg

Models representation

The triangles of the Model become visible in the Viewer.

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


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 opacity80 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 models


Model visibility82 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:the models have disappeared


2d viewer85 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 None


2d viewer86 l.jpg

2D Viewer

Lb: displays label map

Displays results of a segmentation

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


2d viewer87 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 viewer88 l.jpg

2D Viewer

Lb: displays label map

Displays results of a segmentation

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


2d viewer89 l.jpg

2D Viewer

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


2d viewer90 l.jpg

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 l.jpg

Image Fusion

  • Fade slider:

  • fades between foreground

  • and background.

Set the Fade slider to 0.5


2d viewer92 l.jpg

2D Viewer

The volume all is superimposed on the images


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.

Select the Models  Display tab


Clipping models94 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. 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 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 models96 l.jpg

Clipping Models

Clipping Model Result


Conclusion l.jpg

Conclusion

  • Intuitive Interface for Loading and Visualizing Data

  • Slicer Outcome = fusion of Volumes and Surface

  • Open-source tool for developing your own module


  • Login