Data Loading and Visualization-3735

Surgical Planning Laboratoryhttp://www.slicer.org-1-

Brigham and Women’s Hospital

Slicer Training 1 Loading and Viewing Data

Sonia Pujol, Ph.D.

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



Acknowledgments

National Alliance for Medical Image ComputingNIH 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

Questions Answers

Exercises

• Slicer 2.6http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started

• Sample Tutorial Data: tutorial-with-dicom.ziphttp://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101



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



Slicer Interface

Tk window

Viewer

Menu



Slicer Menu

Select the Volumes Module



Panels and Tabs

The Panel of the Volumes Module

appears



Slicer Menu

Panels

Sliders

Buttons

Control Window



Main MenuObserve the different options of the Main Menu

•ViewSelecting view mode

•ModulesSlicer Modules

•File–Opening files–Saving files–Closing files–Exit

•HelpLinks to Slicer Modules information



Viewer window

• Upper part is

3D Viewer

• Lower part is 2D Viewer3 separate views

Independent controls

Observe the Viewer Window



Slicer Modules

The architecture of Slicer is modular

Select Modules in the SubMenu



Slicer Modules

The list of Slicer Modules categories appears

Settings

IO

Application

Filtering

Segmentation

Registration

Measurement

Visualization

Examples

Unfiled

Alpha



Slicer Modules: tutorialsSettings

IO

Application

Filtering

Segmentation

Registration

Measurement

Visualization

Examples

Unfiled

Alpha

•Editor …………….. SlicerTraining 2

•Level-Sets ……….. SlicerTraining 3

•fMRIEngine ………. SlicerTraining 5

•vtkFreeSurferReaders ... SlicerTraining 6

•DTMRI ……………. SlicerTraining 4



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






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 …………………..


• Scenes …………………….Scene = Volume + Model



Loading Data

Slicer Advantage

Putting together Images and Surface



Data representation

• Volume = collection of image files• Image file = header + raw dataThe header contains the parameters of the image.

Header

Raw Data

Header

Raw Data

Header

Raw Data

Header

Raw Data



Data representation

• Volume = collection of image files• Image file = header + raw dataThe header contains the parameters of the image.

• Representation of an image:

2D Array of pixels containing the intensity values

Header

Raw Data

Header

Raw Data

Header

Raw Data

Header

Raw Data

Pixel (a,b)

Intensity

I (a,b)

a

b



Loading DICOM Volumes

Click on Add Volume in the Slicer Menu



Left-click on the Menu

Properties and change Basicto DICOM


The Panel Propsappears by default.



Click on Select DICOM Volume


The DICOM panel appears



Select the directory dicom in

the Tutorial-with-dicom dataset





The list of DICOM studies appears.

Click OK




Name : The name that the

volume will have within Slicer

Change to something descriptive: Cortex and click on Header

Slicer loads the dicom study




The DICOM Headerinformation panel appears

Click Apply




Slicer loads theDICOM volume ofthe 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 VolumesV 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

Position the mouse on the images inside the Viewer

Left-click and move the mouse to the left

• Rotation

The images move to the left





Right-click and move the mouse down

The viewer gets closer to the model

• Zoom





Right-click and move the mouse up

The viewer moves away from the model

• Zoom



Viewing Volumes

Select the 3D View

The View Menu contains

different options to visualize the data



Viewing Volumes

3D Viewfocuses on 3D



Viewing Volumes

Select 4x512





Viewing Volumes

4x512 view: larger image views to see details



Viewing Volumes

Select 1x512





Viewing Volumes

1x512: one large TRANSVERSEview and three smallimages

1x512 COR: one large CORONAL viewand three small images1x512 SAG: one large SAGITTAL viewand three small images



Viewing Volumes

The View Menu containsdifferent options to visualizethe data

Select 4x256



Viewing Volumes

4x256 view: smaller equal-sized images

Come back to Normal View



2D Viewer

• Three 2D windows (red, yellow, and green)• Slider selects which slice of volume to display • Field shows the slice number

1

2

1

2

3

3



2D Viewer

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

Superimposed over the background layer

4

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




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 Header1. 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



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.


2

1

The Header section of the Props tab appears.




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.

34

56

7

3

4

5

6

7



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.

8

9

10

8

9

10

Click Apply to load the volume.





The spgr volume appears in the

Viewer



Loading Data

Slicer can load

• Volumes …………………..





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 …………………..





Loading a Scene

•Select File Open Scene

in the Main Menu•Select the file tutorial.xml in the directory Tutorial-with-dicom/tutorial.

A Scene is represented as an Xml file.



Loading a Scene

The viewer displays the

tutorial Scene



Loading a Scene

The elements of the Scene are listed in the Menu Window



Overview






Manipulating a Model

The model appears in the

3D Viewer.

•Rotate the model: with left mouse button •Zoom the model: with right mouse button




Put the mouse on the 3D Slicer icon




The Control Window appears




Position the mouse on the R letter

(Right) inside the window




The View Panel shows the model

from the right side of the patient




Click on the Spin button




The model starts spinning inside the

Viewer Panel.




Click on the Rock button




The model starts rocking inside the

Viewer Panel.




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 Opacity1. Click on Models in the

Main Menu

2. Select the Display Tab

The properties Panel of the model appears

3. OpacitySet the opacity of the Skin model to 0.5



Model Opacity

Skin model

Opacity = 0.5



Model VisibilityVisibility 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

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





2D Viewer

Left click on Lb in the Axial View and select the Label Map named all.





2D Viewer

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



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



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

Health & Medicine

Data Loading and Visualization-3735