Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Training 1 Loading and...

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 Imaging

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 this tutorial

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



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

Questions Answers

35 Exercises



Goal of the tutorial

Final result of the series of exercises



Overview of Training 1

• Part 1: Slicer Interface

• Part 2: Loading Data

• Part 3: Interacting with Data



Slicer Interface

Viewer

Menu

Tk window



Slicer Menu

Main Menu

Panels

Sliders

Buttons

Select the Volumes Module

Control Window



Panels and Tabs

• Each panel has tabs along the top

• Leftmost tab is Help• Panel may contain

controls and displays

The Panel of the Volumes Module

appears



Slicer Modules

• The architecture of Slicer is modular

Select Modules in the SubMenu



Slicer Modules

The list of Slicer Modules appears

Settings

IO

Application

Filtering

Segmentation

Registration

Measurement

Visualization

Examples

Unfield

Alpha



Slicer Modules: tutorialsSettings

IO

Application

Filtering

Segmentation

Registration

Measurement

Visualization

Examples

Unfiled

Alpha

•fMRIEngine ………. SlicerTraining 5

•Editor …………….. SlicerTraining 2

•Level-Sets ……….. SlicerTraining 3

•DTMRI ……………. SlicerTraining 4



Submenus

• HelpLinks to Slicer information

•File–Opening files–Saving files–Close–Exit

•ViewSelecting view mode

•ModulesSlicer Modules

Observe the different options of the Main Menu



Viewer window

• Upper part is 3D Viewer

• Lower part is 2D Viewer– 3 separate views– Independent controls

Observe the Viewer Window



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



Loading Data

Slicer can load

• Volumes …………………..

• Models …………………….A model is a 3D reconstruction of the anatomy

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



Loading Data

Slicer Power

Putting together Images and Surface



Loading Data

Slicer can load

• Volumes …………………..





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 Volumes: Overview1. Main Data

2. Add VolumeProps 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



1. Main Data Add Volume Props

2. From Properties Change Basic DICOM

DICOM Volumes



3. Select DICOM Volume

A dialog box appears

4. Select directory and click OK

DICOM Volumes

A DICOM panel appears

Slicer searches for every DICOM file.



DICOM Volumes

• Name The name that the volume will have within Slicer

• Optional Description You may enter a description.

5. Change to something descriptive: “Cortex“

6. Click Header



Loading DICOM Volumes

The DICOM Header information panel appears

…Slicer loads the data

7. Click Apply



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

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 (1 of 5)

Select 1x512





Viewing Volumes

1x512 view: one large, 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

• 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

1

2

1

2

3

3



Superimpose

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

Superimposed over the background layer

4

5

4

5



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

6

6



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



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 Header1. 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



Volumes without Header• 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- useful when several DICOM

acquisitions are lumped together.

Click OK



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

1. Main Data Add ModelProps tab appears

2. Browse

3. Name field

4. Color pull-down menu

5. Click Apply to read in the model.

In dialog box, select the model named Vessels and click Open.

Make descriptive: Vessels

Select color for the 3D Viewer



Loading Models

The model of the vessels appears in

the Viewer.



Loading Data

Slicer can load

• Volumes …………………..





Loading a Scene

• File Open Scene.• Find the file tutorial.xml • Double-click it, • Wait for the volumes and models to load.

• A Scene is represented as an Xml file



Loading a Scene

The viewer displays the

tutorial Scene



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



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.



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 Models have disappeared



2D Viewer

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



2D Viewer

The volume all is superimposed on the images



Image Fusion

•Fade slider:

fades between foreground

and background.

Set the Fade slider to 0.5



2D Viewer

Fade slider effect



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



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 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

Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Training 1 Loading and...

Documents

Transcript of Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Training 1 Loading and...