Slicer Tutorial Module: DTMRI Data: Dartmouth DTI

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Slicer TutorialModule: DTMRIData: Dartmouth DTI

May 26-27, 2005

National Alliance for Medical Image Computing http://na-mic.org

Pre-requisites

• Slicer 2.5 already installed fromhttp://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Getting_Started

• Dartmouth DTI Data Set (first of six normals on BIRN servers) downloaded using instructions inhttp://www.na-mic.org/Wiki/index.php/DataRepository

• Dartmouth DTI “protocol” saved in slicer2/Modules/vtkDTMRI/data/ NAMIC-Dartmouth-2b12g-Volume


Tutorial: Slicer DTMRI Module

• Introducing the Module– Load Diffusion Data– Convert to Tensor– Compute Fractional Anisotropy (FA)– Perform Tractography– Save Tracts and Scene

• Use Case from BWH– Compute Statistics on FA of ROI


Load Dartmouth DTI images

1: Click Add Volume

2: Use the Basic Reader

3: Click File Browse

4: Pick First File

5: Switch to Manual

6: Click Apply


Load Dartmouth images (contd)

7: Set Thickness to 3

8: Set Order to Axial SI

9: Little Endian “Yes”

10: Click Apply

11: DWI ImagesAppear

Q: Where is the MRML file? What does it contain?


Convert To Tensors

12: Go to DTMRIModule

13: Pick ConvertTab

14: Protocol isNAMIC-Dartmouth-2b12g-Volume

15: Pick Convert(ignore warningmessages)

16: Resulting Viewerwindow looks like this:


Converted Tensor Image16: Resulting viewer windowlooks like this:

Q: What is it that we are viewing in this image?What is in the protocol file we just used?


Adjust Image Win-LevelSelect “Volumes” and

Adjust Window and LevelResulting Image

Aside

Select the AvGradient volume


Tractography Steps

1. Compute Fractional Anisotropy (FA)

2. Create Tracts• Individually• From segmented ROI


Tractography Step 1: Compute Fractional Anisotropy (FA)

Select DTMRI

Select Scalars (if you don’t see it, select More until you do)

Select FAResulting Image

Apply

Q: What does the MRML file contain now?Q1: Where is the MRML file? What does it contain?Q2: How do you read the FA value at a certain RAS location off the screen?


Tractography Steps

1. Compute Fractional Anisotropy (FA)

2. Create Tracts• Individually• From segmented ROI


Tractography Step 2:Create Individual Tracts

• Setup color of tracts

• Setup 3D view

• Create one tract

• Add slices to 3D view. Zoom and rotate to optimize view.

• Add more tracts individually.

• Add tracts using a segmented ROI.


Tractography Step 2: Go to Tractography Tab

More

Select Display

Select Tractography


Tractography Step 2 (contd): Select color for display of tracts

Select Color

Click on new colorCurrent Selection of Tract Color


Tractography Step 2 (contd): Set up 3D window for viewing tracts

Click on “A” toorient volume view

Notice volumeorientation


Tractography Step 2 (contd): Create a single tract

To create a single tract originating at a point in the corpus collosum: position mouse on the point and hit the “s” key.


Tractography Step 2 (contd):

View tract in 3D window

See the tiny tract in the 3D window.



Zoom in 3D window

Drag Right Mouse Button Down in 3D Window to Zoom In.



Show Slices in 3D window

Click “v” to show slices in 3D window.



Show Slices in 3D window

Click on the left arrow tip to rotate volume…



Rotate and Zoom Volume to optimize view

Drag Left Mouse Button in 3D window to Rotate, and Right Mouse Button to Zoom. Do this until you get to a view you like.



Add more tracts

Add tracts by moving mouse to different points in corpus collosum and hitting the “s” key. Watch tracts appear in the volume window.

Q: What happens if you hold the “s” key down and drag the mouse in the corpus collosum?



Segment ROI (then use it to seed tracts)

Select new color

Start Editor

Effects Tab

Draw

Draw Module



Segment ROI (then use it to seed tracts)

Draw Outlinewith Mouse

Hit Apply to Fill Outline.

Note name of segmented volume.



Generate Tracts from Segmented ROI

Resulting TractsAppear in 3D view.




Zoom and Rotate 3D view by dragging right and left mouse buttons




Add a Slice to 3D view


Tractography Steps

1. Compute Fractional Anisotropy (FA)2. Create Tracts

• Individually• From segmented ROI

3. Save Tracts• Save 3D Model of Tracts• Add Model to Current Scene• Save scene


Save TractsSave 3D Model of Tracts

Give a name such as “savedTractsTutorial” and it Will be saved as “savedTractsTutorial.xml”

Q: Can you open this xml file in a web browser?What does it contain? How many models? Why?


Save TractsAdd Model to Scene

This is the tractFile that was just saved


Save TractsSave Scene


Open Saved Scene


Use Case: Measure FA Statistics in ROI


Measure FA Statistics in ROI

Manually draw a labelmap over your region of interest.

VolumeMath Module:

Modules Measurement VolumeMath


MaskStat Button in VolumeMath

We use the MaskStat button, which:

1) uses our labelmap as a “mask” over the FA volume

2) calculates “stats” on the region contained under the labelmap

First, however, we have to “cast” our FA volume as a different file type.

(*note: this is an extra step that will be resolved in the near future, but for now it is necessary!)


“Cast” FA Volume

The FA volume must be cast as a different file type (“short”) for the computation to work

1) click Cast button

2) Volume to Cast: FractionalAnisotropy

3) Cast Output: FractionalAnisotropy

4) Output Type: Short

5) click Run


MaskStat

1) click MaskStat button

2) Volume to Mask: FractionalAnisotropy

3) LabelMap: Working

4) Masked Output: Create New

5) make sure Mask color (e.g., 2) is the same as your labelmap

6) optional: choose a directory to place the output text file

7) click Run


MaskStat Result

result in Slicer

result in output text file


Do Some DTI!

Documents

Slicer Tutorial Module: DTMRI Data: Dartmouth DTI