Slicer Tutorial Module: DTMRI Data: Dartmouth DTI
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Transcript of 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
National Alliance for Medical Image Computing http://na-mic.org
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
National Alliance for Medical Image Computing http://na-mic.org
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
National Alliance for Medical Image Computing http://na-mic.org
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?
National Alliance for Medical Image Computing http://na-mic.org
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:
National Alliance for Medical Image Computing http://na-mic.org
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?
National Alliance for Medical Image Computing http://na-mic.org
Adjust Image Win-LevelSelect “Volumes” and
Adjust Window and LevelResulting Image
Aside
Select the AvGradient volume
National Alliance for Medical Image Computing http://na-mic.org
Tractography Steps
1. Compute Fractional Anisotropy (FA)
2. Create Tracts• Individually• From segmented ROI
National Alliance for Medical Image Computing http://na-mic.org
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?
National Alliance for Medical Image Computing http://na-mic.org
Tractography Steps
1. Compute Fractional Anisotropy (FA)
2. Create Tracts• Individually• From segmented ROI
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2: Go to Tractography Tab
More
Select Display
Select Tractography
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd): Select color for display of tracts
Select Color
Click on new colorCurrent Selection of Tract Color
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd): Set up 3D window for viewing tracts
Click on “A” toorient volume view
Notice volumeorientation
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
View tract in 3D window
See the tiny tract in the 3D window.
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
Zoom in 3D window
Drag Right Mouse Button Down in 3D Window to Zoom In.
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
Show Slices in 3D window
Click “v” to show slices in 3D window.
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
Show Slices in 3D window
Click on the left arrow tip to rotate volume…
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
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.
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
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?
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
Segment ROI (then use it to seed tracts)
Select new color
Start Editor
Effects Tab
Draw
Draw Module
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
Segment ROI (then use it to seed tracts)
Draw Outlinewith Mouse
Hit Apply to Fill Outline.
Note name of segmented volume.
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
Generate Tracts from Segmented ROI
Resulting TractsAppear in 3D view.
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
Generate Tracts from Segmented ROI
Zoom and Rotate 3D view by dragging right and left mouse buttons
National Alliance for Medical Image Computing http://na-mic.org
Tractography Step 2 (contd):
Generate Tracts from Segmented ROI
Add a Slice to 3D view
National Alliance for Medical Image Computing http://na-mic.org
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
National Alliance for Medical Image Computing http://na-mic.org
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?
National Alliance for Medical Image Computing http://na-mic.org
Save TractsAdd Model to Scene
This is the tractFile that was just saved
National Alliance for Medical Image Computing http://na-mic.org
Save TractsSave Scene
National Alliance for Medical Image Computing http://na-mic.org
Open Saved Scene
National Alliance for Medical Image Computing http://na-mic.org
Use Case: Measure FA Statistics in ROI
National Alliance for Medical Image Computing http://na-mic.org
Measure FA Statistics in ROI
Manually draw a labelmap over your region of interest.
VolumeMath Module:
Modules Measurement VolumeMath
National Alliance for Medical Image Computing http://na-mic.org
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!)
National Alliance for Medical Image Computing http://na-mic.org
“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
National Alliance for Medical Image Computing http://na-mic.org
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
National Alliance for Medical Image Computing http://na-mic.org
MaskStat Result
result in Slicer
result in output text file
National Alliance for Medical Image Computing http://na-mic.org
Do Some DTI!