Slicer Tutorial Module: DTMRI Data: Dartmouth DTI

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Slicer TutorialModule DTMRIData Dartmouth DTI

• May 26-27, 2005

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Pre-requisites

• Slicer 2.5 already installed from
• http//www.na-mic.org/Wiki/index.php/SlicerSlice
  r2.5_Getting_Started
• Dartmouth DTI Data Set (first of six normals on
  BIRN servers) downloaded using instructions in
• http//www.na-mic.org/Wiki/index.php/DataReposito
  ry
• Dartmouth DTI protocol saved in
  slicer2/Modules/vtkDTMRI/data/ NAMIC-Dartmouth-2b1
  2g-Volume

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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

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Load Dartmouth DTI images
2 Use the Basic Reader
3 Click File Browse
4 Pick First File
1 Click Add Volume
5 Switch to Manual
6 Click Apply
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Load Dartmouth images (contd)
7 Set Thickness to 3
11 DWI Images Appear
8 Set Order to Axial SI
9 Little Endian Yes
10 Click Apply
Q Where is the MRML file? What does it contain?
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Convert To Tensors
13 Pick Convert Tab
15 Pick Convert (ignore warning messages)
14 Protocol is NAMIC-Dartmouth-2b12g-Volume
12 Go to DTMRI Module
16 Resulting Viewer window looks like this
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Converted Tensor Image
16 Resulting viewer window looks like this
Q What is it that we are viewing in this
image? What is in the protocol file we just used?
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Adjust Image Win-Level
Aside
Select Volumes and
Select the AvGradient volume
Adjust Window and Level
Resulting Image
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Tractography Steps

• Compute Fractional Anisotropy (FA)
• Create Tracts
• Individually
• From segmented ROI

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Tractography Step 1 Compute Fractional
Anisotropy (FA)
Select DTMRI
Select Scalars (if you dont see it, select More
until you do)
Select FA
Resulting 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?
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Tractography Steps

• Compute Fractional Anisotropy (FA)
• Create Tracts
• Individually
• From segmented ROI

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Tractography Step 2Create 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.

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Tractography Step 2 Go to Tractography Tab
Select Display
More
Select Tractography
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Tractography Step 2 (contd) Select color for
display of tracts
Select Color
Click on new color
Current Selection of Tract Color
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Tractography Step 2 (contd) Set up 3D window
for viewing tracts
Notice volume orientation
Click on A to orient volume view
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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.
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Tractography Step 2 (contd) View tract in 3D
window
See the tiny tract in the 3D window.
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Tractography Step 2 (contd) Zoom in 3D window
Drag Right Mouse Button Down in 3D Window to Zoom
In.
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Tractography Step 2 (contd) Show Slices in 3D
window
Click v to show slices in 3D window.
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Tractography Step 2 (contd) Show Slices in 3D
window
Click on the left arrow tip to rotate volume
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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.
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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?
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Tractography Step 2 (contd) Segment ROI (then
use it to seed tracts)
Draw Module
Start Editor
Effects Tab
Draw
Select new color
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Tractography Step 2 (contd) Segment ROI (then
use it to seed tracts)
Draw Outline with Mouse
Note name of segmented volume.
Hit Apply to Fill Outline.
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Tractography Step 2 (contd) Generate Tracts
from Segmented ROI
Resulting Tracts Appear in 3D view.
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Tractography Step 2 (contd) Generate Tracts
from Segmented ROI
Zoom and Rotate 3D view by dragging right and
left mouse buttons
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Tractography Step 2 (contd) Generate Tracts
from Segmented ROI
Add a Slice to 3D view
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Tractography Steps

• Compute Fractional Anisotropy (FA)
• Create Tracts
• Individually
• From segmented ROI
• Save Tracts
• Save 3D Model of Tracts
• Add Model to Current Scene
• Save scene

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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?
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Save TractsAdd Model to Scene
This is the tract File that was just saved
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Save TractsSave Scene
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Open Saved Scene
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Use Case Measure FA Statistics in ROI
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Measure FA Statistics in ROI
Manually draw a labelmap over your region of
interest.
VolumeMath Module Modules ? Measurement ?
VolumeMath
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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!)
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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
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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
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MaskStat Result
result in Slicer
result in output text file
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Do Some DTI!