NA-MIC National Alliance for Medical Image Computing Slicer Tutorial Module: DTMRI Data: Dartmouth DTI May 26-27, 2005

National Alliance for Medical Image Computing Pre-requisites Slicer 2.5 already installed from Dartmouth DTI Data Set (first of six normals on BIRN servers) downloaded using instructions in Dartmouth DTI “protocol” saved in slicer2/Modules/vtkDTMRI/data/ NAMIC-Dartmouth-2b12g-Volume

National Alliance for Medical Image Computing 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 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 Load Dartmouth images (contd) 7: Set Thickness to 3 8: Set Order to Axial SI 9: Little Endian “Yes” 10: Click Apply 11: DWI Images Appear Q: Where is the MRML file? What does it contain?

National Alliance for Medical Image Computing Convert To Tensors 12: Go to DTMRI Module 13: Pick Convert Tab 14: Protocol is NAMIC-Dartmouth-2b12g-Volume 15: Pick Convert (ignore warning messages) 16: Resulting Viewer window looks like this:

National Alliance for Medical Image Computing 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?

National Alliance for Medical Image Computing Adjust Image Win-Level Select “Volumes” and Adjust Window and Level Resulting Image Aside Select the AvGradient volume

National Alliance for Medical Image Computing Tractography Steps 1.Compute Fractional Anisotropy (FA) 2.Create Tracts Individually From segmented ROI

National Alliance for Medical Image Computing Tractography Step 1: Compute Fractional Anisotropy (FA) Select DTMRI Select Scalars (if you don’t 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?

National Alliance for Medical Image Computing Tractography Steps 1.Compute Fractional Anisotropy (FA) 2.Create Tracts Individually From segmented ROI

National Alliance for Medical Image Computing 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 Tractography Step 2: Go to Tractography Tab More Select Display Select Tractography

National Alliance for Medical Image Computing Tractography Step 2 (contd) : Select color for display of tracts Select Color Click on new color Current Selection of Tract Color

National Alliance for Medical Image Computing Tractography Step 2 (contd) : Set up 3D window for viewing tracts Click on “A” to orient volume view Notice volume orientation

National Alliance for Medical Image Computing 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 Tractography Step 2 (contd) : View tract in 3D window See the tiny tract in the 3D window.

National Alliance for Medical Image Computing 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 Tractography Step 2 (contd) : Show Slices in 3D window Click “v” to show slices in 3D window.

National Alliance for Medical Image Computing Tractography Step 2 (contd) : Show Slices in 3D window Click on the left arrow tip to rotate volume…

National Alliance for Medical Image Computing 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 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 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 Tractography Step 2 (contd) : Segment ROI (then use it to seed tracts) Draw Outline with Mouse Hit Apply to Fill Outline. Note name of segmented volume.

National Alliance for Medical Image Computing Tractography Step 2 (contd) : Generate Tracts from Segmented ROI Resulting Tracts Appear in 3D view.

National Alliance for Medical Image Computing 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 Tractography Step 2 (contd) : Generate Tracts from Segmented ROI Add a Slice to 3D view

National Alliance for Medical Image Computing 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 Save Tracts Save 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 Save Tracts Add Model to Scene This is the tract File that was just saved

National Alliance for Medical Image Computing Save Tracts Save Scene

National Alliance for Medical Image Computing Open Saved Scene

National Alliance for Medical Image Computing Use Case: Measure FA Statistics in ROI

National Alliance for Medical Image Computing 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 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 “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 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 MaskStat Result result in Slicer result in output text file

National Alliance for Medical Image Computing Do Some DTI!