Hands-on Diffusion Tensor Imaging Training

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Hands-on Diffusion Tensor Imaging Training
Randy Gollub, M.D, Ph.D. Massachusetts General
Hospital Harvard Medical School
Sonia Pujol, Ph.D. Brigham and Womens Hospital
Harvard Medical School
13th Annual Meeting of the Organization for
Human Brain Mapping OHBM 2007
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Acknowledgments

• National Alliance for Medical Image Computing
• NIH U54EB005149
• Neuroimage Analysis Center
• NIH P41RR013218
• Laboratory of Mathematics in Imaging,
• Brigham and Womens Hospital

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NA-MIC Kit

• End User Application 3D Slicer, FiberViewer
• Software and methodologies for Medical Image
  Computing
• ITK, VTK, KWidgets, CMake, Dart, CTest, CPack

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OHBM 2007 Workshop
Guiding you step-by-step through a complete DTI
analysis of the corpus callosum which includes
the generation of tensors, calculation of scalar
metrics and tractography tools.
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Material

• Slicer 2.6
• http//www.na-mic.org/Wiki/index.php/SlicerSlicer
  2.6_Getting_Started
• DTI Sample Data Set
• Dwi-dicom.zip
• SlicerSampleDTI.zip
• http//wiki.na-mic.org/Wiki/index.php/TrainingOHB
  M2007_Training_Workshop

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3D Slicer

• Open-source application available for Windows,
  Linux, Solaris and Mac

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3D Slicer

• Open-source application available for Windows,
  Linux, Solaris and Mac
• 447,233 lines of code

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3D Slicer

• Open-source application available for Windows,
  Linux, Solaris and Mac
• 447,233 lines of code
• Neuroscience and Image-guided therapy

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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.

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DTI Analysis with Slicer

• Slicer can load
• DWI Volumes .
• Tensors
• Tracts
• DTI Scenes .

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Slicer Interface
Viewer
Menu
Tk window
Slicer101 Compendium SlicerTraining 1 Loading
and Viewing Data
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DWI Exemplar Dataset 1

• 2 Baselines and 12 Gradients

Volume interleaved
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DWI Exemplar Dataset 2

• 1 Baseline and 6 Gradients
• Volume interleaved

Slice interleaved
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Hands-on Session Overview

• Session 1 Data Loading and Visualization
• Session 2 From DWI to DTI
• Session 3 Scalar maps calculation
• Session 4 Fiber Tract 3D Visualization

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Session 1 Data Loading and Visualization

National Alliance for Medical Image Computing
NA-MIC Training Workshop OHBM 2007
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DWI Exemplar Dataset 1

• 2 Baselines and 12 Gradients

Volume interleaved
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Loading the DWI Training Dataset 1
Click on Add Volume to load the Dwi-dicom
training dataset
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Loading DWI data
The Props Panel of the module Volumes appears.
Select Nrrd Reader in the Properties field
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Loading DWI data
Click on Browse and load the file
namic01-dwi.nhdr in the directory Dwi-dicom
Check that the path to the file is correct. If
needed, manually enter it
Click on Apply
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Loading the DWI training dataset 1
Slicer loads the Nrrd DWI dataset
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Loading the DWI training dataset 1
Left-click on the button Or, and select the
orientation Slices
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Loading the DWI training dataset 1
The anatomical slices are now aligned with the
sampling grid
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Loading the DWI training dataset 1
Change the FOV to 2000
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Loading the DWI training dataset 1
The sagittal and coronal viewers display the 14
MR volumes 2 baselines and 12 diffusion weighted
volumes. This corresponds to a volume-interleaved
dataset.
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Interacting with DWI data
Left-Click on the V button to display the axial
and sagittal slices inside the viewer.
Use the axial slider to slice trough the
baselines and diffusion weighted MR volumes.
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Interacting with DWI data

• Position the mouse inside the 3D Viewer.
• Window/Linux users
• Left-click and move the mouse to the left
  (right)
• Mac users
• Move the mouse button to the left
• ? the volume moves to the left (right).

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Interacting with DWI data

• Position the mouse inside the 3D Viewer.
• Window/Linux users
• Left-click and move the mouse up (down)
• Mac users
• Move the mouse button up (down)
• ? the volume moves up (down).

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Hands-on Session Overview

• Session 1 Data Loading and Visualization
• Session 2 From DWI to DTI
• Session 3 Scalar maps calculation
• Session 4 Fiber Tract 3D Visualization

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Session 2 From Diffusion Weighted Imaging to
Diffusion Tensor Imaging

National Alliance for Medical Image Computing
NA-MIC Training Workshop OHBM 2007
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Converting DWI data to tensors
Si represent the signal intensities in presence
of the gradients gi
(Stejskal and Tanner 1965, Basser 1994 )
Slicer computes the symmetric 3x3 tensor matrix D
for each voxel
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DT-MRI Module
Select Modules in the Main Menu
Select Visualization?DTMRI
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DT-MRI Module
The panel Input of the DTMRI module appears
Click on the tab Conv
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DT-MRI Module
The panel Conv of the DTMRI module appears
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Converting DWI data to tensors
Select the Input Volume namic01-dwi-nhdr and
click on ConvertVolume
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Converting DWI data to tensors

• At the end of the calculation, Slicer displays
  the average of all diffusion weighted images
  (_AvGradient) and the baseline volume
  (_Baseline).
• The tensors volume is available from the DT-MRI
  module for additional calculations.

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Converting DWI data to tensors
Slicer displays the anatomical views of the
average of all 12 diffusion weighted images
(average over all gradient directions)
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Adjusting Window Level
Click on the Module Volumes and select the tab
Display
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Adjusting Window Level
Select the Active Volume namic01-dwi-nhdr_AvGradie
nt
Use the sliders Win and Lev to adjust the Window
level
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Adjusting Window Level
Inspect the anatomy using the axial, sagittal and
coronal sliders.
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Converting DWI data to tensors
Left-click on Bg and select the volume
namic01-dwi nhdr_Baseline
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Converting DWI data to tensors
Slicer displays the baseline images.
Browse the baseline images to check if the
anatomy is correct
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Converting DWI data to tensors
Click on the module Data

• Slicer displays the list of available volumes
• DWI dataset
• Tensor volume
• Average Gradient volume
• Average Gradient mask
• Baseline volume

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Glyphs Visualization
Click on the DTMRI module and select the panel
Glyph
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Glyphs Visualization
Select the Active DTMRI volume namic01-dwi-nhdr_Te
nsor
Select Glyphs on Slice for the axial (red)
view Set Display Glyphs On
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Glyphs Visualization
Slicer displays the orientation of the glyphs in
the Axial view.
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Glyphs Visualization
Right-click and move the mouse down
The 3D Viewer gets closer to the volume.
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Glyphs Visualization
Observe the orientation of the glyphs in the
Corpus Callosum
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Glyphs Visualization
Click on Off to leave the glyphs visualization
mode.
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Closing the scene
Click on the module Data and select File? Close
in the Main Menu to clear the scene
For details on the Nrrd file format, see Slicer
101 Compendium Training 8 Nrrd File Format
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DWI Exemplar Dataset 2

• 1 Baseline and 6 Gradients
• Volume interleaved

Slice interleaved
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Loading the DWI Training Dataset 2
Click on Add Volume to load the SlicerSampleDTI
training dataset
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Loading the DWI Training Dataset 2
Select the Props Panel
Use the Basic Reader and click on Browse Navigate
to the folder containing the tutorial data Select
the first file D.001 Click Open
Select ImageHeaders Auto Click Apply
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Loading the DWI Training Dataset 2
The DWI images appear in the Viewer
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DWI Training Dataset 2
Observe the axial slices using the slider
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DWI Training Dataset 2
A sequence of white stripes appears in the
diffusion weighted images. They correspond to
intersections with the baseline images in Slicer
Axial/Sagittal/Coronal (AxiSagCor) slice mode.
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DWI Training Dataset 2
Baseline
Superior
Gradient
In Axial/Sagittal/Coronal mode the slices planes,
which are aligned with the RAS coordinates, are
cutting through the DWI volume
Inferior
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Slices mode
Superior
Inferior
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DWI Training Dataset 2
Left click on Or and select the orientation
Slices in the Menu
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DWI Training Dataset 2
The original slices appear in the Viewer
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Loading the DWI Training Dataset 2
Superior
In AxiSlice/SagiSlice/CorSlice mode the slices
are aligned with the DWI volume
Inferior
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Loading the DWI Training Dataset 2
Notice that the viewer displays the stack of S0
and diffusion weighted images Si this
corresponds to a slice-interleaved dataset.
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Loading the DWI Training Dataset 2
Browse the original axial slices corresponding to
the baseline (S0) image.
Example display the slice 209
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Loading the DWI Training Dataset 2
Adjust the window level and observe the baseline
image (S0)
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Adjusting Image Window Level
Select the Volumes module
Select the Display panel
Select the volume D
Adjust Window and Level
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Loading the DWI Training Dataset 2
Observe the baseline image (S0)
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Loading the DWI Training Dataset 2
Notice that the image intensity for each of the
six gradient orientations is much lower than the
S0 image.
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Converting DWI data to tensors
Select Modules in the Main Menu
Select Visualization? DTMRI
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Converting DWI data to tensors
Select the Conversion Panel Conv
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Acquisition protocol

• Acquisition parameters are essential for tensor
  calculation, and further DTI analysis.
• Parameters such as gradient directions might not
  be included in the header of the image files.
• In this example, the datasets were acquired with
  a known protocol BWH_6g1bSlice.

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Converting DWI data to tensors
Select InputVolume D
Select Protocol BWH_6g.1bSlice
Click on Prop to display the parameters of the
acquisition protocol
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Acquisition protocol

• The parameters of the acquisition protocol used
  to
• acquire the DTI Sample Data BWH_6g.1bSlice at
• Brigham and Womens Hospital correspond to
• n6 gradients
• Gradient directions 0.707107 0.707107 0 ,
• 0 0.707107 0.707107 , 0.707107 0 0.707107 ,
• 0 0.707107 -0.707107 , 0.707107 -0.707107 0,
• -0.707107 0 0.707107
• Gradient order Slice interleaved
• b1 baseline and B-value 1000

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Converting DWI data to tensors
Click on Convert Volume
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Converting DWI data to tensors
Slicer displays the anatomical views of the
average of all 6 diffusion weighted images
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Converting DWI data to tensors
Left Click on the button Bg and select the volume
D_Baseline
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Converting DWI data to tensors
Observe the volume D_Baseline
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Hands-on Session Overview

• Session 1 Data Loading and Visualization
• Session 2 From DWI to DTI
• Session 3 Scalar maps calculation
• Session 4 Fiber Tract 3D Visualization

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Session 3 Scalar Maps Processing

National Alliance for Medical Image Computing
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Scalar maps

• The tensors derived from diffusion tensor imaging
  describe complex diffusion in tissues.
• Scalar measures that map the three-dimensional
  eigenvalues of the diffusion tensor into scalar
  values provide efficient solutions for extracting
  desired aspects of the tensors.
• In the following section, well compute exemplar
  scalar maps the Relative Anisotropy map and the
  Fractional Anisotropy map.

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Computing Relative Anisotropy

• The Relative Anisotropy (RA) represents the ratio
  of the anisotropic part of D to its isotropic
  part
• where

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Computing Relative Anisotropy
Select the panel Scalars
Browse the menu Create Volume to see the list of
calculations that Slicer can perform on the
D_Tensor dataset.
Select Relative Anisotropy
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Computing Relative Anisotropy
The Relative Anisotropy Panel appears
Select the Region of Interest ROIMask
The Scale Factor is set by default to 1000,
because the standard range of RA values (0.0 to
1.0) is not compatible with Slicer
Click on Apply
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Computing Relative Anisotropy
The Viewer displays the RA volume.
Move the mouse in the slices to see RA values for
each voxel.
Observe High RA values in the Corpus Callosum and
low RA values in Grey matter areas
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Computing Fractional Anisotropy

• The Fractional Anisotropy (FA) is a measure of
  the diffusion anisotropy that can be calculated
  without explicitly computing any eigenvalue
• where D and trace(D) are the norm and trace of
  the Diffusion Tensor.

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Computing Fractional Anisotropy
Select the panel Scalars
Browse the menu Create Volume to see the list of
calculations that Slicer can perform on the
D_Tensor dataset.
Select Fractional Anisotropy
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Computing Fractional Anisotropy
The Fractional Anisotropy Panel appears
Select the Region of Interest ROIMask
The Scale Factor is set by default to 1000,
because the standard range of FA values (0.0 to
1.0) is not compatible with Slicer
Click on Apply
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Computing Fractional Anisotropy
The Viewer displays the FA volume.
Move the mouse in the slices to see FA values for
each voxel.
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Computing Fractional Anisotropy
Note high FA values over large tracts such as the
corpus callosum Note low FA values over gray
matter
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ROI Drawing
Select the Editor module in the main Menu.
Select the Volumes panel.
Select the Original Grayscale FractionalAnisotropy
_D_Tensor
Select the Working Labelmap NEW and keep the
Default Descriptive Name Working.
Click on Start Editing
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ROI Drawing
Select the Effects panel
Left click on Draw in the Effects Menu
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ROI Drawing
The Draw Panel of the Editor Module appears
Left-click on Output, and select the color label
2 (pink)
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ROI Drawing
Draw the contour of the Corpus Callosum with the
mouse in the sagittal slice Click Apply
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Statistical analysis
Select Modules ?Measurement ?VolumeMath in the
Main Menu
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Statistical analysis
Select MaskStat
The MaskStat functionality uses the labelmap as a
mask over the FA volume, and calculates
statistical values on the region contained under
the labelmap.
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Statistical analysis
Set Volume to Mask to FractionalAnisotropy_D_Tens
or Set LabelMap to Working Set Masked Output to
Create New
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Statistical analysis
Click on Mask, select the same color as your
labelmap (Label 2, pink)
Click on Run
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Statistical Analysis
A pop-up window shows statistical values
(multiplied by the Scale Factor) of the
Fractional Anisotropy in the Corpus Callosum. The
results have been saved in the file None_hist.txt
written on the disk.
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Hands-on Session Overview

• Session 1 Data Loading and Visualization
• Session 2 From DWI to DTI
• Session 3 Scalar maps calculation
• Session 4 Fiber Tract 3D Visualization

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Session 4 Fiber Tracts 3D Visualization

National Alliance for Medical Image Computing
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Motivations for DTI visualization

• Clinical drivers applications for nerve fiber
  tract visualization, tract measurements and tract
  clustering include
• neurosurgical planning for tumor resections
• study of fiber tract abnormality in schizophrenia
• white matter disruption in multiple sclerosis

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Fiber tract visualization
DTI data contain useful information related to
the anatomy of nerve fiber tracts. In the
following section, visualize white matter fiber
tract trajectories in the Corpus Callosum.
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Tractography Panel
Select the DTMRI module and click on the Panel
More
Select the Panel Tract inside the DTMRI module
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Tractography Panel
Select the Tab Settings
Left-click on Color
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Tractography Panel
A Color selection panel appears
Select a new color for the tracts
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Create a single tract
Position the mouse on a point inside the Corpus
Callosum, and hit the s key.
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Create a single tract
A tract appears in the 3D Viewer.

• ZOOM IN
• Position the mouse on the images inside the
  Viewer
• Right-click and move the mouse down
• Press the apple button, click and move the mouse
  button down

Linux/Unix/Windows
Mac users
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Create a single tract
The 3D window shows a closer view of the tract.
Click on the V buttons to display the anatomical
slices in the Viewer.
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Create a single tract
Position the mouse on different points in the
corpus callosum and hit the s key.
The tracts that correspond to the visited points
appear in the 3D Viewer.
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Generate Multiple Tracts
Hold down the s key and move the mouse in the
corpus callosum
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Generate Multiple Tracts
Multiple tracts are generated for each point
visited by the mouse.
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Generate Multiple Tracts

• Zoom Out

• Position the mouse on the images inside the
  Viewer
• Right-click and move the mouse up
• Press the apple button, click and move the mouse
  button up

Linux/Unix/Windows
Mac users
The viewer moves away from the model
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Region of Interest Seeding

• Slicer has functionalities to generate tracts
• automatically from a pre-defined Region Of
• Interest (ROI).
• In the previous section, we manually segmented
• the corpus callosum from the Fractional
• Anisotropy Map. This defines our working
• region of interest

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ROI Seeding
Go back to the DT-MRI module and select Seed in
the Tracts Panel
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ROI Seeding
Select the ROI Working
Select the color label of the ROI (2)
Click on Seed Tracts
A warning message appears, Click Yes if you are
ready to process the data.
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Corpus Callosum Tracts
Slicer displays the fiber tracts of the corpus
callosum overlaid on the FA map.
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Corpus Callosum Tracts
Click on Spin to visualize the tracts from
different angles.
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Corpus Callosum Tracts
The fiber tracts overlaid on the FA map start
spinning inside the Viewer Panel, providing
dynamic visualization.
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Corpus Callosum Tracts
For details on the DT-MRI advanced
functionalities, including selective seeding and
tract clustering, see Slicer 101 Compendium
Slicer Training4DT-MRI module
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Conclusion

• Intuitive interface for manual and automatic
  tracts generation
• Enhanced visualization of the anatomy by fusion
  of tracts and DWI images
• Open-source environment

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Slicer Compendium

• A series of courses have been developed to
  facilitate the use of advanced image analysis
  techniques available into Slicer to clinicians
  and scientists.
• Our compendium is available at
• http//www.namic.org/Wiki/index.php/SlicerWorksho
  psUser_Training_101

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Slicer Compendium
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Appendix
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Color By Orientation
In the DTMRI Module, click on Display and Select
Display Tracts Off
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Color By Orientation
Select the DT-MRI module and click on the Tab
Scalars.
Select ColorByOrientation Click Apply
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Color By Orientation
Browse through the volume to observe the
orientation of major fiber bundles
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ROI Drawing
Go back to the Editor module in the main Menu.
Select the Volumes panel.
Select the Original Grayscale FractionalAnisotropy
_D_Tensor
Select the Working Labelmap NEW and edit the
Descriptive Name to be Working2.
Click on Start Editing
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ROI Drawing
Select the Effects panel
Left click on Draw in the Effects Menu
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ROI Drawing
Left-click on Bg and display the Fractional
Anisotropy map in background.
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ROI Drawing
Left-click on Output, and select the color label
7 (blue-green)
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ROI Drawing
Draw the contour of the cingulum with the
mouse. Click Apply
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ROI Seeding
Go back to the DT-MRI module, select the Tract
panel, and select Seed.
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ROI Seeding
Select the ROI Working2
Select the color label of the ROI (7)
Click on Seed Tracts
A warning message appears, Click Yes if you are
ready to process the data.
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Tracts visualization
Observe the spatial orientation of fibers tracts
in the Corpus Callosum and in the Cingulum