Hands-on Diffusion Tensor Imaging Training

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

Hands-on Diffusion Tensor Imaging Training

Randy Gollub, M.D, Ph.D.

Massachusetts General Hospital

Harvard Medical School

Sonia Pujol, Ph.D.

Brigham and Women’s Hospital

Harvard Medical School

13th Annual Meeting of the Organization for Human Brain Mapping – OHBM 2007

Pujol S., Gollub R.National Alliance for Medical Image Computing

Acknowledgments

National Alliance for Medical Image ComputingNIH U54EB005149

Neuroimage Analysis Center NIH P41RR013218

Laboratory of Mathematics in Imaging, Brigham and Women’s Hospital


NA-MIC Kit

• End User Application: 3D Slicer, FiberViewer

• Software and methodologies for Medical Image Computing

• ITK, VTK, KWidgets, CMake, Dart, CTest, CPack


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.


Material

•Slicer 2.6http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started

•DTI Sample Data Set Dwi-dicom.zipSlicerSampleDTI.ziphttp://wiki.na-mic.org/Wiki/index.php/Training:OHBM2007_Training_Workshop


3D Slicer

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


3D Slicer


• 447,233 lines of code


3D Slicer


• 447,233 lines of code

• Neuroscience and Image-guided therapy


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.


DTI Analysis with SlicerSlicer can load

• DWI Volumes …………………….

• Tensors……………………………

• Tracts………………………………

• DTI Scenes ……………………….


Slicer Interface

ViewerMenu

Tk window

Slicer101 Compendium: SlicerTraining 1: Loading and Viewing Data


DWI Exemplar Dataset 1

• 2 Baselines and 12 Gradients

Volume interleaved



• 1 Baseline and 6 Gradients

• Volume interleavedSlice interleaved


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

Si S0 e b ˆ g iT D ˆ g i


Session 1 Data Loading and Visualization

National Alliance for Medical Image Computing

NA-MIC Training Workshop

OHBM 2007



• 2 Baselines and 12 Gradients

Volume interleaved


Loading the DWI Training Dataset 1

Click on Add Volume to load the Dwi-dicom training dataset


Loading DWI data

Select Nrrd Reader in the Properties field

The Props Panel of the module Volumes appears.


Loading DWI data

Click on Apply

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


Loading the DWI training dataset 1

Slicer loads the Nrrd DWI dataset


Left-click on the button Or, and select the orientation Slices



The anatomical slices are now aligned with the sampling grid



Change the FOV to 2000



The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes.

This corresponds to a volume-interleaved dataset.



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.


Interacting with DWI dataPosition 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).


Interacting with DWI dataPosition 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).









Session 2 From Diffusion Weighted Imaging to Diffusion Tensor Imaging



OHBM 2007


Converting DWI data to tensors

zzzyzx

yzyyyx

xzxyxx

DDD

DDD

DDD

(Stejskal and Tanner 1965, Basser 1994 )

{Si} represent the signal intensities in presence of the gradients gi


Slicer computes the symmetric 3x3 tensor matrix D for each voxel


DT-MRI Module

Select Modules in the Main Menu

Select VisualizationDTMRI


DT-MRI Module

The panel Input of the DTMRI module appears

Click on the tab Conv


DT-MRI Module

The panel Conv of the DTMRI module appears



Select the Input Volume namic01-dwi.nhdr and click on ConvertVolume


• 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.




Slicer displays the anatomical views of the average of all 12 diffusion weighted images (average over all gradient directions)


Adjusting Window Level

Click on the Module Volumes and select the tab Display



Select the Active Volume

namic01-dwi-nhdr_AvGradient

Use the sliders Win and Lev to adjust the Window level



Inspect the anatomy using the axial, sagittal and coronal sliders.


Left-click on Bg and select the volume namic01-dwi nhdr_Baseline



Browse the baseline images to check if the anatomy is correct


Slicer displays the baseline images.



Click on the module Data

Slicer displays the list of available volumes:

• DWI dataset

• Tensor volume

•Average Gradient volume

•Average Gradient mask

•Baseline volume


Glyphs Visualization

Click on the DTMRI module and select the panel Glyphs



Select the Active DTMRI volume namic01-dwi-nhdr_Tensor

Select Glyphs on Slice for the axial (red) view

Set Display Glyphs On



Slicer displays the orientation of the glyphs in the Axial view.



Right-click and move the mouse down

The 3D Viewer gets closer to the volume.



Observe the orientation of the glyphs in the Corpus Callosum



Click on Off to leave the glyphs visualization mode.


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



• 1 Baseline and 6 Gradients

• Volume interleavedSlice interleaved



Click on Add Volume to load the SlicerSampleDTI training dataset



Select ImageHeaders: AutoClick Apply

Select the Props Panel

Use the Basic Readerand click on BrowseNavigate to the folder containing

the tutorial dataSelect the first file D.001Click Open



The DWI imagesappear in the Viewer


Observe the axial slices using the slider

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.



Inferior

Superior

In Axial/Sagittal/Coronal mode the slices planes, which are aligned with the RAS coordinates, are cutting through the DWI volume


Baseline

Gradient


Slices mode

Inferior

Superior


Left click on Or and select the orientation Slices in the Menu



The original slices appear in the Viewer



Inferior

Superior

In AxiSlice/SagiSlice/CorSlice mode the slices are aligned with the DWI volume




Notice that the viewer displays the stack of S0 and diffusion weighted images {Si}: this corresponds to a slice-interleaved dataset.


Browse the original axial slices corresponding to the baseline (S0) image.


Example: display the slice 209



Adjust the window level and observe the baseline image (S0)


Adjusting Image Window Level

Select the Volumes module

Adjust Window and Level

Select the volume D

Select the Display panel



Observe the baseline image (S0)


Notice that the image intensity for each of the six gradient orientations is much lower than the S0 image.




Select Modules in the Main Menu

Select VisualizationDTMRI



Select the Conversion Panel: Conv


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.



Select InputVolume D

Select Protocol BWH_6g.1bSlice

Click on Prop to display the parameters of the acquisition protocol


Acquisition protocolThe parameters of the acquisition protocol used toacquire the DTI Sample Data BWH_6g.1bSlice atBrigham and Women’s Hospital correspond to:• n=6 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• b=1 baseline and B-value = 1000



Click on Convert Volume



Slicer displays the anatomical views of the average of all 6 diffusion weighted images



Left Click on the button Bg and select the volume D_Baseline



Observe the volume D_Baseline









Session 3 Scalar Maps Processing



OHBM 2007


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, we’ll compute exemplar scalar maps: the Relative Anisotropy map and the Fractional Anisotropy map.


Computing Relative Anisotropy

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

where

3

))()()(( 23

22

21

RA

3

13

1

ii



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



Click on Apply

Select the Region of Interest ROI:Mask

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

The Relative Anisotropy Panel appears



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


• 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.

Computing Fractional Anisotropy

D

IDtraceDFA

)(31

2

3



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



Click on Apply

Select the Region of Interest ROI:Mask

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

The Fractional Anisotropy Panel appears



The Viewer displays the FA volume.

Move the mouse in the slices to see FA values for each voxel.



Note high FA values over large tracts such as the corpus callosum Note low FA values over gray matter


ROI Drawing

Select the Editor module in the main Menu.

Select the Volumes panel.

Select the Original Grayscale FractionalAnisotropy_D

Select the Working Labelmap NEW and keep the Default Descriptive Name Working.

Click on Start Editing


ROI Drawing

Select the Effects panel

Left click on Draw in the Effects Menu


ROI Drawing

The Draw Panel of the Editor Module appears

Left-click on Output, and select the color label #2 (pink)


ROI Drawing

Draw the contour of the Corpus Callosum with the mouse in the sagittal slice


Statistical analysis

Select Modules Measurement

VolumeMath in the Main Menu



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.



Set Volume to Mask to FractionalAnisotropy_D_Tensor

Set LabelMap to Working

Set Masked Output to Create New



Click on Run

Click on Mask, select the same color asyour labelmap (Label 2, pink)


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 FractionalAnisotropy_D_Tensor_hist.txt written on the disk.









Session 4 Fiber Tracts 3D Visualization



OHBM 2007


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


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.


Tractography Panel

Select the DTMRI module and click on the Panel More

Select the Panel Tract inside the DTMRI module


Tractography Panel

Select the Tab Settings

Left-click on Color


Tractography Panel

A Color selection panel appears

Select a new color for the tracts


Create a single tract

Position the mouse on a point inside the Corpus Callosum, and hit the s key.



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



Click on the V buttons to display the anatomical slices in the Viewer.

The 3D window shows a closer view of the 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.


Generate Multiple Tracts

Hold down the s key and move the mouse in the corpus callosum



Multiple tracts are generated for each point visited by the mouse.



The viewer moves away from the model

• Zoom OutPosition 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


Region of Interest Seeding

Slicer has functionalities to generate tractsautomatically from a pre-defined Region OfInterest (ROI).In the previous section, we manually segmentedthe corpus callosum from the FractionalAnisotropy Map. This defines our workingregion of interest


ROI Seeding

Go back to the DT-MRI module and select Seed in the Tracts Panel


ROI Seeding

Select the ROI Working

Click on Seed Tracts

Select the color label of the ROI (#2)

A warning message appears,Click Yes if you are ready to process the data.


Corpus Callosum Tracts

Slicer displays the fiber tracts of the corpus callosum overlaid on the FA map.



Click on Spin to visualize the tracts from different angles.



The fiber tracts overlaid on the FA map start spinning inside the Viewer Panel, providing dynamic visualization.



For details on the DT-MRI advanced functionalities, including selective seeding and tract clustering, see Slicer 101 Compendium: Slicer Training4:DT-MRI module


Conclusion

• Intuitive interface for manual and automatic tracts generation

• Enhanced visualization of the anatomy by fusion of tracts and DWI images

• Open-source environment


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/

Slicer:Workshops:User_Training_101


Slicer Compendium


Appendix


Color By Orientation

Click on Display and Select Display Tracts Off



Select the DT-MRI module and click on the Tab Scalars.

Select ColorByOrientation



Browse through the volume to observe the orientation of major fiber bundles


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 keep the Default Descriptive Name Working2.

Click on Start Editing


ROI Drawing

Select the Effects panel

Left click on Draw in the Effects Menu


ROI Drawing

Left-click on Bg and display the Fractional Anisotropy map in background.


ROI Drawing

Left-click on Output, and select the color label #7 (blue-green)


ROI Drawing

Draw the contour of the cingulum with the mouse.


ROI Seeding

Go back to the DT-MRI module and select Seed in the Tracts Panel


ROI Seeding

Select the ROI Working2

Click on Seed Tracts

Select the color label of the ROI (#7)

A warning message appears,Click Yes if you are ready to process the data.


Tracts visualization

Observe the spatial orientation of fibers tracts in the Corpus Callosum and in the Cingulum

Documents

Hands-on Diffusion Tensor Imaging Training