diffusion tensor imaging analysis-3749

Surgical Planning Laboratoryhttp://www.slicer.org-1-

Brigham and Women’s Hospital

Diffusion Tensor Imaging

Sonia Pujol, Ph.D.Randy Gollub, M.D., Ph.D.

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 Thanks to Carl-Fredrik Westin, Lauren O’Donnell, Raul SanJose Estepar, Carlos Isorna, Maxime Boucher, Matthan Caan



Material

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

• DTI Sample Data Set Dwi-dicom.zipSlicerSampleDTI.zip

http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101



Goal of this tutorial

Guiding you step-by-step through the DWI data analysis capabilities of Slicer, including generation of tensors, calculation of scalar metrics and tractography tools.

Final result of the tutorial



Slicer DT-MRI Module



Overview

• Part 1: Loading and Converting DTI Data

• Part 2: Computing Fractional Anisotropy

• Part 3: Generating Fiber Tracts

• Part 4: Selective Seeding

• Part 5: Clustering



Diffusion Weighted Imaging (DWI)

Diffusion Sensitizing Gradients

Diffusion Weighted Images



Diffusion Weighted Imaging (DWI)

Example: Correlation between the orientation of the 11th gradient and the signal intensity in the Splenium of the Corpus Callosum



Loading DTI DataSlicer can load

• DWI Volumes …………………….

• Tensors……………………………

• Tracts………………………………

• DTI Scenes ……………………….



DWI Training Dataset 1

• 2 Baselines and 12 Gradients



DWI Training Dataset 2

• 1 Baseline and 6 Gradients



Loading the DWI Training Dataset 1

Click on Add Volume to load the Dicom-DWI 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 DWI data

Slicer loads the Nrrd DWI dataset



Loading DWI data

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



Loading DWI data

The anatomical slices are now aligned with the sampling grid



Loading DWI data

Change the FOV to 2000



Loading DWI data

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



Loading 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.



DT-MRI Module

Select Modules in the Main Menu

Select VisualisationDTMRI



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



Converting DWI data to tensors

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




zzzyzx

yzyyyx

xzxyxx

DDD

DDD

DDD

(Stejskal and Tanner 1965, Basser 1994 )

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

Si S0 e b ˆ g iT D ˆ g i

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



• 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 DTMRI 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




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

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 (T2) images.




Click on the module Data

Slicer displays the list of DTI volumes




Select File Close in the Main Menu to clear the scene



Loading the DWI Training Dataset 2

Click on Add Volume



Loading Slicer Sample DWI data

Select ImageHeaders: AutoClick Apply

Select the Props Panel

Use the Basic ReaderClick 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




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




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}



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.




DT-MRI Module

Select Modules in the Main Menu

Select VisualizationDTMRI



DT-MRI Module

Select the Conversion Panel: Conv

Select the module DTMRI



Convert DWI data to tensors

Select InputVolume D

Select Protocol BWH_6g.1bSlice

Click on Prop to display the parameters of the acquisition protocol



Acquisition protocol

Slicer displays the parameters of the acquisition protocol usedto acquire the DTI Sample Data BWH_6g.1bSlice atBrigham and Women’s Hospital, corresponding 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• B-value = 1000



Convert DWI data to tensors

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



Overview








Computing Fractional Anisotropy

In the DT-MRI module, click on More to navigate in the different panels




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



• 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.


D

IDtraceDFA

)(31

2

3




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



Fractional Anisotropy Statistics

Goal Measure Fractional

Anisotropy Statistics in a

Region of Interest (ROI)



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



ROI Drawing

Click on Apply in the Editor Module



Measure FA Statistics in ROI

Select Modules Measurement

VolumeMath in the Main Menu



MaskStat

Select MaskStat

The MaskStat functionality uses the labelmap as a mask over the FA volume, and calculates “stats” on the region contained under the labelmap.



MaskStat

Set Volume to Mask to FractionalAnisotropy_D_Tensor

Set LabelMap to Working

Set Masked Output to Create New



MaskStat

Click on Run

Click on Mask, select the same color as your labelmap

Click on Browse to select a directory toplace the output text file and enter the filenameFractionalAnisotropy_D_Tensor_hist.txt



MaskStat Result

A window shows the statistics (multiplied by the Scale Factor): minimal, maximal, mean and standard deviation of the FA values.

The results have been saved in the file FractionalAnisotropy_D_Tensor_hist.txt written on the disk.



Save FA volume and ROI

Select the module EditorSelect the panel Volumesand click on Save

Enter a FilenamePrefix andselect the format NRRD(.nhdr)

Click on Save



Save FA volume and ROI

Slicer generates a Nrrdheader file (FA.nhdr), and a

raw compressed file (FA.raw.gz).

Save the Working volumecontaining the label map usingthe same process.

(Slicer Training #7: Saving data.)



Overview








Tractography Panel

Select the DTMRI module and click on the Panel More

Select the Panel Tracts 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.

Drag right mouse button down in the 3D Viewer to zoom in.




Click on the V buttons

The 3D window shows a closer view of the tract.




Slicer displays the slices in the 3D window.

Drag left mouse button in the 3D Viewer to rotate the volume,

Drag right mouse button to zoom in,until you get to a convenient view.



Generate Multiple Tracts

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.




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




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



ROI Seeding

Slicer has functionalities to generate tracts

from a pre-defined Region Of Interest (ROI).

Training dataset ROI: • ROI1: Temporal stem, between frontal and temporal

lobes• ROI2: Posterior temporal lobe• ROI3: Splenium of the corpus callosum



ROI Drawing

Select the Editor module in the main Menu.

Select the Volumes panel and click Setup

Select the Original Grayscale FractionalAnisotropy_D_Tensor

Select the Labelmap Working.

Click on Start Editing



ROI Drawing

Select the Effects panel

Left click on Draw in the Effects Menu



ROI Drawing

Select the color label #7 in the module Editor



ROI1: Temporal stem

Draw a region of interest in the Temporal stem(slice #156)

Select View1x512 COR in the Main Menu

Click on Apply in the module Editor



ROI Drawing




ROI2: Posterior temporal lobe

Draw a region of interest in the Posterior Temporal Lobe (slice #128)

Select View1x512 COR in the Main Menu.

Click on Apply in the module Editor



ROI Drawing




ROI3: Splenium

Draw a region of interest in the Splenium of the Corpus Callosum (slice #131)

Select View1x512 SAG in the Main Menu.

Click on Apply in the module Editor.



Come back to the DTMRI module and select the panel Tracts.

Click on the tab Seed and select the SeedROI Working

ROI Seeding

Select the color label #7 corresponding to the ROI1

Surgical Planning Laboratoryhttp://www.slicer.org-

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Click on Seed Tracts

ROI Seeding

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


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ROI1 Seeding

Slicer displays the tracts from ROI1


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ROI Seeding





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ROI2 Seeding



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ROI Seeding





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ROI3 Seeding



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Selective Seeding

Slicer displays the tracts from the 3 segmented ROIs


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Overview







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Selective Seeding

AND and NOT operators can be used to

select tracts generated from different

Regions Of Interest.


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Selective Seeding

Slicer displays the tracts from the 3 segmented ROIs


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AND/NOT operators: example

• ROI1: Temporal stem, between frontal and temporal lobes

• ROI2: Posterior temporal lobe• ROI3: Splenium of the corpus callosum

• Target: Inferior Occipito-frontal Fasciculus from the Frontal lobe to Occipital Lobe, through Temporal lobe


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Selective SeedingClick on the tab Select in the Panel TractSelect the ROI Labelmap Working

Enter the labels of the ROI1 (label #7) and ROI2 (label #10) in the list of labels called AND.


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Selective Seeding

Click on Find Tracts through ‘ROI’

Enter the label of the ROI3 (label #5) in the list of labels called NOT.


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Selective Seeding

Slicer displays the resulting tracts of the Inferior Occipito-frontal Fasciculus in red.


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Selective Seeding

The tracts that were not selected appear transparent.


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Deleting Tracts

Select the tab Display and click on Delete to delete all the tracts and clear the scene.


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Deleting Tracts

Slicer removes all the tracts generated from the ROIs.


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Overview







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ROI Seeding

Select Seed in the Tracts Panel


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Select the ROI Working


ROI Seeding

Select the color label of the ROI (#2)



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The resulting tracts appearin the 3D Viewer.

ROI Seeding


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Corpus Callosum Tracts


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Clustering Method

Estimation of a similarity measurement

for all pairs of tracts


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Similarity Measurement

The similarity measurement is

based on the mean closestpoint distance between the

tracts.


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Clustering Method*

High dimensional clustering space


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Clustering Method*

Cluster-colored tracts

(*) White Matter Tract Clustering and Correspondence in Populations O’Donnel L, Westin C-F

Medical Image Computing and Computer-Assisted Interventions (MICCAI2005)


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Tract Clustering Algorithm

Click on More and select the panel TC

In this tutorial example, we cluster the fiber tracts generated from the ROI in the Corpus Callosum


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Tract Clustering AlgorithmThe Number of Clusters is the number of bundles expected.


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N is the Sampling resolution along the fibers

In this example, N=8

The default settings of the algorithm is N=15


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Tract Clustering AlgorithmThe ShapeFeature corresponds to the Similarity Measurement


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Tract Clustering AlgorithmThe ShapeFeature corresponds to the Similarity Measurement

The default setting of the algorithm is MeanClosestPoint


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Click on Cluster to start the algorithm


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Tract Clustering Result

Slicer displays the result of the tract clustering in the Corpus Callosum.


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Tract Clustering Result

Slicer displays the result of the tract clustering in the Corpus Callosum.


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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

diffusion tensor imaging analysis-3749

Technology

dwi data slicer

dwi images

dwi volumes

dwi data left

dwi dataleft

dwi data change thefovto

dti data slicer

dwi training dataset