Post on 19-Nov-2014
description
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Diffusion Tensor Imaging
Sonia Pujol, Ph.D.Randy Gollub, M.D., Ph.D.
National Alliance for Medical Image Computing
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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
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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
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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
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Slicer DT-MRI Module
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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
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Diffusion Weighted Imaging (DWI)
Diffusion Sensitizing Gradients
Diffusion Weighted Images
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Diffusion Weighted Imaging (DWI)
Example: Correlation between the orientation of the 11th gradient and the signal intensity in the Splenium of the Corpus Callosum
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Loading DTI DataSlicer can load
• DWI Volumes …………………….
• Tensors……………………………
• Tracts………………………………
• DTI Scenes ……………………….
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DWI Training Dataset 1
• 2 Baselines and 12 Gradients
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DWI Training Dataset 2
• 1 Baseline and 6 Gradients
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Loading the DWI Training Dataset 1
Click on Add Volume to load the Dicom-DWI training dataset
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Loading DWI data
Select Nrrd Reader in the Properties field
The Props Panel of the module Volumes appears.
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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
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Loading DWI data
Slicer loads the Nrrd DWI dataset
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Loading DWI data
Left-click on the button Or, and select the orientation Slices
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Loading DWI data
The anatomical slices are now aligned with the sampling grid
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Loading DWI data
Change the FOV to 2000
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Loading DWI data
The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes
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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.
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DT-MRI Module
Select Modules in the Main Menu
Select VisualisationDTMRI
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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
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
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• 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.
Converting DWI data to tensors
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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_AvGradient
Use the sliders Win and Lev to adjust the Window level
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Adjusting 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.
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Left-click on Bg and select the volume namic01-dwi nhdr_Baseline
Converting DWI data to tensors
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Browse the baseline images to check if the anatomy is correct
Converting DWI data to tensors
Slicer displays the baseline (T2) images.
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Converting DWI data to tensors
Click on the module Data
Slicer displays the list of DTI volumes
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Converting DWI data to tensors
Select File Close in the Main Menu to clear the scene
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Loading the DWI Training Dataset 2
Click on Add Volume
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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
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The DWI imagesappear in the Viewer
Loading Slicer Sample DWI data
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Observe the axial slices using the slider
Loading Slicer Sample DWI data
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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.
Loading Slicer Sample DWI data
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Inferior
Superior
In Axial/Sagittal/Coronal mode the slices planes, which are aligned with the RAS coordinates, are cutting through the DWI volume
Loading Slicer Sample DWI data
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Left click on Or and select the orientation Slices in the Menu
Loading Slicer Sample DWI data
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The original slices appear in the Viewer
Loading Slicer Sample DWI data
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Inferior
Superior
In AxiSlice/SagiSlice/CorSlice mode the slices are aligned with the DWI volume
Loading Slicer Sample DWI data
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Loading Slicer Sample DWI data
Notice that the viewer displays the stack of S0 and diffusion weighted images {Si}
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Browse the original axial slices corresponding to the baseline (S0) image.
Loading Slicer Sample DWI data
Example: display the slice 209
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Loading Slicer Sample DWI data
Adjust the window level and observe the baseline image (S0)
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Adjusting Image Window Level
Select the Volumes module
Adjust Window and Level
Select the volume D
Select the Display panel
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Loading Slicer Sample DWI data
Observe the baseline image (S0)
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Notice that the image intensity for each of the six gradient orientations is much lower than the S0 image.
Loading Slicer Sample DWI data
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DT-MRI Module
Select Modules in the Main Menu
Select VisualizationDTMRI
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DT-MRI Module
Select the Conversion Panel: Conv
Select the module DTMRI
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Convert 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
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
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Convert 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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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
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Computing Fractional Anisotropy
In the DT-MRI module, click on More to navigate in the different panels
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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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• 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
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Computing 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
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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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Fractional Anisotropy Statistics
Goal Measure Fractional
Anisotropy Statistics in a
Region of Interest (ROI)
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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
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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
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ROI Drawing
Click on Apply in the Editor Module
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Measure FA Statistics in ROI
Select Modules Measurement
VolumeMath in the Main Menu
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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.
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MaskStat
Set Volume to Mask to FractionalAnisotropy_D_Tensor
Set LabelMap to Working
Set Masked Output to Create New
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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
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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.
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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
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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.)
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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
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Tractography Panel
Select the DTMRI module and click on the Panel More
Select the Panel Tracts 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.
Drag right mouse button down in the 3D Viewer to zoom in.
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Create a single tract
Click on the V buttons
The 3D window shows a closer view of the tract.
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Create a single 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.
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Generate Multiple Tracts
Position the mouse on different points in the corpus callosum and hit the s key.
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Generate Multiple Tracts
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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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
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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
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ROI Drawing
Select the Effects panel
Left click on Draw in the Effects Menu
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ROI Drawing
Select the color label #7 in the module Editor
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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
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ROI Drawing
Select the color label #10 in the module Editor
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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
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ROI Drawing
Select the color label #5 in the module Editor
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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.
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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
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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
Select the color label #10 corresponding to the ROI2
Click on Seed Tracts
A warning message appears,Click Yes if you are ready to process the data.
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ROI2 Seeding
Slicer displays the tracts from ROI2
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ROI Seeding
Select the color label #5 corresponding to the ROI3
Click on Seed Tracts
A warning message appears,Click Yes if you are ready to process the data.
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ROI3 Seeding
Slicer displays the tracts from ROI3
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Selective Seeding
Slicer displays the tracts from the 3 segmented ROIs
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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
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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
• Part 1: Loading and Converting DTI Data
• Part 2: Computing Fractional Anisotropy
• Part 3: Generating Fiber Tracts
• Part 4: Selective Seeding
• Part 5: Clustering
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ROI Seeding
Select Seed in the Tracts Panel
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Select the ROI Working
Click on Seed Tracts
ROI Seeding
Select the color label of the ROI (#2)
A warning message appears,Click Yes if you are ready to process the data.
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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
Surgical Planning Laboratoryhttp://www.slicer.org-
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Brigham and Women’s Hospital
Tract Clustering AlgorithmThe Number of Clusters is the number of bundles expected.
Surgical Planning Laboratoryhttp://www.slicer.org-
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Brigham and Women’s Hospital
Tract Clustering Algorithm
N is the Sampling resolution along the fibers
In this example, N=8
The default settings of the algorithm is N=15
Surgical Planning Laboratoryhttp://www.slicer.org-
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Brigham and Women’s Hospital
Tract Clustering AlgorithmThe ShapeFeature corresponds to the Similarity Measurement
Surgical Planning Laboratoryhttp://www.slicer.org-
130-
Brigham and Women’s Hospital
Tract Clustering AlgorithmThe ShapeFeature corresponds to the Similarity Measurement
The default setting of the algorithm is MeanClosestPoint
Surgical Planning Laboratoryhttp://www.slicer.org-
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Brigham and Women’s Hospital
Tract Clustering Algorithm
Click on Cluster to start the algorithm
Surgical Planning Laboratoryhttp://www.slicer.org-
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Brigham and Women’s Hospital
Tract Clustering Result
Slicer displays the result of the tract clustering in the Corpus Callosum.
Surgical Planning Laboratoryhttp://www.slicer.org-
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Brigham and Women’s Hospital
Tract Clustering Result
Slicer displays the result of the tract clustering in the Corpus Callosum.
Surgical Planning Laboratoryhttp://www.slicer.org-
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Brigham and Women’s Hospital
Conclusion
• Intuitive interface for manual and automatic tracts generation
• Enhanced visualization of the anatomy by fusion of tracts and DWI images
• Open-source environment