NA-MIC National Alliance for Medical Image Computing Hands-on Diffusion Tensor Imaging Training...
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Transcript of NA-MIC National Alliance for Medical Image Computing 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
Pujol S., Gollub R.National Alliance for Medical Image Computing
NA-MIC Kit
• End User Application: 3D Slicer, FiberViewer
• Software and methodologies for Medical Image Computing
• ITK, VTK, KWidgets, CMake, Dart, CTest, CPack
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
3D Slicer
• Open-source application available for Windows, Linux, Solaris and Mac
Pujol S., Gollub R.National Alliance for Medical Image Computing
3D Slicer
• Open-source application available for Windows, Linux, Solaris and Mac
• 447,233 lines of code
Pujol S., Gollub R.National Alliance for Medical Image Computing
3D Slicer
• Open-source application available for Windows, Linux, Solaris and Mac
• 447,233 lines of code
• Neuroscience and Image-guided therapy
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
DTI Analysis with SlicerSlicer can load
• DWI Volumes …………………….
• Tensors……………………………
• Tracts………………………………
• DTI Scenes ……………………….
Pujol S., Gollub R.National Alliance for Medical Image Computing
Slicer Interface
ViewerMenu
Tk window
Slicer101 Compendium: SlicerTraining 1: Loading and Viewing Data
Pujol S., Gollub R.National Alliance for Medical Image Computing
DWI Exemplar Dataset 1
• 2 Baselines and 12 Gradients
Volume interleaved
Pujol S., Gollub R.National Alliance for Medical Image Computing
DWI Exemplar Dataset 2
• 1 Baseline and 6 Gradients
• Volume interleavedSlice interleaved
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Session 1 Data Loading and Visualization
National Alliance for Medical Image Computing
NA-MIC Training Workshop
OHBM 2007
Pujol S., Gollub R.National Alliance for Medical Image Computing
DWI Exemplar Dataset 1
• 2 Baselines and 12 Gradients
Volume interleaved
Pujol S., Gollub R.National Alliance for Medical Image Computing
Loading the DWI Training Dataset 1
Click on Add Volume to load the Dwi-dicom training dataset
Pujol S., Gollub R.National Alliance for Medical Image Computing
Loading DWI data
Select Nrrd Reader in the Properties field
The Props Panel of the module Volumes appears.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
Loading the DWI training dataset 1
Slicer loads the Nrrd DWI dataset
Pujol S., Gollub R.National Alliance for Medical Image Computing
Left-click on the button Or, and select the orientation Slices
Loading the DWI training dataset 1
Pujol S., Gollub R.National Alliance for Medical Image Computing
The anatomical slices are now aligned with the sampling grid
Loading the DWI training dataset 1
Pujol S., Gollub R.National Alliance for Medical Image Computing
Change the FOV to 2000
Loading the DWI training dataset 1
Pujol S., Gollub R.National Alliance for Medical Image Computing
The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes.
This corresponds to a volume-interleaved dataset.
Loading the DWI training dataset 1
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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).
Pujol S., Gollub R.National Alliance for Medical Image Computing
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).
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Session 2 From Diffusion Weighted Imaging to Diffusion Tensor Imaging
National Alliance for Medical Image Computing
NA-MIC Training Workshop
OHBM 2007
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
DT-MRI Module
Select Modules in the Main Menu
Select VisualizationDTMRI
Pujol S., Gollub R.National Alliance for Medical Image Computing
DT-MRI Module
The panel Input of the DTMRI module appears
Click on the tab Conv
Pujol S., Gollub R.National Alliance for Medical Image Computing
DT-MRI Module
The panel Conv of the DTMRI module appears
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Select the Input Volume namic01-dwi.nhdr and click on ConvertVolume
Pujol S., Gollub R.National Alliance for Medical Image Computing
• 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.
Converting DWI data to tensors
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Slicer displays the anatomical views of the average of all 12 diffusion weighted images (average over all gradient directions)
Pujol S., Gollub R.National Alliance for Medical Image Computing
Adjusting Window Level
Click on the Module Volumes and select the tab Display
Pujol S., Gollub R.National Alliance for Medical Image Computing
Adjusting Window Level
Select the Active Volume
namic01-dwi-nhdr_AvGradient
Use the sliders Win and Lev to adjust the Window level
Pujol S., Gollub R.National Alliance for Medical Image Computing
Adjusting Window Level
Inspect the anatomy using the axial, sagittal and coronal sliders.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Left-click on Bg and select the volume namic01-dwi nhdr_Baseline
Converting DWI data to tensors
Pujol S., Gollub R.National Alliance for Medical Image Computing
Browse the baseline images to check if the anatomy is correct
Converting DWI data to tensors
Slicer displays the baseline images.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
Glyphs Visualization
Click on the DTMRI module and select the panel Glyphs
Pujol S., Gollub R.National Alliance for Medical Image Computing
Glyphs Visualization
Select the Active DTMRI volume namic01-dwi-nhdr_Tensor
Select Glyphs on Slice for the axial (red) view
Set Display Glyphs On
Pujol S., Gollub R.National Alliance for Medical Image Computing
Glyphs Visualization
Slicer displays the orientation of the glyphs in the Axial view.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Glyphs Visualization
Right-click and move the mouse down
The 3D Viewer gets closer to the volume.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Glyphs Visualization
Observe the orientation of the glyphs in the Corpus Callosum
Pujol S., Gollub R.National Alliance for Medical Image Computing
Glyphs Visualization
Click on Off to leave the glyphs visualization mode.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
DWI Exemplar Dataset 2
• 1 Baseline and 6 Gradients
• Volume interleavedSlice interleaved
Pujol S., Gollub R.National Alliance for Medical Image Computing
Loading the DWI Training Dataset 2
Click on Add Volume to load the SlicerSampleDTI training dataset
Pujol S., Gollub R.National Alliance for Medical Image Computing
Loading the DWI Training Dataset 2
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
Loading the DWI Training Dataset 2
The DWI imagesappear in the Viewer
Pujol S., Gollub R.National Alliance for Medical Image Computing
Observe the axial slices using the slider
DWI Training Dataset 2
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
DWI Training Dataset 2
Pujol S., Gollub R.National Alliance for Medical Image Computing
Inferior
Superior
In Axial/Sagittal/Coronal mode the slices planes, which are aligned with the RAS coordinates, are cutting through the DWI volume
DWI Training Dataset 2
Baseline
Gradient
Pujol S., Gollub R.National Alliance for Medical Image Computing
Slices mode
Inferior
Superior
Pujol S., Gollub R.National Alliance for Medical Image Computing
Left click on Or and select the orientation Slices in the Menu
DWI Training Dataset 2
Pujol S., Gollub R.National Alliance for Medical Image Computing
The original slices appear in the Viewer
DWI Training Dataset 2
Pujol S., Gollub R.National Alliance for Medical Image Computing
Inferior
Superior
In AxiSlice/SagiSlice/CorSlice mode the slices are aligned with the DWI volume
Loading the DWI Training Dataset 2
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Browse the original axial slices corresponding to the baseline (S0) image.
Loading the DWI Training Dataset 2
Example: display the slice 209
Pujol S., Gollub R.National Alliance for Medical Image Computing
Loading the DWI Training Dataset 2
Adjust the window level and observe the baseline image (S0)
Pujol S., Gollub R.National Alliance for Medical Image Computing
Adjusting Image Window Level
Select the Volumes module
Adjust Window and Level
Select the volume D
Select the Display panel
Pujol S., Gollub R.National Alliance for Medical Image Computing
Loading the DWI Training Dataset 2
Observe the baseline image (S0)
Pujol S., Gollub R.National Alliance for Medical Image Computing
Notice that the image intensity for each of the six gradient orientations is much lower than the S0 image.
Loading the DWI Training Dataset 2
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Select Modules in the Main Menu
Select VisualizationDTMRI
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Select the Conversion Panel: Conv
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Select InputVolume D
Select Protocol BWH_6g.1bSlice
Click on Prop to display the parameters of the acquisition protocol
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Click on Convert Volume
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Slicer displays the anatomical views of the average of all 6 diffusion weighted images
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Left Click on the button Bg and select the volume D_Baseline
Pujol S., Gollub R.National Alliance for Medical Image Computing
Converting DWI data to tensors
Observe the volume D_Baseline
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Session 3 Scalar Maps Processing
National Alliance for Medical Image Computing
NA-MIC Training Workshop
OHBM 2007
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
Computing 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
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
• 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
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
Computing Fractional Anisotropy
The Viewer displays the FA volume.
Move the mouse in the slices to see FA values for each voxel.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Computing Fractional Anisotropy
Note high FA values over large tracts such as the corpus callosum Note low FA values over gray matter
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Drawing
Select the Effects panel
Left click on Draw in the Effects Menu
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Drawing
The Draw Panel of the Editor Module appears
Left-click on Output, and select the color label #2 (pink)
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Drawing
Draw the contour of the Corpus Callosum with the mouse in the sagittal slice
Pujol S., Gollub R.National Alliance for Medical Image Computing
Statistical analysis
Select Modules Measurement
VolumeMath in the Main Menu
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Statistical analysis
Set Volume to Mask to FractionalAnisotropy_D_Tensor
Set LabelMap to Working
Set Masked Output to Create New
Pujol S., Gollub R.National Alliance for Medical Image Computing
Statistical analysis
Click on Run
Click on Mask, select the same color asyour labelmap (Label 2, pink)
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Session 4 Fiber Tracts 3D Visualization
National Alliance for Medical Image Computing
NA-MIC Training Workshop
OHBM 2007
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Tractography Panel
Select the DTMRI module and click on the Panel More
Select the Panel Tract inside the DTMRI module
Pujol S., Gollub R.National Alliance for Medical Image Computing
Tractography Panel
Select the Tab Settings
Left-click on Color
Pujol S., Gollub R.National Alliance for Medical Image Computing
Tractography Panel
A Color selection panel appears
Select a new color for the tracts
Pujol S., Gollub R.National Alliance for Medical Image Computing
Create a single tract
Position the mouse on a point inside the Corpus Callosum, and hit the s key.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
Create a single tract
Click on the V buttons to display the anatomical slices in the Viewer.
The 3D window shows a closer view of the tract.
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Generate Multiple Tracts
Hold down the s key and move the mouse in the corpus callosum
Pujol S., Gollub R.National Alliance for Medical Image Computing
Generate Multiple Tracts
Multiple tracts are generated for each point visited by the mouse.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Generate Multiple Tracts
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Seeding
Go back to the DT-MRI module and select Seed in the Tracts Panel
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Corpus Callosum Tracts
Slicer displays the fiber tracts of the corpus callosum overlaid on the FA map.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Corpus Callosum Tracts
Click on Spin to visualize the tracts from different angles.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Corpus Callosum Tracts
The fiber tracts overlaid on the FA map start spinning inside the Viewer Panel, providing dynamic visualization.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Corpus Callosum Tracts
For details on the DT-MRI advanced functionalities, including selective seeding and tract clustering, see Slicer 101 Compendium: Slicer Training4:DT-MRI module
Pujol S., Gollub R.National Alliance for Medical Image Computing
Conclusion
• Intuitive interface for manual and automatic tracts generation
• Enhanced visualization of the anatomy by fusion of tracts and DWI images
• Open-source environment
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
Slicer Compendium
Pujol S., Gollub R.National Alliance for Medical Image Computing
Appendix
Pujol S., Gollub R.National Alliance for Medical Image Computing
Color By Orientation
Click on Display and Select Display Tracts Off
Pujol S., Gollub R.National Alliance for Medical Image Computing
Color By Orientation
Select the DT-MRI module and click on the Tab Scalars.
Select ColorByOrientation
Pujol S., Gollub R.National Alliance for Medical Image Computing
Color By Orientation
Browse through the volume to observe the orientation of major fiber bundles
Pujol S., Gollub R.National Alliance for Medical Image Computing
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
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Drawing
Select the Effects panel
Left click on Draw in the Effects Menu
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Drawing
Left-click on Bg and display the Fractional Anisotropy map in background.
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Drawing
Left-click on Output, and select the color label #7 (blue-green)
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Drawing
Draw the contour of the cingulum with the mouse.
Pujol S., Gollub R.National Alliance for Medical Image Computing
ROI Seeding
Go back to the DT-MRI module and select Seed in the Tracts Panel
Pujol S., Gollub R.National Alliance for Medical Image Computing
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.
Pujol S., Gollub R.National Alliance for Medical Image Computing
Tracts visualization
Observe the spatial orientation of fibers tracts in the Corpus Callosum and in the Cingulum