Difference between revisions of "Documentation/Nightly/Modules/TractographyFiducialSeeding"

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This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
 
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
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Author: Demian Wassermann, SPL<br>
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Author: Alex Yarmarkovich, Isomics, SPL<br>
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Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br>
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Contributor1: Demian Wassermann, SPL<br>
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Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br>
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Contributor2: Steve Pieper, Isomics, SPL<br>
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Contact:  Demian Wassermann, <email>demian@bwh.harvard.edu</email><br>
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Contact:  Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email><br>
 
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{{documentation/{{documentation/version}}/module-section|Module Description}}
 
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Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
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This module is used for interactive seeding of DTI fiber tracts starting from a list of fiducial points or vertices of a model, or a label map volume.[[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
  
  
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Most frequently used for these scenarios:
 
Most frequently used for these scenarios:
  
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* Use Case 1:
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* Use Case 1: Create DTI fiber tracts starting from a list of fiducial points. Tracks created from a small number of fiducial points are are highly interactive and can be used in exploration mode while moving fiducials with the help of transformations. This mode can be useful in pre-op planning or for tracking tools during the surgery.
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* Use Case 2:
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* Use Case 2: Create DTI fiber tracts starting from vertices of a model. This mode can be useful for exploring tracts around a tumor model.
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* Use Case 2: Create DTI fiber tracts starting from a label map volume. Tracks created from a label map ROI can be used in interactive mode while modifying the label map using Editor module.
  
 
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[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial Slicer 4 Diffusion Tensor Tutorial]
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[[Documentation/4.0/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|Slicer 4 Diffusion Tensor Tutorial]]
  
 
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{|style="width: 100%"
 
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* Input panel1:
 
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** First input
 
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** Second input
 
 
* Parameters panel:
 
* Parameters panel:
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** First parameter
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** Parameters: select an existing setting for the module or create a new one.
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** Second parameter
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** Presets: select an Slicer4 or Slicer3 parameters setting for the module.
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* Output panel:
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* IO panel:
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** First output
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** Input DTI volume: select an existing tensor volume.
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** Second output
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** Input FiducialList, Model, or Label Map: select an existing fiducial list, or a model, or a label map volume to be used as seeds for tracking.
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* Viewing panel:
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** Output FiberBundle: Select the bundle that you want to create or modify from a list.
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** Enable Seeding Tracts: A toggle to enable/disable seeding. Disable if you want to change multiple parameters without re-running module at each step.
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* Seeding Placement Option panel (only shown when fiducials or a model is selected):
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** Fiducail Region Size: The size of the box around each fiducial used for seeding (mm).
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** Fiducail Seeding Step Size: Step between the seeding samples in the box (mm).
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** Seed Selected Fiducials: Flag indicating whether to use only selected fiducials for seeding or all of them.
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** Maximum Number of Seeds: Used with models to specify the limit of the number of vertices to be used for seeding.
 
| align="right" |
 
| align="right" |
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[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
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[[Image:Tractography_Fiducial_Seeding.PNG|thumb|280px|Fiducial Tractography Seeding]]
 
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|-
 
|
 
|
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* Input panel2:
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* Label Map Options panel:
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** First input
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** Use Index Space: if selected seed at IJK voxel grid
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** Second input
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** Seed Spacing: spacing in between seed points within in the labelmap (in mm), only matters if use Use Index Space is off.
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* Parameters panel:
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** Random Grid: use random placement.
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** First parameter
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** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
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** Second parameter
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** ROI Labels: a comma separated list of label to start seeding
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* Output panel:
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** Write Fibers to Disk: option to save the results to disk for further analysis.
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** First output
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** Output Directory: path where the results are saved.
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** Second output
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** File Prefix Name: name that would be used for each output bundle.
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* Viewing panel:
 
 
| align="right" |
 
| align="right" |
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[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
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[[Image:Tractography_LabelMap_Seeding.PNG|thumb|280px|Label Map Tractography Seeding]]
 
|}
 
|}
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* Tractography Seeding Parameters panel:
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** Minimum Path Length: Select only tracts that are longer than this value (mm).
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** Maximum Path Length: Select only tracts that are shorter than this value (mm).
 +
** Stopping Criteria: Select Linear Measure or FA to be used as stopping criteria.
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** Stopping Value: Select Linear Measure or FA stopping value, tracking will stop when the value drops below this one.
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** Stopping Track Curvature: Select the curvature stopping value in degree per mm, tracking will stop when the radius of curvature is smaller than this one.
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 +
* Enabling Options panel:
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** Create Tracts Initially As: Select Tubes or Lines
  
 
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
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* Point to other modules that have similar functionality
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* Tractography Label Map Seeding
  
 
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Latest revision as of 02:15, 27 November 2019

Home < Documentation < Nightly < Modules < TractographyFiducialSeeding


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
Author: Alex Yarmarkovich, Isomics, SPL
Contributor1: Demian Wassermann, SPL
Contributor2: Steve Pieper, Isomics, SPL
Contact: Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email>

Surgical Planning Laboratory  


Module Description

This module is used for interactive seeding of DTI fiber tracts starting from a list of fiducial points or vertices of a model, or a label map volume.references giving more details on the algorithm.


Use Cases

Most frequently used for these scenarios:

  • Use Case 1: Create DTI fiber tracts starting from a list of fiducial points. Tracks created from a small number of fiducial points are are highly interactive and can be used in exploration mode while moving fiducials with the help of transformations. This mode can be useful in pre-op planning or for tracking tools during the surgery.
  • Use Case 2: Create DTI fiber tracts starting from vertices of a model. This mode can be useful for exploring tracts around a tumor model.
  • Use Case 2: Create DTI fiber tracts starting from a label map volume. Tracks created from a label map ROI can be used in interactive mode while modifying the label map using Editor module.

Tutorials

Slicer 4 Diffusion Tensor Tutorial

Panels and their use

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

  • Parameters panel:
    • Parameters: select an existing setting for the module or create a new one.
    • Presets: select an Slicer4 or Slicer3 parameters setting for the module.
  • IO panel:
    • Input DTI volume: select an existing tensor volume.
    • Input FiducialList, Model, or Label Map: select an existing fiducial list, or a model, or a label map volume to be used as seeds for tracking.
    • Output FiberBundle: Select the bundle that you want to create or modify from a list.
    • Enable Seeding Tracts: A toggle to enable/disable seeding. Disable if you want to change multiple parameters without re-running module at each step.
  • Seeding Placement Option panel (only shown when fiducials or a model is selected):
    • Fiducail Region Size: The size of the box around each fiducial used for seeding (mm).
    • Fiducail Seeding Step Size: Step between the seeding samples in the box (mm).
    • Seed Selected Fiducials: Flag indicating whether to use only selected fiducials for seeding or all of them.
    • Maximum Number of Seeds: Used with models to specify the limit of the number of vertices to be used for seeding.
Fiducial Tractography Seeding
  • Label Map Options panel:
    • Use Index Space: if selected seed at IJK voxel grid
    • Seed Spacing: spacing in between seed points within in the labelmap (in mm), only matters if use Use Index Space is off.
    • Random Grid: use random placement.
    • Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
    • ROI Labels: a comma separated list of label to start seeding
    • Write Fibers to Disk: option to save the results to disk for further analysis.
    • Output Directory: path where the results are saved.
    • File Prefix Name: name that would be used for each output bundle.
Label Map Tractography Seeding
  • Tractography Seeding Parameters panel:
    • Minimum Path Length: Select only tracts that are longer than this value (mm).
    • Maximum Path Length: Select only tracts that are shorter than this value (mm).
    • Stopping Criteria: Select Linear Measure or FA to be used as stopping criteria.
    • Stopping Value: Select Linear Measure or FA stopping value, tracking will stop when the value drops below this one.
    • Stopping Track Curvature: Select the curvature stopping value in degree per mm, tracking will stop when the radius of curvature is smaller than this one.
  • Enabling Options panel:
    • Create Tracts Initially As: Select Tubes or Lines

Similar Modules

  • Tractography Label Map Seeding

References

Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation

Information for Developers

Work in progress
 Section under construction.


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