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

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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>
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Author: Alex Yarmarkovich, Isomics, SPL<br>
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Contributor1: Demian Wassermann, SPL<br>
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Title: Tractography Interactive Seeding
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Contributor2: Steve Pieper, Isomics, SPL<br>
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Contact:  Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email><br>
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Author(s)/Contributor(s): Alex Yarmarkovich, Steve Pieper, Demian Wassermann, Isaiah Norton (SPL, LMI, BWH, SlicerDMRI)
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License: 3D Slicer Contribution and Software License Agreement
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Acknowledgements: The SlicerDMRI developers gratefully acknowledge funding for this project provided by NIH NCI ITCR U01CA199459 (Open Source Diffusion MRI Technology For Brain Cancer Research), NIH P41EB015898 (National Center for Image-Guided Therapy) and NIH P41EB015902 (Neuroimaging Analysis Center), as well as 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.
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Contact:  slicer-users@bwh.harvard.edu
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Website: http://slicerdmri.github.io/
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|Image:SlicerDMRIScreenshot.jpg|SlicerDMRI
 
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
 
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
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|Image:NAC-logo.png|NAC
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|Image:Fiducials seeding 1.png| Tractography Fiducial Seeding
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|Image:Fiducials seeding 2.png| Tractography Fiducial Seeding
 
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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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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.
  
  
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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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Links to tutorials that use this module:
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* Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial * Slicer4 Neurosurgical Planning Tutorial: https://www.slicer.org/wiki/Documentation/4.5/Training#Slicer4_Neurosurgical_Planning_Tutorial <!-- ---------------------------- -->
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A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:
 
  
 
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** Output FiberBundle: Select the bundle that you want to create or modify from a list.
 
** 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.
 
** 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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* Seed Placement Option panel:
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** Fiducail Region Size: The size of the box around each fiducial used for seeding (mm).
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** Fiducial 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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** Fiducial 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.
 
** 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.
 
** Maximum Number of Seeds: Used with models to specify the limit of the number of vertices to be used for seeding.
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| align="right" |
 
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[[Image:Tractography_Fiducial_Seeding.PNG|thumb|280px|Fiducial Tractography Seeding]]
 
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* Label Map Options panel:
 
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** Use Index Space: if selected seed at IJK voxel grid
 
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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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** Random Grid: use random placement.
 
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** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
 
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** ROI Labels: a comma separated list of label to start seeding
 
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** Write Fibers to Disk: option to save the results to disk for further analysis.
 
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** Output Directory: path where the results are saved.
 
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** File Prefix Name: name that would be used for each output bundle.
 
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[[Image:Tractography_LabelMap_Seeding.PNG|thumb|280px|Label Map Tractography Seeding]]
 
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* Tractography Seeding Parameters panel:
 
* Tractography Seeding Parameters panel:
 
** Minimum Path Length: Select only tracts that are longer than this value (mm).
 
** Minimum Path Length: Select only tracts that are longer than this value (mm).
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
* Tractography Label Map Seeding
 
* Tractography Label Map Seeding
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* UKF Tractography
  
 
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Publications related to this module go here. Links to pdfs would be useful.
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* Interactive Diffusion Tensor Tractography Visualization for Neurosurgical Planning: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112275/
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For extensions: link to the source code repository and additional documentation
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*  http://slicerdmri.github.io/
  
 
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* https://github.com/SlicerDMRI
  
  

Latest revision as of 14:01, 27 November 2019

Home < Documentation < Nightly < Modules < TractographyInteractiveSeeding


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


Introduction and Acknowledgements


Title: Tractography Interactive Seeding

Author(s)/Contributor(s): Alex Yarmarkovich, Steve Pieper, Demian Wassermann, Isaiah Norton (SPL, LMI, BWH, SlicerDMRI)

License: 3D Slicer Contribution and Software License Agreement

Acknowledgements: The SlicerDMRI developers gratefully acknowledge funding for this project provided by NIH NCI ITCR U01CA199459 (Open Source Diffusion MRI Technology For Brain Cancer Research), NIH P41EB015898 (National Center for Image-Guided Therapy) and NIH P41EB015902 (Neuroimaging Analysis Center), as well as 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.

Contact: slicer-users@bwh.harvard.edu

Website: http://slicerdmri.github.io/

SlicerDMRI  
Surgical Planning Laboratory  
NAC  
Tractography Fiducial Seeding  
Tractography Fiducial Seeding  


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.


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

Links to tutorials that use this module:

Panels and their use

  • 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.
  • Seed Placement Option panel:
    • Fiducial Region Size: The size of the box around each fiducial used for seeding (mm).
    • Fiducial 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.
  • 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
  • UKF Tractography

References

Information for Developers
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