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

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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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Contact:  <email>slicer-users@bwh.harvard.edu</email><br>
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Contact:  Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email><br>
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Website: http://slicerdmri.github.io/
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|Image:Logo-splnew.jpg|Surgical Planning Laboratory
 
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|Image:Fiber select.PNG|Tract selection
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|Image:Wholebraintractography.png|Whole brain tractography
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|Image:CCSelectedTracts.png|Corpus callosum (CC) tract selection
 
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This module is used for selecting a subset of DTI fiber tracts including or excluding certain fibers passing through a selected set of labels in the label map volume.
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[https://www.slicer.org/slicerWiki/index.php/Documentation/4.5/Training#Fiber_Bundle_Selection_and_Scalar_Measurements|Fiber Bundle Selection and Scalar Measurements]
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Links to tutorials that use this module
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* Slicer4 Fiber Bundle Selection and Scalar Measurements Tutorial: https://www.slicer.org/wiki/Documentation/4.5/Training#Fiber_Bundle_Selection_and_Scalar_Measurements * Tractography selection and measurements in command line interface (CLI) mode: http://dmri.slicer.org/tutorials/tractography_measurement
 
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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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* Parameters panel:
 
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** Parameters: select an existing setting for the module or create a new one.
 
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* IO panel:
 
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** Input Label Map: select an existing label map volume.
 
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** Input FiberBundle: Select the fibers that you want to filter.
 
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** Output FiberBundle: Select the bundle that you want to create or modify from a list.
 
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* Label Regions Definition panel :
 
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** Labels to include: A comma separated list of label values to include in the output fiber bundles set.
 
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** Combine Include Labels: OR or AND logical operation to combine individual label values in the above list.
 
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** Labels to exclude: A comma separated list of label values to exclude from the output fiber bundles set.
 
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** Combine Exclude Labels: OR or AND logical operation to combine individual label values in the above list.
 
  
 
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* Tractography Label Map Seeding
 
* Tractography Label Map Seeding
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*  http://slicerdmri.github.io/
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Latest revision as of 13:59, 27 November 2019

Home < Documentation < Nightly < Modules < FiberBundleLabelSelect


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


Introduction and Acknowledgements


Title: Tractography ROI Selection
Author(s)/Contributor(s): Demian Wassermann, Fan Zhang, Lauren O'Donnell (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: <email>slicer-users@bwh.harvard.edu</email>
Website: http://slicerdmri.github.io/

SlicerDMRI  
Surgical Planning Laboratory  
NAC  
Whole brain tractography  
Corpus callosum (CC) tract selection  


Module Description

Fiber bundle label select allows a user to select tracts passing or not passing through single or multiple labels. (Selection region label maps may be created with the Editor module or other segmentation tools.)


Use Cases

Most frequently used for these scenarios:

  • Use Case 1: Filter out a subset of DTI fiber tracts which are passing through selected region(s) defined in the label map volume.
  • Use Case 2: Filter out a subset of DTI fiber tracts which are NOT passing through selected region(s) defined in the label map volume.
  • Use Case 3: A combination of Case 1 and Case 2.

Tutorials

Links to tutorials that use this module

Panels and their use

Parameters:

  • IO: Input/output parameters
    • Selection Region Label Map (InputLabel_A): Label map volume defining selection region
    • Input Fiber Bundle (InputFibers): Input tractography for region-based selection.
    • Output Fiber Bundle (OutputFibers): Selected tractography result from region-based selection.
  • Tract selection region labels:
    • Inclusion labels (comma-separated) (PassLabel): Comma-separated list of label values defining inclusion region. Fibers passing through these labels will be retained.
    • Inclusion label combination logic (PassOperation): AND: Fiber must pass through all specified labels.
      OR: Fiber must pass through any specified label (at least one).
    • Exclusion labels (comma-separated) (NotPassLabel): Comma-separated list of label values defining exclusion region. Fibers passing through these labels will be removed.
    • Exclusion label combination logic (NoPassOperation): AND: Any fiber passing through all specified labels is excluded.
      OR: Fibers passing through any specified label (at least one) are excluded.
  • Advanced Settings: Advanced settings
    • Sampling distance (mm) (SamplingDistance): Sampling Distance


List of parameters generated transforming this XML file using this XSL file. To update the URL of the XML file, edit this page.


Similar Modules

  • Tractography Label Map Seeding


References

Information for Developers

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