Difference between revisions of "Documentation/4.3/Modules/FiberBundleLabelSelect"

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* Parameters panel:
 
* Parameters panel:
 
** Parameters: select an existing setting for the module or create a new one.
 
** Parameters: select an existing setting for the module or create a new one.
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[[Image:Fiber select.PNG|thumb|280px|FiberBundleLabelSelect]]
 
* IO panel:
 
* IO panel:
 
** Input Label Map: select an existing label map volume.
 
** Input Label Map: select an existing label map volume.
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* Label Regions Definition panel :
 
* Label Regions Definition panel :
 
** Labels to include: A comma separated list of label values to include in the output fiber bundles set.
 
** Labels to include: A comma separated list of label values to include in the output fiber bundles set.
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** Fiducail Seeding Step Size: Step between the seeding samples in the box (mm).
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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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** Seed Selected Fiducials: Flag indicating whether to use only selected fiducials for seeding or all of them.
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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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** 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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** Combine Exclude Labels: OR or AND logical operation to combine individual label values in the above list.
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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:
 
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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).
 
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** 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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Latest revision as of 17:33, 21 November 2019

Home < Documentation < 4.3 < Modules < FiberBundleLabelSelect


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
Contact: Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email>

Surgical Planning Laboratory  


Module Description

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.

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

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.
FiberBundleLabelSelect
  • IO panel:
    • Input Label Map: select an existing label map volume.
    • Input FiberBundle: Select the fibers that you want to filter.
    • Output FiberBundle: Select the bundle that you want to create or modify from a list.
  • Label Regions Definition panel :
    • Labels to include: A comma separated list of label values to include in the output fiber bundles set.
    • Combine Include Labels: OR or AND logical operation to combine individual label values in the above list.
    • Labels to exclude: A comma separated list of label values to exclude from the output fiber bundles set.
    • Combine Exclude Labels: OR or AND logical operation to combine individual label values in the above list.

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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