Difference between revisions of "Documentation/Nightly/Modules/TractographyLabelMapSeeding"
From Slicer Wiki
m (Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 ") |
|||
| Line 36: | Line 36: | ||
{{documentation/{{documentation/version}}/module-section|Tutorials}} | {{documentation/{{documentation/version}}/module-section|Tutorials}} | ||
Links to tutorials that use this module | Links to tutorials that use this module | ||
| − | * Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/ | + | * Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial <!-- ---------------------------- --> |
| − | |||
| − | <!-- ---------------------------- --> | ||
{{documentation/{{documentation/version}}/module-section|Panels and their use}} | {{documentation/{{documentation/version}}/module-section|Panels and their use}} | ||
{{documentation/{{documentation/version}}/module-parametersdescription}} | {{documentation/{{documentation/version}}/module-parametersdescription}} | ||
| Line 44: | Line 42: | ||
<!-- ---------------------------- --> | <!-- ---------------------------- --> | ||
{{documentation/{{documentation/version}}/module-section|Similar Modules}} | {{documentation/{{documentation/version}}/module-section|Similar Modules}} | ||
| − | * TractographyInteractiveSeeding: https://www.slicer.org/ | + | * TractographyInteractiveSeeding: https://www.slicer.org/wiki/Documentation/Nightly/Modules/TractographyInteractiveSeeding <!-- ---------------------------- --> |
| − | |||
| − | <!-- ---------------------------- --> | ||
{{documentation/{{documentation/version}}/module-section|References}} | {{documentation/{{documentation/version}}/module-section|References}} | ||
* http://slicerdmri.github.io/ | * http://slicerdmri.github.io/ | ||
Latest revision as of 13:15, 27 November 2019
Home < Documentation < Nightly < Modules < TractographyLabelMapSeeding
|
For the latest Slicer documentation, visit the read-the-docs. |
Introduction and Acknowledgements
|
Contact: <email>slicer-users@bwh.harvard.edu</email> | |||||||||||
|
Module Description
Seed tractography from a Diffusion Tensor Image (DTI) within a region defined by a label map.
Use Cases
Most frequently used for these scenarios:
- Use Case 1: Using a label map, trace all the fibers emanating from it.
- Use Case 2: Using a brain mask, perform a full brain tractography.
Tutorials
Links to tutorials that use this module
- Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial
Panels and their use
Parameters:
- IO: Input/output parameters
- Input DTI Volume (InputVolume): DTI volume in which to seed (generate) tractography.
- Input Label Map (InputROI): Label map defining region for seeding tractography.
- Output Fiber Bundle (OutputFibers): Tractography result
- Seeding Options: Options for seed placement
- Start Threshold (ClTh): Minimum Linear Measure for the seeding to start.
- Tractography Seeding Parameters: Parameters for the tractography method
- Minimum Length (MinimumLength): Minimum length of the fibers (in mm)
- Maximum Length (MaximumLength): Maximum length of fibers (in mm)
- Stopping Criteria (ThresholdMode): Tensor measurement used to start and stop the tractography
- Stopping Value (StoppingValue): Tractography will stop when the stopping measurement drops below this value
- Stopping Track Curvature (StoppingCurvature): Tractography will stop if radius of curvature becomes smaller than this number units are degrees per mm
- Integration Step Length(mm) (IntegrationStepLength): Distance between points on the same fiber in mm
- Label definition: Selection of label(labels) for ROI definition
- Seeding label (ROIlabel): Label value that defines seeding region.
- Advanced:
- Use Index Space (UseIndexSpace): Seed at IJK voxel grid
- Seed Spacing (SeedSpacing): Spacing (in mm) between seed points, only matters if use Use Index Space is off
- Random Grid (RandomGrid): Enable random placing of seeds
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
- TractographyInteractiveSeeding: https://www.slicer.org/wiki/Documentation/Nightly/Modules/TractographyInteractiveSeeding
