Difference between revisions of "Documentation/4.2/Modules/fibertrack"

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== Usage ==
 
== Usage ==
  
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===Use Cases, Examples===
 
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This module is especially appropriate for these use cases:
 
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* Use Case 1:
 
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* Use Case 2:
 
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Examples of the module in use:
 
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* Example 1:
 
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* Example 2:
 
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===Tutorials===
 
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* Tutorial 1
 
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** Data Set 1
 
 
===Quick Tour of Features and Use===
 
===Quick Tour of Features and Use===
  

Revision as of 22:19, 27 November 2012

Home < Documentation < 4.2 < Modules < fibertrack


FiberTrack

FiberTrack

User Interface
Output

General Information

Module Type & Category

Type: CLI

Category: Diffusion.NIRALPipeline


Authors, Collaborators & Contact

Author: Casey Goodlett

Contributors:

Contact: name, email

Module Description

Program title FiberTrack
Program description \nThis program implements a simple streamline tractography method based on the principal eigenvector of the tensor field. A fourth order Runge-Kutta integration rule used to advance the streamlines.\nAs a first parameter you have to input the tensor field (with the --input_tensor_file option). Then the region of interest image file is set with the --input_roi_file. Next you want to set the output fiber file name after the --output_fiber_file option. \nYou can specify the label value in the input_roi_file with the --target_label, --source_label and --fobidden_label options. By default target label is 1, source label is 2 and forbidden label is 0. The source label is where the streamlines are seeded, the target label defines the voxels through which the fibers must pass by to be kept in the final fiber file and the forbidden label defines the voxels where the streamlines are stopped if they pass through it. There is also a --whole_brain option which, if enabled, consider both target and source labels of the roi image as target labels and all the voxels of the image are considered as sources.\nDuring the tractography, the --fa_min parameter is used as the minimum value needed at different voxel for the tracking to keep going along a streamline. The --step_size parameter is used for each iteration of the tracking algorithm and defines the length of each step. The --max_angle option defines the maximum angle allowed between two successive segments along the tracked fiber.
Program version 1.1.0
Program documentation-url http://www.google.com/

Usage

Quick Tour of Features and Use

A list panels in the interface, their features, what they mean, and how to use them.

  • I/O:
    • Input Tensor Image [----input_tensor_file] [-i]: Tensor Image
    • Input ROI Image [----input_roi_file] [-r]: The filename of the image which contains the labels used for seeding and constraining the algorithm.
    • Output Fiber File [----output_fiber_file] [-o]: The filename for the fiber file produced by the algorithm. This file must end in a .fib or .vtk extension for ITK spatial object and vtkPolyData formats respectively.
  • Source/Target:
    • Source Label [----source_label] [-s]: The label of voxels in the labelfile to use for seeding tractography. One tract is seeded from the center of each voxel with this label Default value: 2
    • Target Label [----target_label] [-t]: The label of voxels in the labelfile used to constrain tractography. Tracts that do not pass through a voxel with this label are rejected. Set this keep all tracts. Default value: 1
    • Forbidden Label [----forbidden_label] [-f]: Forbidden label Default value: 0
    • Whole Brain [----whole_brain] : If this option is enabled all voxels in the image are used to seed tractography. When this option is enabled both source and target labels function as target labels Default value: false
  • Start/Stop options:
    • Maximum Angle [----max_angle] : Maximum angle of change in radians Default value: 0.785398163397448309615660845819875721
    • Step Size [----step_size] : Step size in mm for the tracking algorithm Default value: 0.5
    • Minimum FA [----min_fa] : The minimum FA threshold to continue tractography Default value: 0.2
  • Advanced options:
    • Force [----force] : Ignore sanity checks. Default value: 0
    • Verbose [----verbose] [-v]: produce verbose output Default value: 0
    • Really Verbose [----really_verbose] : Follow detail of fiber tracking algorithm Default value: 0
User Interface

Development

Notes from the Developer(s)

Algorithms used, library classes depended upon, use cases, etc.

Dependencies

Other modules or packages that are required for this module's use.

Tests

On the Dashboard, these tests verify that the module is working on various platforms:

Known bugs

Links to known bugs in the Slicer3 bug tracker

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usabilityissue category when browsing or contributing.

Source code & documentation

Links to the module's source code:

Source code:

Doxygen documentation:

More Information

Acknowledgment

Hans Johnson(1,3,4); Kent Williams(1); (1=University of Iowa Department of Psychiatry, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering) provided conversions to make DTIProcess compatible with Slicer execution, and simplified the stand-alone build requirements by removing the dependancies on boost and a fortran compiler.

References

Publications related to this module go here. Links to pdfs would be useful.

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