View source for GtractFastMarchingTracking

===Module Type & Category===

Type: CLI

Category: Diffusion.GTRACT



===Authors, Collaborators & Contact===

Author: This tool was developed by Vincent Magnotta and Greg Harris. The original code here was developed by Daisy Espino.

Contributors: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1



===Module Description===

{| style="color:green" border="1"

|Program title || Fast Marching Tracking

|-
|Program version || 4.0.0

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|Program documentation-url || https://www.slicer.org/wiki/Modules:GTRACT |-
|}

* <span style="color:blue">'''''Input Image Files''''' </span> Parameters for specifying the diffusion tensor image set
** <span style="color:green">'''Input Tensor Image Volume'''</span> [<span style="color:orange">--inputTensorVolume</span>] : Required: input tensor image file name
** <span style="color:green">'''Input Anisotropy Image Volume'''</span> [<span style="color:orange">--inputAnisotropyVolume</span>] : Required: input anisotropy image file name
** <span style="color:green">'''Input Cost Image Volume'''</span> [<span style="color:orange">--inputCostVolume</span>] : Required: input vcl_cost image file name
** <span style="color:green">'''Input Starting Seeds LabelMap Volume'''</span> [<span style="color:orange">--inputStartingSeedsLabelMapVolume</span>] : Required: input starting seeds LabelMap image file name
** <span style="color:green">'''Starting Seeds Label'''</span> [<span style="color:orange">--startingSeedsLabel</span>] : Label value for Starting Seeds
* <span style="color:blue">'''''Output Files''''' </span> Output file in which to store tract lines
** <span style="color:green">'''Output Tract Filename'''</span> [<span style="color:orange">--outputTract</span>] : Required: name of output vtkPolydata file containing tract lines and the point data collected along them.
** <span style="color:green">'''Write fiber tracts in XML format'''</span> [<span style="color:orange">--writeXMLPolyDataFile</span>] : Flag to make use of the XML format for vtkPolyData fiber tracts.
* <span style="color:blue">'''''Fast Marching Tracking Parameters''''' </span> Input parameters controlling the Fast Marching Cost Function
** <span style="color:green">'''Number of Iterations'''</span> [<span style="color:orange">--numberOfIterations</span>] : Number of iterations used for the optimization
** <span style="color:green">'''Seed Threshold'''</span> [<span style="color:orange">--seedThreshold</span>] : Anisotropy threshold used for seed selection
** <span style="color:green">'''Tracking Threshold'''</span> [<span style="color:orange">--trackingThreshold</span>] : Anisotropy threshold used for fiber tracking
** <span style="color:green">'''Cost Step Size'''</span> [<span style="color:orange">--costStepSize</span>] : Cost image sub-voxel sampling
** <span style="color:green">'''Maximum Step Size'''</span> [<span style="color:orange">--maximumStepSize</span>] : Maximum step size to move when tracking
** <span style="color:green">'''Minimum Step Size'''</span> [<span style="color:orange">--minimumStepSize</span>] : Minimum step size to move when tracking