View source for Documentation/4.3/Modules/fibertrack

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===FiberTrack===
FiberTrack

{|
|[[Image:FiberTrack.png|thumb|280px|User Interface]]
|[[Image:FiberTrack-fibers.png|thumb|280px|Output]]
|}

== General Information ==

===Module Type & Category===

Type: CLI

Category: Diffusion.NIRALPipeline


===Authors, Collaborators & Contact===

Author: Casey Goodlett

Contributors:

Contact: name, email

===Module Description===
{| style="color:green" border="1"
|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.
{|
|
* <span style="color:blue">'''''I/O'''''</span>: 
** <span style="color:green">'''Input Tensor Image'''</span> [<span style="color:orange">----input_tensor_file</span>] [<span style="color:pink">-i</span>]: Tensor Image

** <span style="color:green">'''Input ROI Image'''</span> [<span style="color:orange">----input_roi_file</span>] [<span style="color:pink">-r</span>]: The filename of the image which contains the labels used for seeding and constraining the algorithm.

** <span style="color:green">'''Output Fiber File'''</span> [<span style="color:orange">----output_fiber_file</span>] [<span style="color:pink">-o</span>]: 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.

* <span style="color:blue">'''''Source/Target'''''</span>: 
** <span style="color:green">'''Source Label'''</span> [<span style="color:orange">----source_label</span>] [<span style="color:pink">-s</span>]: 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''
** <span style="color:green">'''Target Label'''</span> [<span style="color:orange">----target_label</span>] [<span style="color:pink">-t</span>]: 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''
** <span style="color:green">'''Forbidden Label'''</span> [<span style="color:orange">----forbidden_label</span>] [<span style="color:pink">-f</span>]: Forbidden label ''Default value: 0''
** <span style="color:green">'''Whole Brain'''</span> [<span style="color:orange">----whole_brain</span>] : 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''
* <span style="color:blue">'''''Start/Stop options'''''</span>: 
** <span style="color:green">'''Maximum Angle'''</span> [<span style="color:orange">----max_angle</span>] : Maximum angle of change in radians ''Default value: 0.785398163397448309615660845819875721''
** <span style="color:green">'''Step Size'''</span> [<span style="color:orange">----step_size</span>] : Step size in mm for the tracking algorithm ''Default value: 0.5''
** <span style="color:green">'''Minimum FA'''</span> [<span style="color:orange">----min_fa</span>] : The minimum FA threshold to continue tractography ''Default value: 0.2''
* <span style="color:blue">'''''Advanced options'''''</span>: 
** <span style="color:green">'''Force'''</span> [<span style="color:orange">----force</span>] : Ignore sanity checks. ''Default value: 0''
** <span style="color:green">'''Verbose'''</span> [<span style="color:orange">----verbose</span>] [<span style="color:pink">-v</span>]: produce verbose output ''Default value: 0''
** <span style="color:green">'''Really Verbose'''</span> [<span style="color:orange">----really_verbose</span>] : Follow detail of fiber tracking algorithm ''Default value: 0''
|[[Image:FiberTrack.png|thumb|280px|User Interface]]
|}

== More Information ==

More information is available on the project webpage: http://www.nitrc.org/projects/dtiprocess

===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.