Documentation/4.2/Modules/fibertrack - Revision history

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T07:48:01Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

Fbudin: /* References */

2012-11-27T22:22:50Z

References

Fbudin at 22:22, 27 November 2012

2012-11-27T22:22:37Z

Fbudin: /* Usage */

2012-11-27T22:19:57Z

Usage

Fbudin: /* FiberTrack */

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FiberTrack

Fbudin: /* FiberTrack */

2012-11-27T22:19:26Z

FiberTrack

Fbudin: /* Quick Tour of Features and Use */

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Quick Tour of Features and Use

Fbudin: /* FiberTrack */

2012-11-27T19:21:15Z

FiberTrack

Fbudin: Created page with ' NOTOC ===FiberTrack=== FiberTrack {| |User Interface |Output |[[Image:screen…'

2012-11-27T19:17:51Z

Created page with ' __NOTOC__ ===FiberTrack=== FiberTrack {| |thumb|280px|User Interface |thumb|280px|Output |[[Image:screen…'

New page

__NOTOC__

===FiberTrack===
FiberTrack

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

== 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 ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1:
* Example 2:

===Tutorials===
* Tutorial 1
** Data Set 1
===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''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|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 [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunkMyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000:description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php 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:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== 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.

← Older revision		Revision as of 07:48, 14 June 2013
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	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.		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.~~

← Older revision		Revision as of 22:19, 27 November 2012
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	== Usage ==		== Usage ==

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

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

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

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 |}
-== Development ==
+== More Information ==
-===Tests===
+More information is available on the project webpage: http://www.nitrc.org/projects/dtiprocess
 ===Acknowledgment===

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 ** <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:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
+|[[Image:FiberTrack.png|thumb|280px|User Interface]]
 |}
 == Development ==

Documentation/4.2/Modules/fibertrack - Revision history

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

Fbudin: /* References */

Fbudin at 22:22, 27 November 2012

Fbudin: /* Usage */

Fbudin: /* FiberTrack */

Fbudin: /* FiberTrack */

Fbudin: /* Quick Tour of Features and Use */

Fbudin: /* FiberTrack */

Fbudin: Created page with ' __NOTOC__ ===FiberTrack=== FiberTrack {| |User Interface |Output |[[Image:screen…'

Fbudin: Created page with ' NOTOC ===FiberTrack=== FiberTrack {| |User Interface |Output |[[Image:screen…'