Documentation/4.2/Modules/UKFTractography - Revision history

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

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Reckbo2 at 16:43, 28 January 2013

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 -h, --help 	Displays usage information and exits.
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 Fiber Scalar Fields
 --recordFA 	Whether to store FA. Attaches field 'FA', and 'FA2' for 2-tensor case to fiber.
 --recordNMSE 	Whether to store NMSE. Attaches field 'NMSE' to fiber.
 --recordTrace 	Whether to store Trace. Attaches field 'Trace', and 'Trace2' for 2-tensor case to fiber.
 --recordFreeWater 	Whether to store the fraction of free water. Attaches field 'FreeWater' to fiber.
 --recordState 	Whether to attach the states to the fiber. Will generate field 'state'.
 --recordCovariance 	Whether to store the covariance. Will generate field 'covariance' in fiber.
 --recordTensors 	Recording the tensors enables Slicer to color the fiber bundles by FA, orientation, and so on. The fields will be called 'TensorN', where N is the tensor number.
 Advanced Options
 --numThreads <int> 	Number of threads used during compuation. Set to the number of cores on your workstation for optimal speed. If left undefined boost will figure out the number of cores, and hence threads, during runtime.
 --normalizedDWIData 	Whether the DWI input data is already normalized
 --weightsOnTensors <std::vector<double>> 	Weights on different tensors when using multiple tensors. There must be one weight for each tensor, and the weights must sum up to 1. Defaults to equally weighted.
 --maxHalfFiberLength <double> 	The max length limit of the half fibers generated during tractography. Here the fiber is "half" because the tractography goes in only one direction from one seed point at a time (default: 10000)
 --Qm <double> 	Process noise for angles/direction (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
 --Ql <double> 	Process noise for eigenvalues (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
 --Qw <double> 	Process noise for free water weights, ignored if no free water estimation (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
 --Rs <double> 	Measurement noise (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
 --stepLength <double> 	Step length i.e. size of the step taken in the most consistent direction during each iteration of tractography given in millimeters (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
 --maxBranchingAngle <double> 	Maximum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle). Branching is supressed when this maxBranchingAngle is set to 0.0
 --minBranchingAngle <double> 	Minimum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle)
 Additional Output Options
 --noTransformPosition 	Don't transform Points back from ijk->RAS when writing the output fiber
 --branchesOnly 	Only output branches, ignore the primary tracts
 --storeGlyphs 	Store tensors' main directions as two-point lines in a separate file named glyphs_{tracts}. When using multiple tensors, only the major tensors' main directions are stored
 --outputNormalizedDWIData 	Whether to output the DWI after normalization (i.e. preprocessing)
 Tractography unrelated options
 --returnparameterfile <std::string> 	Filename in which to write simple return parameters (int, float, int-vector, etc.) as opposed to bulk return parameters (image, geometry, transform, measurement, table).
 --processinformationaddress <std::string> 	Address of a structure to store process information (progress, abort, etc.). (default: 0)
 --xml 	Produce xml description of command line arguments.
 --echo 	Echo the command line arguments.
 --, --ignore_rest 	Ignores the rest of the labeled arguments following this flag.
 --version 	Displays version information and exits.
 -h, --help 	Displays usage information and exits.

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 Input/Output (IO)
 --dwiFile <std::string> 	Input DWI Image
 --seedsFile <std::string> 	Seeds for diffusion. If not specified, full brain tractography will be performed, and the algorithm will start from every voxel in the brain mask where the Generalized Anisotropy is bigger than 0.18
 --labels <std::vector<int>> 	A vector of the ROI labels to be used (default: 1)
 --maskFile <std::string> 	Mask for diffusion tractography
 --tracts <std::string> 	Tracts generated, with first tensor output
 --tractsWithSecondTensor <std::string> 	Tracts generated with second tensor output (if there is one)
 Seeding Options
 --seedsPerVoxel <int> 	Number of seeds per voxel (default: 1)
 --seedFALimit<double> 	Seed points whose FA are below this value are excluded (default: 0.15)
 Model Options
 --numTensor <1|2|3> 	Number of tensors used (default: 2)
 --fullTensorModel 	Whether to use the full tensor model. Which models all three eigenvalues seperately, as opposed to lambda2=lambda3.
 --freeWater 	Adds a term for free water difusion to the model. If checked, the 1T simple model is forced.
 Stopping Criteria
 --minFA <double> 	Abort the tractography when the Fractional Anisotropy is less than this value (default: 0.15)
 --minGA <double> 	Abort the tractography when the Generalized Anisotropy is less than this value (default: 0.1)

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 Input/Output (IO)
 --dwiFile <std::string> 	Input DWI Image
 --seedsFile <std::string> 	Seeds for diffusion. If not specified, full brain tractography will be performed, and the algorithm will start from every voxel in the brain mask where the Generalized Anisotropy is bigger than 0.18
 --labels <std::vector<int>> 	A vector of the ROI labels to be used (default: 1)

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 This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
 Author: Yogesh Rathi, Ph.D, Psychiatry Neuroimaging Laboratory, Brigham & Women's Hospital<br>
-Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br>
-Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br>
+Contact: Ryan Eckbo, <email>reckbo@bwh.harvard.edu</email><br>
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+* 1-Tensor tractography
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+Reference for 2-tensor tractography:
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