Diffusion.Tractography UKF Tractography
For more information, please reference: Malcolm, James G., Martha E. Shenton, and Yogesh Rathi. "Filtered multitensor tractography." Medical Imaging, IEEE Transactions on 29.9 (2010): 1664-1675. (http://www.ncbi.nlm.nih.gov/pubmed/20805043)]]> 1.0 https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/UKFTractography Yogesh Rathi, Stefan Lienhard, Yinpeng Li, Martin Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner, Kent Williams, Hans Johnson, Peter Savadjiev, Carl-Fredrik Westin, Lauren O'Donnell, Jessica Lee. Input/output parameters dwiFile dwiFile input Input diffusion weighted (DWI) volume seedsFile seedsFile input 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 labels A vector of the ROI labels to be used. There are the voxel values where tractography should be seeded. 1 maskFile maskFile input Brain mask for diffusion tractography. Tracking will only be performed inside this mask. tracts tracts output Output fiber tracts. Basic Parameters seedsPerVoxel seedsPerVoxel Tractography parameter used in all models. Each seed generates a fiber, thus using more seeds generates more fibers. In general use 1 or 2 seeds, and for a more thorough result use 5 or 10 (depending on your machine this may take up to 2 days to run). Default: 1. Range: 0-50. 1 0 50 1 seedingThreshold seedingThreshold Tractography parameter used in all models. Seed points whose fractional anisotropy (FA) or mean signal are below this value are excluded. Default: 0.18. Range: 0-1. 0.18 0 1 0.01 stoppingFA stoppingFA Tractography parameter used in tensor model. Tractography will stop when the fractional anisotropy (FA) of the tensor being tracked is less than this value. Note: make sure to also decrease the GA to track through lower anisotropy areas. This parameter is used only in tensor models. Default: 0.15. Range: 0-1. 0.15 0 1 0.01 stoppingThreshold stoppingThreshold Tractography parameter used in all models. Tractography will stop when the mean signal is below this value. Default: 0.1. Range: 0-1. 0.1 0 1 0.01 numThreads numThreads Tractography parameter used in all models. Number of threads used during computation. Set to the number of cores on your workstation for optimal speed. If left undefined, the number of cores detected will be used. -1 numTensor numTensor Number of tensors (tensor model) or orientations (NODDI model) used 2 1 2 stepLength stepLength Tractography parameter used in all models. Step size when conducting tractography. Default: 0.3. Range: 0.1-1. 0.3 0.1 1 0.1 Qm Qm UKF data fitting parameter for tensor or NODDI model: Process noise for angles/direction. Defaults: Noddi-0.001; Single tensor-0.005; other-0.001. Suggested Range: 0.00001 - 0.25. Default of 0.0 indicates the program will assign value based on other model parameters. 0.0 0.0 0.25 0.00001 recordLength recordLength Tractography parameter used in all models. Step size between points saved along fibers. Default: 0.9. Range: 0.1-4. 0.9 0.1 4 0.1 maxHalfFiberLength maxHalfFiberLength Tractography parameter used in all models. The max length limit of the half fibers generated during tractography. A fiber is "half" when the tractography goes in only one direction from one seed point at a time. Default: 250 mm. Range: 1-500 mm. 250 1 500 1 recordNMSE recordNMSE Record output from data fitting: Store normalized mean square error (NMSE) along fibers. false Tensor model parameters freeWater freeWater Adds a term for free water diffusion to the model. The free water model is a tensor with all 3 eigenvalues equal to the diffusivity of free water (0.003). To output the free water fraction, make sure to use the "save free water" parameter. false recordFA recordFA Record output from tensor model: Save fractional anisotropy (FA) of the tensor(s). Attaches field 'FA' or 'FA1' and 'FA2' for 2-tensor case to fiber. true recordTrace recordTrace Record output from tensor model: Save the trace of the tensor(s). Attaches field 'Trace' or 'Trace1' and 'Trace2' for 2-tensor case to fiber. false recordFreeWater recordFreeWater Record output from tensor plus free water model: Save the fraction of free water. Attaches field 'FreeWater' to fiber. false recordTensors recordTensors Record output from tensor model: Save the tensors that were computed during tractography (if using tensor model). The fields will be called 'TensorN', where N is the tensor number. Recording the tensors enables Slicer to color the fiber bundles by FA, orientation, and so on. Recording the tensors also enables quantitative analyses. true Ql Ql UKF data fitting parameter for tensor model: Process noise for eigenvalues. Defaults: 1 tensor-300 ; 2 tensor-50 ; 3 tensor-100. Suggested Range: 1-1000. Default of 0.0 indicates the program will assign value based on other model parameters. 0.0 0 1000 1 Qw Qw UKF data fitting parameter for tensor plus free water model: Process noise for free water weights, ignored if no free water estimation. Defaults: 1 tensor-0.0025; 2 tensor-0.0015. Suggested Range: 0.00001-0.25. Default of 0.0 indicates the program will assign value based on other model parameters. 0.0 0.0 0.25 0.00001 Use NODDI model noddi noddi Use neurite orientation dispersion and density imaging (NODDI) model instead of tensor model. false recordVic recordVic Record output from NODDI model: Store volume fraction of intra-cellular compartment along fibers. false recordKappa recordKappa Record output from NODDI model: concentration parameter that measures the extent of orientation dispersion. false recordViso recordViso Record output from NODDI model: Store volume fraction of CSF compartment along fibers. false Qkappa Qkappa UKF data fitting parameter for NODDI model: Rate of change of kappa (orientation dispersion) value. Higher kappa values indicate more fiber dispersion. Default: 0.01. 0.01 Qvic Qvic UKF data fitting parameter for NODDI model: Rate of change of volume fraction of intracellular component. Default: 0.004. 0.004 Rs Rs UKF Data Term: Measures expected noise in signal. This is used by the UKF method to decide how much to trust the data. This should be increased for very noisy data or reduced for high quality data. Defaults: single tensor/orientation-0.01; other-0.02. Suggested Range: 0.001-0.25. Default of 0.0 indicates the program will assign value based on other model parameters. 0.0 0.0 0.25 0.001 sigmaSignal sigmaSignal UKF Data Term: Sigma for Gaussian kernel used to interpolate the signal at sub-voxel locations. Default: 0.0 0.0 recordState recordState Develop/Debug Only: Store the states along the fiber. Will generate field 'state'. The state is the model for UKF. In the case of the two tensor model, it is a ten-parameter vector. false recordCovariance recordCovariance Develop/Debug Only: Store the covariance matrix along the fiber. Will generate field 'covariance' in fiber. This is the covariance from the unscented Kalman filter. false fullTensorModel fullTensorModel Develop/Debug Only: Use the full tensor model instead of the default model. The default model has both smaller eigenvalues equal, whereas the full model allows 3 different eigenvalues. false maxBranchingAngle maxBranchingAngle Develop/Debug Only: 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. Default: 0.0. Range: 0-90. 0.0 0 90 1 minBranchingAngle minBranchingAngle Develop/Debug Only: 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). Default: 0. Range: 0-90. 0.0 0 90 1 tractsWithSecondTensor tractsWithSecondTensor output Develop/Debug Only: Tracts generated, with second tensor output (if there is one) storeGlyphs storeGlyphs Develop/Debug Only: 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 false writeAsciiTracts a writeAsciiTracts Develop/Debug Only: Write tract file as ASCII text format. Default is not ASCII. Default tracts are written on VTK binary data file. false writeUncompressedTracts u writeUncompressedTracts Develop/Debug Only: Write tract file as a VTK uncompressed data file false