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 maskFile maskFile input Brain mask for diffusion tractography. Tracking will only be performed inside this mask. tracts tracts output Output fiber tracts. Options for seeding tractography. Only one of the three provided options will be used. Option 1 (Minimum Seed FA) is the default. seedingThreshold seedingThreshold (Seeding Option 1) Tractography parameter used in all models. Seed points whose fractional anisotropy (FA) are below this value are excluded. This seeding option is default and will not be used if Seeding Option 2 or 3 is used. Default: 0.18. Range: 0-1. 0.18 0 1 0.01 wmFile wmFile input (Seeding Option 2) A probabilistic segmentation map of the White Matter (WM). The values in the map should be between 0 and 1. Voxels with a probability over WM Probability Threshold (--wmProbThreshold) will be used for seeding. This seeding option will not be used if Seeding Option 3 is used. wmProbThreshold wmProbThreshold (Seeding Option 2) When a WM Segmentation Map (--wmFile) is provided, tracking will be seeded in voxels with values over this threshold. Default: 0.3. Range: 0-1. 0.3 0 1 0.01 seedsFile seedsFile input (Seeding Option 3) Voxels in this map with a label defined in ROI Labels (--seedLabels) for Seeding will be used for seeding. If this option is used, Seeding Options 1 and 2 will not be used. seedLabels seedLabels (Seeding Option 3) A list of the ROI labels to be used when Seeding Label Map (--seedsFile) is provided. There are the voxel values where tractography should be seeded. 1 Options for stopping tractography. Only one of the three provided options will be used. Option 1 (Terminating Mean Signal) is the default. stoppingFA stoppingFA (Stopping Option 1) Tractography parameter used only in tensor models. 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 Terminating Mean Signal (--stoppingThreshold) to track through lower anisotropy areas. This option will not be used if Stopping Option 2 or 3 is provided. Default: 0.15. Range: 0-1. 0.15 0 1 0.01 stoppingThreshold stoppingThreshold (Stopping Option 1) Tractography parameter used by default in all models. Tractography will stop when the mean signal is below this value. This option will not be used if Stopping Option 2 or 3 is provided. Default: 0.1. Range: 0-1. 0.1 0 1 0.01 gmFile gmFile input (Stopping Option 2) A probabilistic segmentation map of the Gray Matter (GM). The values in the map should be between 0 and 1. Tracking will stop in the voxels with a probability over GM Probability Threshold (--gmProbThreshold). This option will not be used if Stopping Option 3 is used. gmProbThreshold gmProbThreshold (Stopping Option 2) When a GM Segmentation Map (--gmFile) is provided, tracking will stop in voxels with values over this threshold. Default: 0.99. Range: 0-1. 0.99 0 1 0.01 csfFile csfFile input (Stopping Option 2) A probabilistic segmentation map of the Cerebrospinal Fluid (CSF). The values in the map should be between 0 and 1. Tracking will stop in voxels with a probability over CSF Probability Threshold (--csfProbThreshold). This option will not be used if Stopping Option 3 is used. csfProbThreshold csfProbThreshold (Stopping Option 2) When a CSF Segmentation Map (--csfFile) is provided, tracking will stop in voxels with values over this threshold. Default: 0.5. Range: 0-1. 0.5 0 1 0.01 stopFile stopFile input (Stopping Option 3) Label map that defines where tracking should stop. Voxels in this map with a label listed in ROI Labels for Stopping (--stopLabels) will be used for stopping. If this option is provided, Stopping Options 1 and 2 will not be used. stopLabels stopLabels (Stopping Option 3) A list of the ROI labels to be used when Stopping Label Map (--stopFile) is provided. There are the voxel values where tractography should stop. 1 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 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 --recordFreeWater flag. 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. To use this flag, --freeWater flag must also be used. 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