3 Yd@spdZddlZddlmZmZmZmZmZmZm Z m Z m Z m Z GdddeZ GdddeZGd d d eZdS) zuAutogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.N) CommandLineCommandLineInputSpecSEMLikeCommandLine TraitedSpecFile Directorytraits isdefinedInputMultiPathOutputMultiPathc@seZdZeddddZeddddZeejddd d Z ed dd dZ ej ej ed dddZ ej dddZej dddZejdddZejdddddZej dddZej dddZej d d!dZej d"d#dZej d$d%dZej d&d'dZej d(d)dZej d*d+dZejd,d-dZejd.d/dZejd0d1dZej d2d3dZejd4d5dZ ejd6d7dZ!ejd8d9dZ"ejd:d;dZ#ejdd?dZ%ejd@dAdZ&ejdBdCdZ'ejdDdEdZ(ejdFdGdZ)ej ej ed dHdIdZ*ej dJdKdZ+dLS)MUKFTractographyInputSpeczInput DWI volumeTz --dwiFile %s)descexistsargstrzSeeds 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 0.18z--seedsFile %sz%A vector of the ROI labels to be used,z --labels %s)rseprzMask for diffusion tractographyz --maskFile %sFz*Tracts generated, with first tensor outputz --tracts %s)Z hash_filesrrz*Write tract file as a VTK binary data filez--writeAsciiTracts )rrz0Write tract file as a VTK uncompressed data filez--writeUncompressedTracts z 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)., z--seedsPerVoxel %d12zNumber of tensors usedz--numTensor %szpAdds a term for free water difusion to the model. (Note for experts: if checked, the 1T simple model is forced) z --freeWater zPWhether to store FA. Attaches field 'FA', and 'FA2' for 2-tensor case to fiber. z --recordFA zQWhether to store the fraction of free water. Attaches field 'FreeWater' to fiber.z--recordFreeWater zXWhether to store Trace. Attaches field 'Trace', and 'Trace2' for 2-tensor case to fiber.z--recordTrace zRecording 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. z--recordTensors z7Whether to store NMSE. Attaches field 'NMSE' to fiber. z --recordNMSE zGWhether to attach the states to the fiber. Will generate field 'state'.z--recordState zKWhether to store the covariance. Will generate field 'covariance' in fiber.z--recordCovariance z-Record length of tractography, in millimetersz--recordLength %fzMAbort the tractography when the Fractional Anisotropy is less than this valuez --minFA %fzNAbort the tractography when the Generalized Anisotropy is less than this valuez --minGA %fzWWhether to use the full tensor model. If unchecked, use the default simple tensor modelz--fullTensorModel zNumber 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. z--numThreads %dz+Step length of tractography, in millimetersz--stepLength %fzThe 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 timez--maxHalfFiberLength %fz6Seed points whose FA are below this value are excludedz--seedFALimit %fz"Process noise for angles/directionz--Qm %fzProcess noise for eigenvaluesz--Ql %fzIProcess noise for free water weights, ignored if no free water estimationz--Qw %fzMeasurement noisez--Rs %faMaximum 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 0.0z--maxBranchingAngle %fzMinimum 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)z--minBranchingAngle %fz=Tracts generated, with second tensor output (if there is one)z--tractsWithSecondTensor %szStore 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 storedz--storeGlyphs N),__name__ __module__ __qualname__rZdwiFileZ seedsFiler r ZIntlabelsZmaskFileZEitherZBooltractsZwriteAsciiTractsZwriteUncompressedTractsZ seedsPerVoxelEnumZ numTensorZ freeWaterZrecordFAZrecordFreeWaterZ recordTraceZ recordTensorsZ recordNMSEZ recordStateZrecordCovarianceZFloatZ recordLengthZminFAZminGAZfullTensorModelZ numThreadsZ stepLengthZmaxHalfFiberLengthZ seedFALimitZQmZQlZQwZRsZmaxBranchingAngleZminBranchingAngletractsWithSecondTensorZ storeGlyphsrrs/var/www/html/virt/lib/python3.6/site-packages/nipype/interfaces/semtools/diffusion/tractography/ukftractography.pyr s    r c@s$eZdZedddZedddZdS)UKFTractographyOutputSpecz*Tracts generated, with first tensor outputT)rrz=Tracts generated, with second tensor output (if there is one)N)rrrrrrrrrrrs rc@s*eZdZdZeZeZdZdddZ dZ dS)UKFTractographyatitle: UKF Tractography category: Diffusion.Tractography description: This module traces fibers in a DWI Volume using the multiple tensor unscented Kalman Filter methology. For more informations check the documentation. version: 1.0 documentation-url: http://www.nitrc.org/plugins/mwiki/index.php/ukftractography:MainPage contributor: Yogesh Rathi, Stefan Lienhard, Yinpeng Li, Martin Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner, Kent Williams, Hans Johnson, Peter Savadjiev, Carl-Fredrik Westin. acknowledgements: The development of this module was supported by NIH grants R01 MH097979 (PI Rathi), R01 MH092862 (PIs Westin and Verma), U01 NS083223 (PI Westin), R01 MH074794 (PI Westin) and P41 EB015902 (PI Kikinis). z UKFTractography z tracts.vtpztractsWithSecondTensor.vtp)rrFN) rrr__doc__r Z input_specrZ output_specZ_cmdZ_outputs_filenamesZ _redirect_xrrrrrsr)r osbaserrrrrrr r r r r rrrrrrs 0