EXTRACT_Profile =============== Extract fiber tract statistics from images :Command: ``dmrifiberprofile`` :Module version: 0.1 :Module type: ``fiberprofile`` :Attributes: ``utility`` :Source: `dtiplayground/dmri/fiberprofile/modules/EXTRACT_Profile `_ Protocol options ---------------- ``atlas`` Directory containing set of fiber tracts in the atlas to be analyzed :Type: ``dirpath-remote`` :Default: not set ``tracts`` Selected set of tracts to use. Must uniquely map to a VTK fiber file in the atlas location. Empty - all the tracts (.vtk) of the atlas folder. :Type: ``filepath-remote-mult`` :Default: not set ``inputIsDTI`` Input image is a DTI (column 'Original DTI Image'). The tensors are interpolated along the fibers and FA, MD, AD, RD are computed from them; FA, MD, AD, RD are computed from the tensors of the column ' DTI Image' if the column map has that key (e.g. FWFA from 'FW DTI Image'). Other properties, or all properties if this is off, are sampled from their own scalar image column. A property whose image cell is empty for a subject is not profiled for that subject. :Type: ``boolean`` :Default: ``true`` ``tensorInterpolation`` Interpolation of the DTI along the fibers (only if the input is a DTI) :Type: ``list`` :Default: ``logEuclidean`` :Choices: - ``logEuclidean`` -- Linear interpolation of the matrix logarithms of the tensors (no swelling effect). Voxels without a positive definite tensor are left out. - ``linear`` -- Linear interpolation of the tensor components (as fiberprocess) ``propertiesToProfile`` List of selected properties to profile along tracts :Type: ``string`` :Default: ``FA, MD, RD, AD`` ``useDisplacementField`` Convert image to atlas space using displacement field. If set to false, the image will not be transformed to atlas space. :Type: ``boolean`` :Default: ``true`` ``parameterToColumnHeaderMap`` Datasheet column of each parameter: Case ID, Original DTI Image, Deformation Field, ' DTI Image' (additional tensor images, e.g. FW DTI Image), and the image of each scalar property :Type: ``dictionary`` :Default: ``Case ID``: ``id``, ``Original DTI Image``: ``Original DTI image``, ``Deformation Field``: ``Concatenated Deformation field``, ``FA``: ``FA from original``, ``MD``: ``MD from original``, ``AD``: ``AD from original``, ``RD``: ``RD from original`` ``resultCaseColumnwise`` In output CSV, store cases as columns instead of rows :Type: ``boolean`` :Default: ``true`` ``planeOfOrigin`` Determines plane that sets the origin of the profile arc length :Type: ``list`` :Default: ``Median`` :Choices: - ``Median`` -- Origin of profile will be median of tract - ``CoG`` -- Origin of profile will be center of gravity ``arcLength`` Source of the arc length of the fiber points :Type: ``list`` :Default: ``stored`` :Choices: - ``stored`` -- Use the arc lengths stored in parametrized tracts (point data SamplingDistance2Origin, e.g. written by dmrifiberprofile parametrize-fibers); computed from the plane of origin if the tract has none - ``compute`` -- Always compute the arc lengths from the plane of origin ``cleanup`` Remove the profiles of each scan (.fvp, per property and tract folders) and fiber files after processing; kept, they are reused by a later run when their settings and input files are unchanged :Type: ``list`` :Default: ``noCleanup`` :Choices: - ``noCleanup`` -- Keep the profile of each scan (.fvp) and fiber files; a later run reuses the profiles whose settings and input files are unchanged - ``duringProcessing`` -- Remove the profiles of each scan (.fvp) and fiber files the moment they're no longer needed (everything is recomputed by a later run) - ``endOfProcessing`` -- Remove the profiles of each scan (.fvp) and fiber files after processing is complete (everything is recomputed by a later run) ``stepSize`` Distance (mm) along the tract between profile samples; samples are at multiples of the step size from the plane of origin :Type: ``float`` :Default: ``1`` ``supportBandwidth`` Standard deviation (mm) of the Gaussian kernel; points within this distance of a sample are averaged :Type: ``float`` :Default: ``3`` ``noNaN`` Remove fibers with NaN values of the profiled property (for each subject) :Type: ``boolean`` :Default: ``false`` ``writeFiberFiles`` Write the fibers of each subject with the sampled property values and arc lengths (one VTK file per subject, property and tract, e.g. to view the values along the fibers). Not needed for the profiles; removed by the cleanup like the .fvp profiles :Type: ``boolean`` :Default: ``false`` ``mask`` Optional mask file to use during profile extraction. Mask has to be defined in atlas space. :Type: ``file`` :Default: not set ``maskThreshold`` Fibers whose average mask value along the fiber is below this threshold are removed (only used with a mask) :Type: ``float`` :Default: ``0.5``