Sample values of an associated image along tracks
tcksample [ options ] tracks image values
- tracks: the input track file
- image: the image to be sampled
- values: the output sampled values
By default, the value of the underlying image at each point along the track is written to either an ASCII file (with all values for each track on the same line), or a track scalar file (.tsf). Alternatively, some statistic can be taken from the values along each streamline and written to a vector file.
- -stat_tck statistic compute some statistic from the values along each streamline (options are: mean,median,min,max)
- -nointerp do not use trilinear interpolation when sampling image values
- -precise use the precise mechanism for mapping streamlines to voxels (obviates the need for trilinear interpolation) (only applicable if some per-streamline statistic is requested)
- -use_tdi_fraction each streamline is assigned a fraction of the image intensity in each voxel based on the fraction of the track density contributed by that streamline (this is only appropriate for processing a whole-brain tractogram, and images for which the quantiative parameter is additive)
- -info display information messages.
- -quiet do not display information messages or progress status. Alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
- -debug display debugging messages.
- -force force overwrite of output files. Caution: Using the same file as input and output might cause unexpected behaviour.
- -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).
- -help display this information page and exit.
- -version display version information and exit.
- If using -precise option: Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT: Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013, 67, 298-312
Author: Robert E. Smith (email@example.com)
Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.
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MRtrix3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see http://www.mrtrix.org/