tcksample [ options ]  tracks image values
  • tracks: the input track file
  • image: the image to be sampled
  • values: the output sampled values


sample values of an associated image along tracks

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)
  • -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)

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status.
  • -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)
  • -failonwarn terminate program if a warning is produced
  • -help display this information page and exit.
  • -version display version information and exit.

Author: Robert E. Smith (

Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors

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