Convert a fixel-based sparse-data image into some form of scalar image


fixel2voxel [ options ]  fixel_in operation image_out
  • fixel_in: the input fixel data file
  • operation: the operation to apply, one of: mean, sum, product, min, max, absmax, magmax, count, complexity, sf, dec_unit, dec_scaled, split_data, split_dir.
  • image_out: the output scalar image.


Fixel data can be reduced to voxel data in a number of ways:

  • Some statistic computed across all fixel values within a voxel: mean, sum, product, min, max, absmax, magmax
  • The number of fixels in each voxel: count
  • Some measure of crossing-fibre organisation: complexity, sf (‘single-fibre’)
  • A 4D directionally-encoded colour image: dec_unit, dec_scaled
  • A 4D scalar image of fixel values with one 3D volume per fixel: split_data
  • A 4D image of fixel directions, stored as three 3D volumes per fixel direction: split_dir


  • -number N use only the largest N fixels in calculation of the voxel-wise statistic; in the case of “split_data” and “split_dir”, output only the largest N fixels, padding where necessary.
  • -weighted fixel_in weight the contribution of each fixel to the per-voxel result according to its volume. E.g. when estimating a voxel-based measure of mean axon diameter, a fixel’s mean axon diameter should be weigthed by its relative volume within the voxel. Note that AFD can be used as a psuedomeasure of fixel volume.

Standard options

  • -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.


  • Reference for ‘complexity’ operation:Riffert, T. W.; Schreiber, J.; Anwander, A. & Knosche, T. R. Beyond Fractional Anisotropy: Extraction of bundle-specific structural metrics from crossing fibre models. NeuroImage, 2014, 100, 176-191

Author: Robert E. Smith ( & David Raffelt (

Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.

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