fixel2voxel [ options ]  fixel_in operation image_out
  • fixel_in: the input sparse fixel image.
  • operation: the operation to apply, one of: mean, sum, product, rms, var, std, min, max, absmax, magmax, count, complexity, sf, dec_unit, dec_scaled, split_size, split_value, split_dir.
  • image_out: the output scalar image.


convert a fixel-based sparse-data image into some form of scalar image. This could be: - Some statistic computed across all fixel values within a voxel: mean, sum, product, rms, var, std, 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 with one 3D volume per fixel: split_size, split_value- A 4D image with three 3D volumes per fixel direction: split_dir


  • -weighted weight the contribution of each fixel to the per-voxel result according to its volume (note that this option is not applicable for all operations, and should be avoided if the value stored in the fixel image is itself the estimated fibre volume)

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.


  • 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 (in press)

Author: Robert E. Smith (

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

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