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, none.

  • 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 image containing all fixel data values in each voxel unmodified: none

The -weighted option deals with the case where there is some per-fixel metric of interest that you wish to collapse into a single scalar measure per voxel, but each fixel possesses a different volume, and you wish for those fixels with greater volume to have a greater influence on the calculation than fixels with lesser volume. For instance, when estimating a voxel-based measure of mean axon diameter from per-fixel mean axon diameters, a fixel’s mean axon diameter should be weigthed by its relative volume within the voxel in the calculation of that voxel mean.


  • -number N use only the largest N fixels in calculation of the voxel-wise statistic; in the case of operation “none”, output only the largest N fixels in each voxel.

  • -fill value for “none” operation, specify the value to fill when number of fixels is fewer than the maximum (default: 0.0)

  • -weighted fixel_in weight the contribution of each fixel to the per-voxel result according to its 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).

  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.

  • -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

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Author: Robert E. Smith ( & David Raffelt (

Copyright: Copyright (c) 2008-2024 the MRtrix3 contributors.

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