fixelstats [ options ]  input
  • input: the input fixel image.


Compute fixel image statistics


Statistics options

  • -output field output only the field specified. Multiple such options can be supplied if required. Choices are: mean, median, std, min, max, count. Useful for use in scripts.
  • -mask image only perform computation within the specified binary mask image.
  • -histogram file generate histogram of intensities and store in specified text file. Note that the first line of the histogram gives the centre of the bins.
  • -bins num the number of bins to use to generate the histogram (default = 100).
  • -dump file dump the voxel intensities to a text file.

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: David Raffelt (

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

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