Perform filtering operations on fixel-based data


fixelfilter [ options ]  input filter output
  • input: the input: either a fixel data file, or a fixel directory (see Description)
  • filter: the filtering operation to perform; options are: connect, smooth
  • output: the output: either a fixel data file, or a fixel directory (see Description)


If the first input to the command is a specific fixel data file, then a filtered version of only that file will be generated by the command. Alternatively, if the input is the location of a fixel directory, then the command will create a duplicate of the fixel directory, and apply the specified filter operation to all fixel data files within the directory.


  • -matrix file provide a fixel-fixel connectivity matrix for filtering operations that require it

Options specific to the “connect” filter

  • -threshold_value value specify a threshold for the input fixel data file values (default = 0.5)
  • -threshold_connectivity value specify a fixel-fixel connectivity threshold for connected-component analysis (default = 0.10000000000000001)

Options specific to the “smooth” filter

  • -fwhm value the full-width half-maximum (FWHM) of the spatial component of the smoothing filter (default = 10mm)
  • -minweight value apply a minimum threshold to smoothing weights (default = 0.01)
  • -mask image only perform smoothing within a specified binary fixel mask

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.


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 (

Copyright: Copyright (c) 2008-2020 the MRtrix3 contributors.

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