Perform filtering operations on 3D / 4D mask images


maskfilter [ options ]  input filter output
  • input: the input image.

  • filter: the type of filter to be applied (clean, connect, dilate, erode, median)

  • output: the output image.


The available filters are: clean, connect, dilate, erode, median.

Each filter has its own unique set of optional parameters.


Options for mask cleaning filter

  • -scale value the maximum scale used to cut bridges. A certain maximum scale cuts bridges up to a width (in voxels) of 2x the provided scale. (Default: 2)

Options for connected-component filter

  • -axes axes specify which axes should be included in the connected components. By default only the first 3 axes are included. The axes should be provided as a comma-separated list of values.

  • -largest only retain the largest connected component

  • -connectivity use 26-voxel-neighbourhood connectivity (Default: 6)

Options for dilate / erode filters

  • -npass value the number of times to repeatedly apply the filter

Options for median filter

  • -extent voxels specify the extent (width) of kernel size in voxels. This can be specified either as a single value to be used for all axes, or as a comma-separated list of the extent for each axis. The default is 3x3x3.

Stride options

  • -strides spec specify the strides of the output data in memory; either as a comma-separated list of (signed) integers, or as a template image from which the strides shall be extracted and used. The actual strides produced will depend on whether the output image format can support it.

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 (, David Raffelt (, Thijs Dhollander ( and J-Donald Tournier (

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

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