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).
  • -help display this information page and exit.
  • -version display version information and exit.

Author: Robert E. Smith (, David Raffelt (, Thijs Dhollander ( and J-Donald Tournier (

Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, you can obtain one at

MRtrix3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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