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Generate an image for visualisation purposes from an ACT 5TT segmented anatomical image


5tt2vis [ options ]  input output
  • input: the input 4D tissue-segmented image
  • output: the output 3D image for visualisation


  • -bg value image intensity of background (default: 0)
  • -cgm value image intensity of cortical grey matter (default: 0.5)
  • -sgm value image intensity of sub-cortical grey matter (default: 0.75)
  • -wm value image intensity of white matter (default: 1)
  • -csf value image intensity of CSF (default: 0.15)
  • -path value image intensity of pathological tissue (default: 2)

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 (

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.

For more details, see

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