Generate a mask image appropriate for seeding streamlines on the grey matter-white matter interface


5tt2gmwmi [ options ]  5tt_in mask_out
  • 5tt_in: the input 5TT segmented anatomical image
  • mask_out: the output mask image


  • -mask_in image Filter an input mask image according to those voxels that lie upon the grey matter - white matter boundary. If no input mask is provided, the output will be a whole-brain mask image calculated using the anatomical image only.

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.


Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. Anatomically-constrained tractography:Improved diffusion MRI streamlines tractography through effective use of anatomical information. NeuroImage, 2012, 62, 1924-1938

Author: Robert E. Smith (robert.smith@florey.edu.au)

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 http://mozilla.org/MPL/2.0/

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 http://www.mrtrix.org/