5ttedit

Synopsis

Manually set the partial volume fractions in an ACT five-tissue-type (5TT) image using mask images

Usage

5ttedit [ options ]  input output
  • input: the 5TT image to be modified
  • output: the output modified 5TT image

Options

  • -cgm image provide a mask of voxels that should be set to cortical grey matter
  • -sgm image provide a mask of voxels that should be set to sub-cortical grey matter
  • -wm image provide a mask of voxels that should be set to white matter
  • -csf image provide a mask of voxels that should be set to CSF
  • -path image provide a mask of voxels that should be set to pathological tissue
  • -none image provide a mask of voxels that should be cleared (i.e. are non-brain); note that this will supersede all other provided masks

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.

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

Copyright: Copyright (c) 2008-2019 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/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.