Compose any number of linear transformations and/or warps into a single transformation


transformcompose [ options ]  input [ input ... ] output
  • input: the input transforms (either linear or non-linear warps). List transforms in the order you like them to be applied to an image (as if you were applying them seperately with mrtransform).
  • output: the output file. If all input transformations are linear, then the output will also be a linear transformation saved as a 4x4 matrix in a text file. If a template image is supplied, then the output will always be a deformation field (see below). If all inputs are warps, or a mix of linear and warps, then the output will be a deformation field defined on the grid of the last input warp supplied.


The input linear transforms must be supplied in as a 4x4 matrix in a text file (as per the output of mrregister).The input warp fields must be supplied as a 4D image representing a deformation field (as output from mrrregister -nl_warp).


  • -template image define the output grid defined by a template image

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: David Raffelt (

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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