warpcorrect

Synopsis

Replaces voxels in a deformation field that point to a specific out of bounds location with nan,nan,nan

Usage

warpcorrect [ options ]  in out
  • in: the input warp image.
  • out: the output warp image.

Description

This can be used in conjunction with the warpinit command to compute a MRtrix compatible deformation field from non-linear transformations generated by any other registration package.

Options

  • -marker coordinates single value or a comma separated list of values that define out of bounds voxels in the input warp image. Default: (0,0,0).
  • -tolerance value numerical precision used for L2 matrix norm comparison. Default: 9.99999975e-06.

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: David Raffelt (david.raffelt@florey.edu.au) & Max Pietsch (mail@maxpietsch.com)

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/.