Performs a global DWI intensity normalisation on a group of subjects using the median b=0 white matter value as the reference


dwiintensitynorm input_dir mask_dir output_dir fa_template wm_mask [ options ]
  • input_dir: The input directory containing all DWI images
  • mask_dir: Input directory containing brain masks, corresponding to one per input image (with the same file name prefix)
  • output_dir: The output directory containing all of the intensity normalised DWI images
  • fa_template: The output population specific FA template, which is threshold to estimate a white matter mask
  • wm_mask: The output white matter mask (in template space), used to estimate the median b=0 white matter value for normalisation


The white matter mask is estimated from a population average FA template then warped back to each subject to perform the intensity normalisation. Note that bias field correction should be performed prior to this step.


Options for the dwiintensitynorm script

  • -fa_threshold The threshold applied to the Fractional Anisotropy group template used to derive an approximate white matter mask (default: 0.4)

Standard options

  • -continue <TempDir> <LastFile> Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file
  • -force Force overwrite of output files if pre-existing
  • -help Display help information for the script
  • -nocleanup Do not delete temporary files during script, or temporary directory at script completion
  • -nthreads number Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)
  • -tempdir /path/to/tmp/ Manually specify the path in which to generate the temporary directory
  • -quiet Suppress all console output during script execution
  • -info Display additional information and progress for every command invoked
  • -debug Display additional debugging information over and above the output of -info

Author: David Raffelt (david.raffelt@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/