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.
- -fa_threshold The threshold applied to the Fractional Anisotropy group template used to derive an approximate white matter mask
- -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) 2008-2017 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/.
MRtrix 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/.