Multi-Tissue Bias field correction and Intensity Normalisation (MTBIN)
mtbin [ options ] input output [ input output ... ]
- input output: list of all input and output tissue compartment files. See example usage in the description. Note that any number of tissues can be normalised
This command inputs N number of tissue components (e.g. from multi-tissue CSD), and outputs N corrected tissue components. Intensity normalisation is performed by either determining a common global normalisation factor for all tissue types (default) or by normalising each tissue type independently with a single tissue-specific global scale factor.
Example usage: mtbin wm.mif wm_norm.mif gm.mif gm_norm.mif csf.mif csf_norm.mif.
The estimated multiplicative bias field is guaranteed to have a mean of 1 over all voxels within the mask.
- -mask image define the mask to compute the normalisation within. If not supplied this is estimated automatically
- -value number specify the value to which the summed tissue compartments will be normalised to (Default: sqrt(1/(4*pi)) = 0.282094)
- -bias image output the estimated bias field
- -independent intensity normalise each tissue type independently
- -maxiter number set the maximum number of iterations. Default(100). It will stop before the max iterations if convergence is detected
- -check image check the automatically computed mask
- -info display information messages.
- -quiet do not display information messages or progress status.
- -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)
- -failonwarn terminate program if a warning is produced
- -help display this information page and exit.
- -version display version information and exit.
Author: David Raffelt (email@example.com)
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/.