dwinormalise [ options ] input mask output
- input: the input DWI image containing volumes that are both diffusion weighted and b=0
- mask: the input mask image used to normalise the intensity
- output: the output DWI intensity normalised image
Intensity normalise the b=0 signal within a supplied white matter mask
- -intensity value normalise the b=0 signal to the specified value (Default: 1e+003)
- -percentile value define the percentile of the mask intensties used for normalisation. If this option is not supplied then the median value (50th percentile) will be normalised to the desired intensity value.
DW gradient table import options¶
- -grad encoding specify the diffusion-weighted gradient scheme used in the acquisition. The program will normally attempt to use the encoding stored in the image header. This should be supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units of s/mm^2.
- -fslgrad bvecs bvals specify the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format.
- -bvalue_scaling mode specifies whether the b-values should be scaled by the square of the corresponding DW gradient norm, as often required for multi-shell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes/no, true/false, 0/1 (default: true).
- -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 (firstname.lastname@example.org)
Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors
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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 www.mrtrix.org