dwiextract [ options ] input output
- input: the input DW image.
- output: the output image (diffusion-weighted volumes by default.
Extract either diffusion-weighted volumes or b=0 volumes from an image containing both
- -bzero output b=0 volumes instead of the diffusion weighted volumes.
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).
DW Shell selection options¶
- -shell list specify one or more diffusion-weighted gradient shells to use during processing, as a comma-separated list of the desired approximate b-values. Note that some commands are incompatible with multiple shells, and will throw an error if more than one b-value is provided.
- -stride spec specify the strides of the output data in memory, as a comma-separated list. The actual strides produced will depend on whether the output image format can support it.
- -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) 2008-2016 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 www.mrtrix.org