Extract diffusion-weighted volumes, b=0 volumes, or certain shells from a DWI dataset
dwiextract [ options ] input output
- input: the input DW image.
- output: the output image (diffusion-weighted volumes by default).
- -bzero Output b=0 volumes (instead of the diffusion weighted volumes, if -singleshell is not specified).
- -no_bzero Output only non b=0 volumes (default, if -singleshell is not specified).
- -singleshell Force a single-shell (single non b=0 shell) output. This will include b=0 volumes, if present. Use with -bzero to enforce presence of b=0 volumes (error if not present) or with -no_bzero to exclude them.
DW gradient table import options¶
- -grad file Provide the diffusion-weighted gradient scheme used in the acquisition in a text file. 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. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.
- -fslgrad bvecs bvals Provide the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.
- -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.
Options for importing phase-encode tables¶
- -import_pe_table file import a phase-encoding table from file
- -import_pe_eddy config indices import phase-encoding information from an EDDY-style config / index file pair
Options for selecting volumes based on phase-encoding¶
- -pe desc select volumes with a particular phase encoding; this can be three comma-separated values (for i,j,k components of vector direction) or four (direction & total readout time)
- -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.
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/.