dwiextract¶

Synopsis¶

Extract diffusion-weighted volumes, b=0 volumes, or certain shells from a DWI dataset

Usage¶

dwiextract [ options ]  input output

input: the input DW image.
output: the output image (diffusion-weighted volumes by default).

Options¶

-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 options¶

-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.

Standard options¶

-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 (david.raffelt@florey.edu.au) and Thijs Dhollander (thijs.dhollander@gmail.com)

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/.