.. _dwiextract:

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).

Example usages
--------------

-   *Calculate the mean b=0 image from a 4D DWI series*::

        $ dwiextract dwi.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3

    The dwiextract command extracts all volumes for which the b-value is (approximately) zero; the resulting 4D image can then be provided to the mrmath command to calculate the mean intensity across volumes for each voxel.

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.

DW shell selection options
^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-shells b-values** specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided.  |br|
   WARNING: note that, even though the b=0 volumes are never referred to as shells in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms which include the b=0 volumes in their computations may otherwise return an undesired result.

DW gradient table export options
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-export_grad_mrtrix path** export the diffusion-weighted gradient table to file in MRtrix format

-  **-export_grad_fsl bvecs_path bvals_path** export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format

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
^^^^^^^^^^^^^^

-  **-strides spec** specify the strides of the output data in memory; either as a comma-separated list of (signed) integers, or as a template image from which the strides shall be extracted and used. 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; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.

-  **-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).

-  **-config key value** *(multiple uses permitted)* temporarily set the value of an MRtrix config file entry.

-  **-help** display this information page and exit.

-  **-version** display version information and exit.

References
^^^^^^^^^^

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

--------------



**Author:** David Raffelt (david.raffelt@florey.edu.au) and Thijs Dhollander (thijs.dhollander@gmail.com) and Robert E. Smith (robert.smith@florey.edu.au)

**Copyright:** Copyright (c) 2008-2021 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/.

Covered Software is provided under this License on an "as is"
basis, without warranty of any kind, either expressed, implied, or
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Covered Software is free of defects, merchantable, fit for a
particular purpose or non-infringing.
See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.


