<commit_before>dwiextract
===========

Synopsis
--------

::

    dwiextract [ options ]  input output

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

Description
-----------

Extract either diffusion-weighted volumes or b=0 volumes from an image containing both

Options
-------

-  **-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.

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

-  **-failonwarn** terminate program if a warning is produced

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

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

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


<commit_msg>docs update<commit_after>dwiextract
===========

Synopsis
--------

::

    dwiextract [ options ]  input output

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

Description
-----------

Extract either diffusion-weighted volumes or b=0 volumes from an image containing both

Options
-------

-  **-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 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

-  **-failonwarn** terminate program if a warning is produced

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

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

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



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