.. _cli_reference:

Command Line Tools
==================

The following section outlines the CLI of shimming-toolbox.

.. contents::
   :local:
   :depth: 2

Field mapping
-------------

.. click:: shimmingtoolbox.cli.prepare_fieldmap:prepare_fieldmap_cli
   :prog: st_prepare_fieldmap

.. click:: shimmingtoolbox.cli.unwrap:unwrap_cli
   :prog: st_unwrap


Shimming
--------

.. _st_b0shimming:

.. click:: shimmingtoolbox.cli.b0shim:b0shim_cli
   :prog: st_b0shim
   :nested: full

.. click:: shimmingtoolbox.cli.b1shim:b1shim_cli
   :prog: st_b1shim

Masking
-------

.. click:: shimmingtoolbox.cli.mask:mask_cli
   :prog: st_mask
   :nested: full

File Conversion
---------------

.. click:: shimmingtoolbox.cli.dicom_to_nifti:dicom_to_nifti_cli
   :prog: st_dicom_to_nifti

Coil Profile Generation
-----------------------

.. _st_create_coil_profiles:

.. click:: shimmingtoolbox.cli.create_coil_profiles:coil_profiles_cli
   :prog: st_create_coil_profiles
   :nested: full

Image manipulation
------------------

.. click:: shimmingtoolbox.cli.image:image_cli
   :prog: st_image
   :nested: full

.. click:: shimmingtoolbox.cli.maths:maths_cli
   :prog: st_maths
   :nested: full

Miscellaneous
-------------

.. click:: shimmingtoolbox.cli.download_data:download_data
   :prog: st_download_data

.. click:: shimmingtoolbox.cli.sort_dicoms:sort_dicoms
   :prog: st_sort_dicoms

System Tools
------------

.. click:: shimmingtoolbox.cli.check_env:check_dependencies
   :prog: st_check_dependencies

.. click:: shimmingtoolbox.cli.check_env:dump_env_info
   :prog: st_dump_env_info