Welcome to shimming-toolbox!¶
shimming-toolbox is an open-source Python software package enabling
a variety of MRI shimming (magnetic field homogenization) techniques
and real-time shimming for use
with standard manufacturer-supplied gradient/shim coils or with custom
“multi-coil” arrays. The toolbox provides useful set of command line tools as
well as a fsleyes plugin
dedicated to make shimming more accessible and more reproducible.
Built-in DICOM to NIfTI conversion
Masking tools for the brain and spinal cord
Supports the creation and usage of a variety of coil profiles: Spherical harmonics, shim-only arrays, “AC-DC” multi-coil, etc.
Supports different shimming scenarios: dynamic (slicewise), realtime (shim modulation with respiration), gradient z-shimming, two-region shimming (e.g., fat and brain)
1. Command Line
The primary way to use
shimming-toolbox is through the command line. For example:
$ st_prepare_fieldmap --help Usage: st_prepare_fieldmap [OPTIONS] PHASE... Creates fieldmap (in Hz) from phase images. This function accommodates multiple echoes (2 or more) and phase difference. This function also accommodates 4D phase inputs, where the 4th dimension represents the time, in case multiple fieldmaps are acquired across time for the purpose of real-time shimming experiments. phase: Input path of phase nifti file(s), in ascending order: echo1, echo2, etc. Options: -mag PATH Input path of mag nifti file -unwrapper [prelude] Algorithm for unwrapping -output PATH Output filename for the fieldmap, supported types : '.nii', '.nii.gz' -mask PATH Input path for a mask. Used for PRELUDE -threshold FLOAT Threshold for masking. Used for: PRELUDE -h, --help Show this message and exit.
To facilitate reproducibility, commands can be chained together in a pipeline using multiple Shimming Toolbox commands. An example script is provided.
The different commands of Shimming Toolbox can be found in the CLI Reference page.
2. Graphical User Interface (FSLeyes)
shimming-toolbox also features a graphical user interface (GUI) via a FSLeyes plugin. See the plugin’s installation page for more information.