Installation on Windows
Shimming Toolbox can be used from the Terminal on Windows system.
$ st_prepare_fieldmap -h
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 field maps are acquired across time
for the purpose of real-time shimming experiments. For non Siemens phase
data, see --autoscale-phase option.
PHASE: Input path of phase nifti file(s), in ascending order: echo1, echo2,
--mag PATH Input path of mag nifti file [required]
--unwrapper [prelude|skimage] Algorithm for unwrapping. skimage is
installed by default, prelude requires FSL to
be installed. [default: prelude]
-o, --output PATH Output filename for the fieldmap, supported
types : '.nii', '.nii.gz' [default:
--autoscale-phase BOOLEAN Tells whether to auto rescale phase inputs
according to manufacturer standards. If you
have non standard data, it would be
preferable to set this option to False and
input your phase data from -pi to pi to avoid
unwanted rescaling [default: True]
--mask PATH Input path for a mask. Mask must be the same
shape as the array of each PHASE input.
--threshold FLOAT Threshold for masking if no mask is provided.
Allowed range: [0, 1] where all scaled values
lower than the threshold are set to 0.
--savemask PATH Filename of the mask calculated by the
--gaussian-filter BOOLEAN Gaussian filter for B0 map
--sigma FLOAT Standard deviation of gaussian filter. Used
-v, --verbose [info|debug] Be more verbose
-h, --help Show this message and exit.
prelude(FSL) is only supported on macOS and Linux. To use prelude, install Shimming Toolbox on a macOS or Linux system.
If you would like to use
sct_deepseg_scfor spinal cord segmentation, you need to install SCT.
Installation Procedure for Windows
Conda requires an installation path that does not contain spaces. Your username should not contain spaces to avoid this issue. If your username contains spaces, you can create a new user account with no spaces in the username or use a different OS.
The installer will install
Shimming Toolbox and
dcm2niix into an isolated environment. It will not interfere if you already have
cmd command prompt and run the following commands.
First, download Shimming Toolbox:
git clone https://github.com/shimming-toolbox/shimming-toolbox.git
Next, run the installer:
To use Shimming Toolbox's scripts, you will be prompted to either reboot your computer or follow these instructions:
Open the Start Menu -> Type 'environment' -> Open Edit environment variables for your account
To make sure the installation was successful, run the following command:
Test the Installation
This step is optional but it's a good measure to ensure
Shimming Toolbox is properly installed on your system.
To run the testing suite, run
pytest from the shimming-toolbox source directory:
pytest -m "not prelude"
See https://docs.pytest.org/ for more options.
If all tests pass,
Shimming Toolbox is properly installed with all supported dependencies (SCT).
Testing subsets of soft dependencies
SCT is a soft dependencies, so you may wish to run the
parts of the testing suite that do not depend on it.
To test shimming-toolbox without
pytest -m "not prelude and not sct"
To test only the parts of shimming-toolbox dependent on
sct, the corresponding
-m argument is
The installation script can be found in the
installer folder as
When you run the installer, we first check if the
ST_DIR exists. The
ST_DIR is where the
We then install
conda. Next, we install
shimming-toolbox into the base environment of the new conda installation.