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,
etc.

Options:
--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:
                               ./fieldmap.nii.gz]
--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.
                               [default: 0.05]
--savemask PATH                Filename of the mask calculated by the
                               unwrapper
--gaussian-filter BOOLEAN      Gaussian filter for B0 map
--sigma FLOAT                  Standard deviation of gaussian filter. Used
                               for: gaussian_filter
-v, --verbose [info|debug]     Be more verbose
-h, --help                     Show this message and exit.

Dependencies

Optional dependencies:

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_sc for 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.

Note

The installer will install Shimming Toolbox and dcm2niix into an isolated environment. It will not interfere if you already have dcm2niix installed.

Open a 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:

cd shimming-toolbox
installer\windows_install.bat

Warning

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

Click 'OK'

To make sure the installation was successful, run the following command:

st_b0shim --help

Test the Installation

This step is optional but it's a good measure to ensure Shimming Toolbox is properly installed on your system.

Comprehensive Test

To run the testing suite, run pytest from the shimming-toolbox source directory:

%userprofile%\shimming-toolbox\python\Scripts\activate
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 SCT:

%userprofile%\shimming-toolbox\python\Scripts\activate
pytest -m "not prelude and not sct"

To test only the parts of shimming-toolbox dependent on sct, the corresponding -m argument is "sct"

For Developers

The installation script can be found in the installer folder as windows_installer.bat.

When you run the installer, we first check if the ST_DIR exists. The ST_DIR is where the shimming-toolbox package.

We then install conda. Next, we install shimming-toolbox into the base environment of the new conda installation.