To provide an alternative to the scanner's built-in B0 shimming routine, so that the linear and high-order B0 shims can be set according to well-defined (and potentially application-specific) critera.
The framework allows for nonlinear loss functions, and may be useful for exploring alternative shimming criteria (beyond least-squares) in the future. For example, the user may want to minimize root-mean-square (RMS) B0 inhomogeneity over a user-specified 3D subvolume.
We envision this tool as one component of a more harmonized cross-vendor MRI workflow in support of reproducible MRI research.
- Get this toolbox
$ git clone [email protected]:HarmonizedMRI/B0shimming.git
- Change into the
juliasubdirectory
julia> cd("julia")
-
Start Julia (download from https://julialang.org/). Current version is 1.6.0.
-
Press
]to enter the Julia package manager and do:
(@v1.6) pkg> activate .
(julia) pkg> instantiate
-
Press
backspaceto get back to the Julia prompt. -
Run the example:
julia> include("example.jl")
Each panel in the output image shows the field map (in Hz) before (left) and
after (right) 2nd order shimming of a cylindrical jar phantom:
The code is based on the model
f(s) = H*A*s + f0
f: [N] fieldmap (Hz), where N = number of voxels
f0: [N] observed 'baseline' field map, e.g., after setting all shim currents to zero
H: [N nb] spherical harmonic basis (see julia/getSHbasis.jl). nb = # of basis functions.
A: [nb nb] shim coil expansion coefficients for basis in H (see julia/getcalmatrix.jl)
s: [nShim+1] change in center frequency (cf) and shim currents from baseline (hardware units)
For 2nd order shim systems, nShim = 8 (3 linear and 5 2nd order).
Each column in H is an N-vector, evaluated at the same N spatial locations as f.
The first column corresponds to the center frequency offset.
This toolbox provides support for spherical harmonic basis functions of arbitrary order
(see julia/getSHbasis.jl), but the code should work equally well with other bases.
The goal here is to set the shim current vector s to make f(s) as homogeneous
as possible -- or more generally, to choose s according to some desired property of f
such as minimizing roughness or the maximum through-voxel gradient.
To do this we need to first calibrate the shim system to obtain A,
which contains the basis expansion coefficients for a particular shim system.
We do this by turning the shims on/off one-by-one and acquiring a 3D fieldmap for each shim setting,
and assembling that data into a matrix F:
F: [N nShim] fieldmaps (Hz) obtained by turning on/off individual shim coils
S: [nShim nShim] applied shim currents (pairwise differences) used to obtain F
F should be obtained in a stationary phantom, and only needs to be acquired once for each scanner.
We then obtain A by fitting each column in F
to the basis in H, using least-squares fitting (backslash in Julia); see julia/getcalmatrix.jl.
See julia/example.jl for a complete example, and additional information for how to construct F.