https://github.com/MagneticResonanceImaging/BlochSim.jl
This Julia package provides functionality
for simulating arbitrary MRI pulse sequences.
It includes support for (traditional) single-compartment Bloch simulations
(using Spin objects) as well as multi-compartment Bloch-McConnell simulations
(using SpinMC objects).
This package is registered in the
General registry, so you can
install it at the REPL with ] add BlochSim.
The main functionality is provided by the functions
freeprecess, excite, and spoil
(and their mutating variants freeprecess!, excite!, and spoil!).
These functions can be used to simulate a wide variety of MRI sequences.
In addition, this package provides implementations
for specific scan sequences:
- multi-echo spin echo (MESE) scan (
MESEBlochSim) - spoiled gradient-recalled echo (SPGR) scan (
SPGRBlochSim).
See the examples given in the documentation strings for how to use the provided
functions. To access the documentation for, e.g., freeprecess, simply type
?freeprecess at the Julia REPL after loading the package.
For examples of how to simulate full MRI sequences, see src/mese.jl and src/spgr.jl in this repo, and STFR.jl.
Additionally, the following blog posts cover the basics of the Bloch equations and some examples of how to use this package.
- Simulating MRI Physics with the Bloch Equations
- Mastering MRI Bloch Simulations with BlochSim.jl in Julia
- Simulating MRI Scans with BlochSim.jl
Below are some more concrete examples of how to use this package.
julia> using BlochSim
julia> spin = Spin(1, 1000, 100, 3.75)
Spin{Float64}:
M = Magnetization(0.0, 0.0, 1.0)
M0 = 1.0
T1 = 1000.0 ms
T2 = 100.0 ms
Δf = 3.75 Hz
pos = Position(0.0, 0.0, 0.0) cm
julia> excite!(spin, InstantaneousRF(π/2)) # 90° excitation
julia> spin.M # Mz is not quite 0 due to numerical roundoff
Magnetization vector with eltype Float64:
Mx = 1.0
My = 0.0
Mz = 6.123233995736766e-17
julia> freeprecess!(spin, 100) # Free-precess for 100 ms
julia> spin.M
Magnetization vector with eltype Float64:
Mx = -0.2601300475114444
My = -0.2601300475114445
Mz = 0.09516258196404054
julia> spgr! = SPGRBlochSim(5, 2.5, deg2rad(20)) # Create an object to simulate an SPGR scan
Spoiled Gradient-Recalled Echo (SPGR) Bloch Simulation:
TR = 5.0 ms
TE = 2.5 ms
rf (excitation pulse) = Instantaneous RF pulse with eltype Float64:
α = 0.3490658503988659 rad
θ = 0.0 rad
spoiling = IdealSpoiling()
steady-state
julia> spgr!(spin) # Simulate a steady-state SPGR scan applied to the given spin
julia> spin.M # Steady-state magnetization
Magnetization vector with eltype Float64:
Mx = 0.025553542433162182
My = -0.0015069712547712193
Mz = 0.07442699373678281
julia> spinmc = SpinMC(1, (0.2, 0.8), (400, 1000), (20, 80), (15, 0), (100, 25))
SpinMC{Float64,2}:
M = MagnetizationMC((0.0, 0.0, 0.2), (0.0, 0.0, 0.8))
M0 = 1.0
frac = (0.2, 0.8)
T1 = (400.0, 1000.0) ms
T2 = (20.0, 80.0) ms
Δf = (15.0, 0.0) Hz
r = ((0.0, 0.01), (0.04, 0.0)) 1/ms
pos = Position(0.0, 0.0, 0.0) cm
julia> spgr!(spinmc) # The same SPGR scan can be used on multi-compartment spins
julia> spinmc.M # Steady-state magnetization
2-compartment Magnetization vector with eltype Float64:
Compartment 1:
Mx = -0.09359002635156467
My = 0.02433674787041617
Mz = -0.36973998540693054
Compartment 2:
Mx = 0.1541252837882581
My = 0.00031515000730316224
Mz = 0.5077167235922019
julia> signal(spin) # Grab the observed signal from the spin
0.025553542433162182 - 0.0015069712547712193im
julia> signal(spinmc)
0.060535257436693427 + 0.02465189787771933im- MRIgeneralizedBloch.jl focuses on magnetization transfer
- KomaMRI.jl has Pulseq compatibility
This package was developed based on
Brian Hargreaves' Bloch simulation tutorial.
All tests for this package of the form testX0x (like testA5b or testF3d)
are based on the corresponding section in the tutorial (see
test/matlab.jl).
On 2024-04-08 this repo moved here from https://github.com/StevenWhitaker/BlochSim.jl. Submit issues for outdated URLs.