STFR.jl

This package provides functionality for simulating the signal acquired from a small-tip fast recovery (STFR) MRI scan. The function stfr implements the signal equations found in the following papers:

• J.-F. Nielsen, D. Yoon, and D. C. Noll. Small-tip fast recovery imaging using non-slice-selective tailored tip-up pulses and radiofrequency-spoiling. Mag. Res. Med., 69(3):657-66, March 2013.
  • For RF spoiled STFR.
• H. Sun, J. A. Fessler, D. C. Noll, and J.-F. Nielsen. Strategies for improved 3D small-tip fast recovery imaging. Mag. Res. Med., 72(2):389-98, August 2014.
  • For RF unspoiled STFR.
  • Note that the paper has an error; the corrected equations were used in this package.

The function stfr can be used for either a single-compartment model or a two-compartment model without exchange.

This package also provides a Bloch simulation implementation of STFR (STFRBlochSim) that allows for modeling different RF pulses and spoiling schemes. (See BlochSim.jl for different subtypes of AbstractRF and AbstractSpoiling.) In addition, STFRBlochSim can be used for spins with an arbitrary number of compartments with exchange (see Spin and SpinMC in BlochSim.jl).

Getting Started

First, type ] at the Julia REPL to enter the package prompt. Next, there are two ways to add this package to your Julia environment.

1. Add via PublicRegistry: Type registry add https://github.com/StevenWhitaker/PublicRegistry to add PublicRegistry to the list of Julia package registries. Now you can type add STFR to install the most recent version of STFR as if it were registered in Julia's General registry. Furthermore, running up to update your packages will automatically update STFR as updates become available.
2. Add via URL: Type add https://github.com/StevenWhitaker/STFR.jl#v2.0.0 to add STFR v2.0.0 (note that v2.0.0 can be replaced with whatever version is needed). When an update becomes available, you will need to manually add the updated version of STFR (e.g., with add https://github.com/StevenWhitaker/STFR.jl#v2.0.1).

After the package has been installed, hit backspace to return to the normal Julia prompt, and then type using STFR to load the package.

Examples

Below are some concrete examples of how to use this package.

julia> using STFR

julia> sig = stfr(1, 1000, 100, 3.75 * 2π, 1, 8, 3, π/12, π/12, 0, 4) # Spoiled STFR
0.1587855247046399 - 0.01500965127299392im

julia> stfr(1, 1000, 100, 3.75 * 2π, 1, 8, 3, π/12, π/12, 0, 4, Val(false)) # No RF spoiling
0.009194809492086849 + 0.16021302758102335im

julia> spin = Spin(1, 1000, 100, 3.75) # From BlochSim.jl
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> stfr! = STFRBlochSim(8, 3, 4, π/12, π/12, 0) # Create an object to simulate an STFR scan
Small-Tip Fast Recovery (STFR) Bloch Simulation:
 Tfree = 8 ms
 Tg = 3 ms
 TE = 4 ms
 rftipdown (tip-down excitation pulse) = Instantaneous RF pulse with eltype Float64:
 α = 0.2617993877991494 rad
 θ = 0.0 rad
 rftipup (tip-up RF pulse) = Instantaneous RF pulse with eltype Float64:
 α = -0.2617993877991494 rad
 θ = 0.0 rad
 spoiling = IdealSpoiling()
 steady-state

julia> stfr!(spin) # Simulate a steady-state STFR scan applied to the given spin

julia> spin.M # Steady-state magnetization
Magnetization vector with eltype Float64:
 Mx = 0.15878552470463958
 My = -0.015009651272993887
 Mz = 0.6210482688962908

julia> signal(spin) ≈ sig
true