From 0c7c0306f8e3dacf0affaa67999e66bdcfd31a23 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Fri, 23 Feb 2024 13:43:02 +0000
Subject: [PATCH] Create DW-SE sequence
---
src/MRIBuilder.jl | 4 +-
src/sequences/diffusion_spin_echoes.jl | 70 ++++++++++++++++++++++++++
src/sequences/gradient_echoes.jl | 2 +-
src/sequences/sequences.jl | 2 +
src/sequences/spin_echoes.jl | 6 +--
5 files changed, 78 insertions(+), 6 deletions(-)
create mode 100644 src/sequences/diffusion_spin_echoes.jl
diff --git a/src/MRIBuilder.jl b/src/MRIBuilder.jl
index 08ee4b9..47923a2 100644
--- a/src/MRIBuilder.jl
+++ b/src/MRIBuilder.jl
@@ -34,8 +34,8 @@ export Pathway, duration_transverse, duration_dephase, bval, bmat, get_pathway
import .Parts: dwi_gradients, readout_event, excitation_pulse, refocus_pulse, Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines, SpoiltSliceSelect, SliceSelectRephase, EPIReadout, interpret_image_size
export dwi_gradients, readout_event, excitation_pulse, refocus_pulse, Trapezoid, SliceSelect, LineReadout, opposite_kspace_lines, SpoiltSliceSelect, SliceSelectRephase, EPIReadout, interpret_image_size
-import .Sequences: GradientEcho, SpinEcho
-export GradientEcho, SpinEcho
+import .Sequences: GradientEcho, SpinEcho, DiffusionSpinEcho, DW_SE, DWI
+export GradientEcho, SpinEcho, DiffusionSpinEcho, DW_SE, DWI
import JuMP: @constraint, @objective, objective_function, value, Model
export @constraint, @objective, objective_function, value, Model
diff --git a/src/sequences/diffusion_spin_echoes.jl b/src/sequences/diffusion_spin_echoes.jl
new file mode 100644
index 0000000..9c5523d
--- /dev/null
+++ b/src/sequences/diffusion_spin_echoes.jl
@@ -0,0 +1,70 @@
+module DiffusionSpinEchoes
+import ...Containers: Sequence
+import ...Parts: excitation_pulse, readout_event, interpret_image_size, Trapezoid, gradient_spoiler, refocus_pulse, dwi_gradients
+import ...Containers: start_time
+import ...Variables: get_pulse, get_readout, echo_time, duration_transverse, delay, effective_time, diffusion_time, Δ, TR, TE, repetition_time
+import ...Pathways: Pathway, get_pathway
+import ...BuildSequences: build_sequence
+import ...Scanners: Default_Scanner
+
+const DiffusionSpinEcho = Sequence{:DiffusionSpinEcho}
+const DW_SE = DiffusionSpinEcho
+const DWI = DiffusionSpinEcho
+
+"""
+ DiffusionSpinEcho(; echo_time, delay=0., excitation=(), gradient=(), refocus=(), readout=(), optim=(), resolution/fov/voxel_size/slice_thickness, scanner)
+
+Defines a gradient echo sequence with a single readout event.
+
+`DWI`, `DW_SE`, and `DiffusionSpinEcho` are all synonyms.
+
+By default, an instant excitation pulse and readout event are used.
+If image parameters are provided, this will switch to a sinc pulse and EPI readout.
+
+## Parameters
+- [`excitation`](@ref): properties of the excitation pulse as described in [`excitation_pulse`](@ref).
+- [`gradient`](@ref): properties of the diffusion-weighting gradients as described in [`dwi_gradients`](@ref).
+- [`refocus`](@ref): properties of the refocus pulse as described in [`refocus_pulse`](@ref).
+- [`readout`](@ref): properties of the readout as described in [`readout_event`](@ref).
+- [`spoiler`](@ref): if set adds a spoiler [`gradient_spoiler`](@ref) gradient after the readout (e.g., `spoiler=()` to add a gradient in the z-direction of the `FOV` coordinate system that fully dephases spins over 1 mm).
+- Image parameters ([`resolution`](@ref)/[`fov`](@ref)/[`voxel_size`](@ref)/[`slice_thickness`](@ref)): describe the properties of the resulting image. See [`interpret_image_size`](@ref) for details.
+- [`optim`](@ref): parameters to pass on to the Ipopt optimiser (see https://coin-or.github.io/Ipopt/OPTIONS.html).
+- [`scanner`](@ref): Sets the [`Scanner`](@ref) used to constraint the gradient parameters. If not set, the [`Default_Scanner`](@ref) will be used.
+
+## Variables
+- [`TE`](@ref)/[`echo_time`](@ref): echo time between excitation pulse and spin echo in ms.
+- [`delay`](@ref): delay between the readout and the peak of the spin echo in ms (positive number indicates that readout is after the spin echo). Defaults to zero.
+- [`TR`](@ref)/[`repetition_time`](@ref)/[`duration`](@ref): total duration of the sequence from start of excitation pulse to end of readout or spoiler in ms.
+- [`Δ`](@ref)/[`diffusion_time`](@ref): Time from the start of one diffusion-weighted gradient till the other in ms.
+"""
+function DiffusionSpinEcho(; delay=0., excitation=(), gradient=(), refocus=(), readout=(), optim=(), spoiler=nothing, resolution=nothing, fov=nothing, voxel_size=nothing, slice_thickness=nothing, scanner=Default_Scanner, variables...)
+ build_sequence(scanner; optim...) do
+ (slice_thickness, _, extra_readout_params) = interpret_image_size(fov, resolution, voxel_size, slice_thickness)
+ (g1, g2) = dwi_gradients(; gradient...)
+ parts = Any[
+ :excitation => excitation_pulse(; slice_thickness=slice_thickness, excitation...),
+ nothing,
+ :gradient => g1,
+ nothing,
+ :refocus => refocus_pulse(; slice_thickness=slice_thickness, refocus...),
+ nothing,
+ :gradient2 => g2,
+ nothing,
+ :readout => readout_event(; extra_readout_params..., readout...),
+ ]
+ if !isnothing(spoiler)
+ push!(parts, gradient_spoiler(; spoiler...))
+ end
+ return Sequence(parts; name=:DiffusionSpinEcho, delay=delay, variables...)
+ end
+end
+
+
+get_pulse(ge::DiffusionSpinEcho) = (excitation=ge.excitation, refocus=ge.refocus)
+get_readout(ge::DiffusionSpinEcho) = ge.readout
+get_pathway(ge::DiffusionSpinEcho) = Pathway(ge, [90, 180], 1, :DWI)
+echo_time(ge::DiffusionSpinEcho) = 2 * (effective_time(ge, :refocus) - effective_time(ge, :excitation))
+delay(ge::DiffusionSpinEcho) = duration_transverse(ge) - echo_time(ge)
+diffusion_time(ge::DiffusionSpinEcho) = start_time(ge, :gradient2) - start_time(ge, :gradient)
+
+end
\ No newline at end of file
diff --git a/src/sequences/gradient_echoes.jl b/src/sequences/gradient_echoes.jl
index e845948..4a4d854 100644
--- a/src/sequences/gradient_echoes.jl
+++ b/src/sequences/gradient_echoes.jl
@@ -1,7 +1,7 @@
module GradientEchoes
import ...Containers: Sequence
import ...Parts: excitation_pulse, readout_event, interpret_image_size, Trapezoid, gradient_spoiler
-import ...Variables: get_pulse, get_readout, echo_time, duration_transverse
+import ...Variables: get_pulse, get_readout, echo_time, duration_transverse, TR, TE, repetition_time
import ...Pathways: Pathway, get_pathway
import ...BuildSequences: build_sequence
import ...Scanners: Default_Scanner
diff --git a/src/sequences/sequences.jl b/src/sequences/sequences.jl
index 59cab1d..ff93653 100644
--- a/src/sequences/sequences.jl
+++ b/src/sequences/sequences.jl
@@ -1,8 +1,10 @@
module Sequences
include("gradient_echoes.jl")
include("spin_echoes.jl")
+include("diffusion_spin_echoes.jl")
import .GradientEchoes: GradientEcho
import .SpinEchoes: SpinEcho
+import .DiffusionSpinEchoes: DiffusionSpinEcho, DW_SE, DWI
end
\ No newline at end of file
diff --git a/src/sequences/spin_echoes.jl b/src/sequences/spin_echoes.jl
index 7241b4e..313ab23 100644
--- a/src/sequences/spin_echoes.jl
+++ b/src/sequences/spin_echoes.jl
@@ -1,7 +1,7 @@
module SpinEchoes
import ...Containers: Sequence
import ...Parts: excitation_pulse, readout_event, interpret_image_size, Trapezoid, gradient_spoiler, refocus_pulse
-import ...Variables: get_pulse, get_readout, echo_time, duration_transverse, delay, effective_time
+import ...Variables: get_pulse, get_readout, echo_time, duration_transverse, delay, effective_time, TR, TR, repetition_time
import ...Pathways: Pathway, get_pathway
import ...BuildSequences: build_sequence
import ...Scanners: Default_Scanner
@@ -9,7 +9,7 @@ import ...Scanners: Default_Scanner
const SpinEcho = Sequence{:SpinEcho}
"""
- SpinEcho(; echo_time, delay=0., excitation=(), refocus_pulse=(), readout=(), optim=(), resolution/fov/voxel_size/slice_thickness, scanner)
+ SpinEcho(; echo_time, delay=0., excitation=(), refocus=(), readout=(), optim=(), resolution/fov/voxel_size/slice_thickness, scanner)
Defines a gradient echo sequence with a single readout event.
@@ -27,7 +27,7 @@ If image parameters are provided, this will switch to a sinc pulse and EPI reado
## Variables
- [`TE`](@ref)/[`echo_time`](@ref): echo time between excitation pulse and spin echo in ms (required).
-- [`delay`](@ref): delay between the readout and the peak of the spin echo in ms (positive number indicates that readout is after the spin echo).
+- [`delay`](@ref): delay between the readout and the peak of the spin echo in ms (positive number indicates that readout is after the spin echo). Defaults to zero.
- [`TR`](@ref)/[`repetition_time`](@ref)/[`duration`](@ref): total duration of the sequence from start of excitation pulse to end of readout or spoiler in ms.
"""
function SpinEcho(; delay=0., excitation=(), refocus=(), readout=(), optim=(), spoiler=nothing, resolution=nothing, fov=nothing, voxel_size=nothing, slice_thickness=nothing, scanner=Default_Scanner, variables...)
--
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