Create DW-SE sequence

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

src/sequences/diffusion_spin_echoes.jl

+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

src/sequences/gradient_echoes.jl

 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

src/sequences/sequences.jl

 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

src/sequences/spin_echoes.jl

 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...)