src/MRIBuilder.jl

@@ -40,8 +40,8 @@ export dwi_gradients, readout_event, excitation_pulse, refocus_pulse, Trapezoid,
 import .PostHoc: adjust, merge_sequences
 export adjust, merge_sequences
 
-import .Sequences: GradientEcho, SpinEcho, DiffusionSpinEcho, DW_SE, DWI, MagnetisationTransfer
-export GradientEcho, SpinEcho, DiffusionSpinEcho, DW_SE, DWI, MagnetisationTransfer
+import .Sequences: GradientEcho, SpinEcho, DiffusionSpinEcho, DW_SE, DWI, MagnetisationTransfer, MultiSpinEcho
+export GradientEcho, SpinEcho, DiffusionSpinEcho, DW_SE, DWI, MagnetisationTransfer, MultiSpinEcho
 
 import .SequenceIO: read_sequence, write_sequence
 export read_sequence, write_sequence

src/components/pulses/sinc_pulses.jl

@@ -134,7 +134,7 @@ function make_generic(block::SincPulse)
     normed_times = -variables.N_left(block):0.1:variables.N_right(block) + 1e-5
     times = max.(0., (normed_times .+ variables.N_left(block))) .* variables.lobe_duration(block)
     amplitudes = variables.amplitude(block) .* (normalised_function.(normed_times, variables.N_left(block), variables.N_right(block); apodise=block.apodise))
-    phases = [variables.frequency(block) .* variables.lobe_duration(block)] .* normed_times .* 360
+    phases = [variables.frequency(block) .* variables.lobe_duration(block)] .* normed_times .* 360 .+ variables.phase(block)
     return GenericPulse(times, amplitudes, phases, variables.effective_time(block))
 end
 

src/containers/base_sequences.jl

@@ -182,7 +182,7 @@ function Base.getproperty(seq::T, v::Symbol) where T <: Sequence
     if v in [k for (k, _) in values(seq.blocks)]
         return seq[v]
     end
-    error("Type $(T) has no field, block, or variable $(v)")
+    error("Type $(T) has no field, block, or variable called `$(v)`")
 end
 
 B0(sequence::Sequence) = B0(sequence.scanner)

src/sequences/multi_spin_echoes.jl

+module MultiSpinEchoes
+import ...Containers: Sequence, start_time
+import ...Parts: excitation_pulse, readout_event, interpret_image_size, Trapezoid, gradient_spoiler, refocus_pulse, Repeat
+import ...Variables: get_pulse, get_readout, variables, @defvar, apply_simple_constraint!
+import ...Pathways: Pathway, get_pathway
+import ...BuildSequences: build_sequence
+import ...Scanners: Default_Scanner
+
+const MultiSpinEcho = Sequence{:MultiSpinEcho}
+
+"""
+    SpinEcho(; echo_time, nrepeat, delay=0., excitation=(), refocus=(), readout=(), optim=(), resolution/fov/voxel_size/slice_thickness, scanner)
+
+Defines a gradient echo sequence with a single readout event.
+
+By default, an instant excitation and refocus 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).
+- [`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).
+- Image parameters ([`variables.resolution`](@ref)/[`variables.fov`](@ref)/[`variables.voxel_size`](@ref)/[`variables.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
+- [`variables.TE`](@ref)/[`variables.echo_time`](@ref): echo time between excitation pulse and spin echo in ms (required).
+- [`variables.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.
+- [`variables.duration`](@ref): total duration of the sequence from start of excitation pulse to end of the final readout.
+- [`variables.nrepeat`](@ref): How often to repeat the readout.
+"""
+function MultiSpinEcho(; excitation=(), refocus=(), readout=(), optim=(), spoiler=nothing, resolution=nothing, fov=nothing, voxel_size=nothing, slice_thickness=nothing, delay=0., scanner=Default_Scanner, vars...)
+    build_sequence(scanner; optim...) do
+        (slice_thickness, _, extra_readout_params) = interpret_image_size(fov, resolution, voxel_size, slice_thickness)
+        repeating_part = Sequence(Any[
+            :refocus => refocus_pulse(; slice_thickness=slice_thickness, refocus...),
+            nothing,
+            :readout => readout_event(; extra_readout_params..., readout...),
+            nothing,
+        ])
+        res = Repeat(repeating_part)
+        seq = Sequence(Any[
+            :excitation => excitation_pulse(; slice_thickness=slice_thickness, excitation...),
+            nothing,
+            :repeat => res
+        ]; name=:MultiSpinEcho, delay=delay, vars...)
+        apply_simple_constraint!(
+            (variables.effective_time(repeating_part, :refocus) + start_time(seq, :repeat) - variables.effective_time(seq, :excitation)) * 2,
+            variables.echo_time(seq)
+        )
+        return seq
+    end
+end
+
+
+get_pulse(se::MultiSpinEcho) = (excitation=se.excitation, refocus=se.repeat.block.refocus)
+get_readout(se::MultiSpinEcho) = se.repeat.block.readout
+
+@defvar begin
+    echo_time(se::MultiSpinEcho) = variables.duration(se.repeat.block)
+    delay(se::MultiSpinEcho) = variables.effective_time(se.repeat.block, :readout) - variables.echo_time(se)/2
+    nrepeat(se::MultiSpinEcho) = variables.nrepeat(se.repeat)
+end
+
+end

src/sequences/sequences.jl

@@ -3,10 +3,12 @@ include("gradient_echoes.jl")
 include("spin_echoes.jl")
 include("diffusion_spin_echoes.jl")
 include("magnetisation_transfers.jl")
+include("multi_spin_echoes.jl")
 
 import .GradientEchoes: GradientEcho
 import .SpinEchoes: SpinEcho
 import .DiffusionSpinEchoes: DiffusionSpinEcho, DW_SE, DWI
 import .MagnetisationTransfers: MagnetisationTransfer
+import .MultiSpinEchoes: MultiSpinEcho
 
 end
\ No newline at end of file

src/sequences/spin_echoes.jl

@@ -11,9 +11,9 @@ const SpinEcho = Sequence{:SpinEcho}
 """
     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.
+Defines a spin echo sequence with a single readout event.
 
-By default, an instant excitation pulse and readout event are used.
+By default, an instant excitation and refocus pulse and readout event are used.
 If image parameters are provided, this will switch to a sinc pulse and EPI readout.
 
 ## Parameters