From 55b910a7a99454d830c07cddcbcdb93b73ae8360 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
Date: Wed, 21 Feb 2024 17:09:37 +0000
Subject: [PATCH] Set default shape to instant if there is no overlap with
gradients
---
src/parts/helper_functions.jl | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)
diff --git a/src/parts/helper_functions.jl b/src/parts/helper_functions.jl
index cfa53cd..f2f8c7e 100644
--- a/src/parts/helper_functions.jl
+++ b/src/parts/helper_functions.jl
@@ -36,7 +36,7 @@ For an [`InstantPulse`](@ref) (i.e., `shape=:instant`), only the `flip_angle`, `
- `optimise`: set to true to optimise this RF pulse separately from the embedding sequence.
### Pulse parameters
-- `shape`: The shape of the RF pulse. One of `:sinc` (for [`SincPulse`](@ref)), `:constant`/`:hard` (for [`ConstantPulse`](@ref)), or `:instant` (for [`InstantPulse`](@ref)).
+- `shape`: The shape of the RF pulse. One of `:sinc` (for [`SincPulse`](@ref)), `:constant`/`:hard` (for [`ConstantPulse`](@ref)), or `:instant` (for [`InstantPulse`](@ref)). Default is :sinc for slice-selective pulses or :instant otherwise.
- `flip_angle`: size of the flip due to the RF pulse in degrees (default: 90).
- `phase`: angle of the RF pulse in the x-y plane in degrees (default: 0).
- `frequency`: frequency of the RF pulse relative to the Larmor frequency in kHz (default: 0).
@@ -51,11 +51,15 @@ For an [`InstantPulse`](@ref) (i.e., `shape=:instant`), only the `flip_angle`, `
- `rotate_grad`: name of the parameter with which the slice selection gradient will be rotated after sequence optimisation (default: `:FOV`).
- `scanner`: overrides the [`global_scanner`](@ref) for this part of the sequence. Recommended to set only if not part of a larger sequence.
"""
-function excitation_pulse(; flip_angle=90, phase=0., frequency=0., shape=:sinc, slice_thickness=Inf, rephase=true, Nzeros=3, group=nothing, rotate_grad=:FOV, bandwidth=nothing, duration=nothing, scanner=nothing, optimise=false, other_kwargs...)
+function excitation_pulse(; flip_angle=90, phase=0., frequency=0., shape=nothing, slice_thickness=Inf, rephase=true, Nzeros=3, group=nothing, rotate_grad=:FOV, bandwidth=nothing, duration=nothing, scanner=nothing, optimise=false, other_kwargs...)
bad_keys = [key for (key, value) in pairs(other_kwargs) if !isnothing(value)]
if length(bad_keys) > 0
error("Unrecognised keyword arguments in call of `excitation_pulse`: $bad_keys")
end
+ if isnothing(shape)
+ shape = isinf(slice_thickness) ? :instant : :sinc
+ end
+
build_sequence(scanner; optimise=optimise) do
pulse = _get_pulse(shape, flip_angle, phase, frequency, Nzeros, group, bandwidth, duration)
if pulse isa InstantPulse
@@ -89,7 +93,7 @@ If `slice_thickness` is not set or is set to `:min`, then either `bandwidth` or
### Pulse parameters
For an [`InstantPulse`](@ref) (i.e., `shape=:instant`), only the `flip_angle`, `phase`, and `group` will be used. All other parameters are ignored.
-- `shape`: The shape of the RF pulse. One of `:sinc` (for [`SincPulse`](@ref)), `:constant`/`:hard` (for [`ConstantPulse`](@ref)), or `:instant` (for [`InstantPulse`](@ref)).
+- `shape`: The shape of the RF pulse. One of `:sinc` (for [`SincPulse`](@ref)), `:constant`/`:hard` (for [`ConstantPulse`](@ref)), or `:instant` (for [`InstantPulse`](@ref)). Default is :sinc for slice-selective pulses or :instant otherwise.
- `flip_angle`: size of the flip due to the RF pulse in degrees (default: 180).
- `phase`: angle of the RF pulse in the x-y plane in degrees (default: 0).
- `frequency`: frequency of the RF pulse relative to the Larmor frequency in kHz (default: 0).
@@ -105,11 +109,14 @@ For an [`InstantPulse`](@ref) (i.e., `shape=:instant`), only the `flip_angle`, `
- `scanner`: overrides the [`global_scanner`](@ref) for this part of the sequence. Recommended to set only if not part of a larger sequence.
- `orientation`: vector with orientation of slice select gradient and pulses (defaults: z-direction).
"""
-function refocus_pulse(; flip_angle=180, phase=0., frequency=0., shape=:sinc, slice_thickness=Inf, Nzeros=3, group=nothing, bandwidth=nothing, duration=nothing, spoiler=Inf, scanner=nothing, optimise=false, orientation=[0, 0, 1], other_kwargs...)
+function refocus_pulse(; flip_angle=180, phase=0., frequency=0., shape=nothing, slice_thickness=Inf, Nzeros=3, group=nothing, bandwidth=nothing, duration=nothing, spoiler=Inf, scanner=nothing, optimise=false, orientation=[0, 0, 1], other_kwargs...)
bad_keys = [key for (key, value) in pairs(other_kwargs) if !isnothing(value)]
if length(bad_keys) > 0
error("Unrecognised keyword arguments in call of `refocus_pulse`: $bad_keys")
end
+ if isnothing(shape)
+ shape = isinf(slice_thickness) ? :instant : :sinc
+ end
build_sequence(scanner; optimise=optimise) do
pulse = _get_pulse(shape, flip_angle, phase, frequency, Nzeros, group, bandwidth, duration)
if pulse isa InstantPulse && !isinf(slice_thickness)
--
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