API
This page contains documentation of the public API of MRIReco. In the Julia REPL one can access this documentation by entering the help mode with ? and then writing the function for which the documentation should be shown.
Operators
Operators are implemented as subtypes of AbstractLinearOperator, which is defined in the package LinearOperators.jl. Such operators must provide a function implementing the product and a function implementing the product with the adjoint. Furthermore, the number of rows and columns of the operator must be specified.
Missing docstring for MRIReco.encodingOps2d_simple. Check Documenter's build log for details.
Missing docstring for MRIReco.encodingOps3d_simple. Check Documenter's build log for details.
Missing docstring for MRIReco.encodingOps2d_parallel. Check Documenter's build log for details.
Missing docstring for MRIReco.encodingOps3d_parallel. Check Documenter's build log for details.
Missing docstring for MRIReco.encodingOp2d_multiEcho. Check Documenter's build log for details.
Missing docstring for MRIReco.encodingOp3d_multiEcho. Check Documenter's build log for details.
Missing docstring for MRIReco.encodingOp2d_multiEcho_parallel. Check Documenter's build log for details.
Missing docstring for MRIReco.encodingOp3d_multiEcho_parallel. Check Documenter's build log for details.
Missing docstring for MRIReco.fourierEncodingOp2d. Check Documenter's build log for details.
Missing docstring for MRIReco.fourierEncodingOp3d. Check Documenter's build log for details.
Missing docstring for MRIReco.ExplicitOp(shape::NTuple{D,Int64}, tr::Trajectory, correctionmap::Array{ComplexF64,D}; MRIReco.echoImage::Bool=false, kargs...) where D. Check Documenter's build log for details.
Missing docstring for RegularizedLeastSquares.FFTOp(T::Type, shape::Tuple, shift=true). Check Documenter's build log for details.
Missing docstring for MRIReco.NFFTOp(shape::Tuple, tr::Trajectory; nodes=nothing, kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.FieldmapNFFTOp(shape::NTuple{D,Int64}, tr::Trajectory, correctionmap::Array{ComplexF64,D}; method::String="nfft", echoImage::Bool=true, alpha::Float64=1.75, m::Float64=3.0, K=20, kargs...) where D. Check Documenter's build log for details.
Missing docstring for MRIReco.SamplingOp. Check Documenter's build log for details.
Missing docstring for MRIReco.SensitivityOp. Check Documenter's build log for details.
Missing docstring for MRIReco.SparseOp. Check Documenter's build log for details.
Missing docstring for MRIReco.RegularizedLeastSquares.WeightingOp. Check Documenter's build log for details.
Datatypes
Missing docstring for MRIReco.AcquisitionData. Check Documenter's build log for details.
Missing docstring for MRIReco.AcquisitionData(tr::T,kdata::Array{Matrix{ComplexF64},3} ; seqInfo=Dict{Symbol,Any}() , idx=nothing , encodingSize=Int64[0,0,0] , fov=Float64[0,0,0] , kargs...) where T <: Union{Trajectory,Vector{Trajectory}}. Check Documenter's build log for details.
Missing docstring for MRIReco.trajectory(acqData::AcquisitionData,i::Int64=1). Check Documenter's build log for details.
Missing docstring for MRIReco.numContrasts(acqData::AcquisitionData). Check Documenter's build log for details.
Missing docstring for MRIReco.numChannels. Check Documenter's build log for details.
Missing docstring for MRIReco.numSlices. Check Documenter's build log for details.
Missing docstring for MRIReco.numRepetitions. Check Documenter's build log for details.
Missing docstring for MRIReco.kData. Check Documenter's build log for details.
Missing docstring for MRIReco.multiEchoData. Check Documenter's build log for details.
Missing docstring for MRIReco.multiCoilData. Check Documenter's build log for details.
Missing docstring for MRIReco.multiCoilMultiEchoData. Check Documenter's build log for details.
Missing docstring for MRIReco.profileData. Check Documenter's build log for details.
Missing docstring for MRIReco.samplingDensity. Check Documenter's build log for details.
Missing docstring for MRIReco.changeEncodingSize2D. Check Documenter's build log for details.
Missing docstring for MRIReco.convert3dTo2d. Check Documenter's build log for details.
Missing docstring for MRIReco.RawAcquisitionData. Check Documenter's build log for details.
Missing docstring for MRIReco.trajectory(f::RawAcquisitionData; slice::Int=1, contrast::Int=1). Check Documenter's build log for details.
Missing docstring for MRIReco.rawdata(f::RawAcquisitionData). Check Documenter's build log for details.
Missing docstring for MRIReco.AcquisitionData(f::RawAcquisitionData). Check Documenter's build log for details.
Missing docstring for MRIReco.RawAcquisitionData(f::ISMRMRDFile, dataset="dataset"). Check Documenter's build log for details.
Missing docstring for MRIReco.AcquisitionData(f::ISMRMRDFile, dataset="dataset"). Check Documenter's build log for details.
Trajectories
Missing docstring for MRIReco.Trajectory. Check Documenter's build log for details.
Missing docstring for MRIReco.trajectory(trajName::AbstractString, numProfiles::Int, numSamplingPerProfile::Int; MRIReco.numSlices::Int64=1, TE::Float64=0.0, AQ::Float64=1.e-3, kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.string(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.echoTime(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.acqTimePerProfile(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.numProfiles(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.numSamplingPerProfile(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.numSlices(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.isCircular(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.isCartesian(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.dims(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.kspaceNodes(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.readoutTimes(tr::Trajectory). Check Documenter's build log for details.
Missing docstring for MRIReco.CartesianTrajectory. Check Documenter's build log for details.
Missing docstring for MRIReco.EPITrajectory. Check Documenter's build log for details.
Missing docstring for MRIReco.OneLine2dTrajectory. Check Documenter's build log for details.
Missing docstring for MRIReco.RadialTrajectory. Check Documenter's build log for details.
Missing docstring for MRIReco.SpiralTrajectory. Check Documenter's build log for details.
Missing docstring for MRIReco.SpiralTrajectoryVarDens. Check Documenter's build log for details.
Missing docstring for MRIReco.CartesianTrajectory3D. Check Documenter's build log for details.
Missing docstring for MRIReco.KooshballTrajectory. Check Documenter's build log for details.
Missing docstring for MRIReco.StackOfStarsTrajectory. Check Documenter's build log for details.
Sequences
Missing docstring for MRIReco.MESequence. Check Documenter's build log for details.
Missing docstring for MRIReco.numContrasts(seq::MESequence). Check Documenter's build log for details.
Missing docstring for MRIReco.echoTimes(seq::MESequence). Check Documenter's build log for details.
Missing docstring for MRIReco.flipAngles(seq::MESequence). Check Documenter's build log for details.
Missing docstring for MRIReco.echoAmplitudes(seq::MESequence, R1::Float64, R2::Float64, numStates=nothing). Check Documenter's build log for details.
Missing docstring for MRIReco.epgAmplitudes(seq::MESequence, R1::Real, R2::Real, numStates=nothing). Check Documenter's build log for details.
Missing docstring for MRIReco.epgRotation. Check Documenter's build log for details.
Missing docstring for MRIReco.epgRelaxation. Check Documenter's build log for details.
Missing docstring for MRIReco.epgDephasing. Check Documenter's build log for details.
Missing docstring for MRIReco.rfRotation. Check Documenter's build log for details.
Sampling
Missing docstring for MRIReco.sample. Check Documenter's build log for details.
Missing docstring for MRIReco.sample_kspace(data::AbstractArray,redFac::Float64,patFunc::AbstractString;kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.sample_kspace(acqData::AcquisitionData,redFac::Float64, patFunc::AbstractString; rand=true, profiles=true, seed = 1234, kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.sample_regular(shape::Tuple, redFac::Float64; kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.sample_random(shape::Tuple{Int64,Int64},redFac::Float64;calsize::Int64=0,kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.sample_poissondisk(shape::Tuple{Int64,Int64},redFac::Float64;calsize::Int64=0, seed::Int64=1234,kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.sample_vdpoisson(shape::Tuple{Int64,Int64},redFac::Float64; seed::Int64=1234,kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.sample_lines(shape::Tuple{Int64,Int64},redFac::Float64;sampleFunc="random",kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.calculateIncoherence(acqData::AcquisitionData, recoParams::Dict, slice=1). Check Documenter's build log for details.
Simulation
Missing docstring for MRIReco.simulation(image::Array{T,3}, simParams::Dict) where T<:Union{ComplexF64,Float64}. Check Documenter's build log for details.
Missing docstring for MRIReco.simulation(image::Array{T,3}, simParams::Dict, filename::String; force=false) where T<:Union{ComplexF64,Float64}. Check Documenter's build log for details.
Missing docstring for MRIReco.simulation(image::Array{T,2}, simParams::Dict) where T<:Union{ComplexF64,Float64}. Check Documenter's build log for details.
Missing docstring for MRIReco.simulation(tr::Trajectory , image::Array{ComplexF64} , correctionMap = [] ; opName="fast" , senseMaps=[] , verbose=true , kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.simulation(seq::AbstractSequence, tr::Vector{Trajectory} , image::Array{ComplexF64,3} ; opName="fast" , r1map=[] , r2map=[] , fmap=[] , senseMaps=[] , verbose=true , kargs...). Check Documenter's build log for details.
Missing docstring for MRIReco.addNoise(x::Vector, snr::Float64, complex= true). Check Documenter's build log for details.
Missing docstring for MRIReco.addNoise(acqData::AcquisitionData, snr::Float64). Check Documenter's build log for details.
Missing docstring for MRIReco.addNoise!(acqData::AcquisitionData, snr::Float64). Check Documenter's build log for details.
Missing docstring for MRIReco.birdcageSensitivity. Check Documenter's build log for details.
Missing docstring for MRIReco.measured2DSensitivity. Check Documenter's build log for details.
Missing docstring for MRIReco.quadraticFieldmap. Check Documenter's build log for details.
Reconstruction
MRIReco.reconstruction — Methodreconstruction(acqData::AcquisitionData, recoParams::Dict)Performs image reconstruction of an AcquisitionData object. Parameters are specified in a dictionary.
Reconstruction types are specified by the symbol :reco. Valid reconstruction names are:
- :direct - direct Fourier reconstruction
- :standard - iterative reconstruction for all contrasts, coils & slices independently
- :multiEcho - iterative joint reconstruction of all echo images
- :multiCoil - SENSE-type iterative reconstruction
- :multiCoilMultiEcho - SENSE-type iterative reconstruction of all echo images
MRIReco.reconstruction — Methodreconstruction(acqData::AcquisitionData, recoParams::Dict,filename::String; force=false)performs the same image reconstrucion as reconstruction(acqData::AcquisitionData, recoParams::Dict) and saves the image in a file with name filename. If force=false, the reconstructed image is loaded from the the file filename if the latter is present.
Missing docstring for MRIReco.setupIterativeReco. Check Documenter's build log for details.
Missing docstring for MRIReco.reconstruction_direct_2d. Check Documenter's build log for details.
Missing docstring for MRIReco.reconstruction_direct_3d. Check Documenter's build log for details.
MRIReco.reconstruction_simple — FunctionPerforms iterative image reconstruction independently for the data of all coils, contrasts and slices
Arguments
acqData::AcquisitionData- AcquisitionData objectreconSize::NTuple{2,Int64}- size of image to reconstructreg::Vector{<:AbstractRegularization}- Regularization to be usedsparseTrafo::AbstractLinearOperator- sparsifying transformationweights::Vector{Vector{Complex{<:AbstractFloat}}}- sampling density of the trajectories in acqDatasolver::Type{<:AbstractLinearSolver}- name of the solver to use- (
normalize::Bool=false) - adjust regularization parameter according to the size of k-space data - (
params::Dict{Symbol,Any}) - Dict with additional parameters
MRIReco.reconstruction_multiEcho — FunctionPerforms a iterative image reconstruction jointly for all contrasts. Different slices and coil images are reconstructed independently.
Arguments
acqData::AcquisitionData- AcquisitionData objectreconSize::NTuple{2,Int64}- size of image to reconstructreg::Vector{<:AbstractRegularization}- Regularization to be usedsparseTrafo::AbstractLinearOperator- sparsifying transformationweights::Vector{Vector{Complex{<:AbstractFloat}}}- sampling density of the trajectories in acqDatasolver::Type{<:AbstractLinearSolver}- name of the solver to use- (
normalize::Bool=false) - adjust regularization parameter according to the size of k-space data - (
params::Dict{Symbol,Any}) - Dict with additional parameters
MRIReco.reconstruction_multiCoil — FunctionPerforms a SENSE-type iterative image reconstruction. Different slices and contrasts images are reconstructed independently.
Arguments
acqData::AcquisitionData- AcquisitionData objectreconSize::NTuple{2,Int64}- size of image to reconstructreg::Vector{<:AbstractRegularization}- Regularization to be usedsparseTrafo::AbstractLinearOperator- sparsifying transformationweights::Vector{Vector{Complex{<:AbstractFloat}}}- sampling density of the trajectories in acqDataL_inv::Array{Complex{<:AbstractFloat}}- noise decorrelation matrixsolver::Type{<:AbstractLinearSolver}- name of the solver to usesenseMaps::Array{Complex{<:AbstractFloat}}- coil sensitivities- (
normalize::Bool=false) - adjust regularization parameter according to the size of k-space data - (
params::Dict{Symbol,Any}) - Dict with additional parameters
MRIReco.reconstruction_multiCoilMultiEcho — FunctionPerforms a SENSE-type iterative image reconstruction which reconstructs all contrasts jointly. Different slices are reconstructed independently.
Arguments
acqData::AcquisitionData- AcquisitionData objectreconSize::NTuple{2,Int64}- size of image to reconstructreg::Vector{<:AbstractRegularization}- Regularization to be usedsparseTrafo::AbstractLinearOperator- sparsifying transformationweights::Vector{Vector{Complex{<:AbstractFloat}}}- sampling density of the trajectories in acqDatasolver::Type{<:AbstractLinearSolver}- name of the solver to usesenseMaps::Array{Complex{<:AbstractFloat}}- coil sensitivities- (
normalize::Bool=false) - adjust regularization parameter according to the size of k-space data - (
params::Dict{Symbol,Any}) - Dict with additional parameters
Missing docstring for MRIReco.espirit. Check Documenter's build log for details.
MRIReco.nrmsd — Functionnrmsd(I,Ireco)computes the normalized root mean squared error of the image Ireco with respect to the image I.