NeuroAnalyzer tutorials: General remarks

NeuroAnalyzer functions operate on NeuroAnalyzer objects. The major object is NeuroAnalyzer.NEURO, which is an equivalent of single recording of any type (e.g. EEG or MEG).

mutable struct NEURO
    header::NeuroAnalyzer.HEADER
    time_pts::Vector{Float64}                         # time points for the whole signal
    epoch_time::Vector{Float64}                       # time points for single epoch
    data::Array{<:Number, 3}                          # data must have at least one channel and one epoch
    components::Dict{Any}                             # additional data, e.g. ICs
    markers::DataFrame                                # event markers
    locs::DataFrame                                   # channel locations
    history::Vector{String}                           # list of operations
end

The NeuroAnalyzer.NEURO object contains a header with the following meta-data:

mutable struct HEADER
    subject::Dict
    recording::Dict
    experiment::Dict
end

The subject dictionary contains the following keys:

• :id::String
• :first_name::String
• :middle_name::String
• :last_name::String
• :handedness::String
• :weight::Float64
• :height::Float64

For EEG objects, the recording dictionary contains the following keys:

• :data_type::String: “eeg”
• :file_name::String
• :file_size_mb::Float64
• :file_type::String: e.g. “EDF”, “EDF+”, “BDF”, “BDF+”, “Digitrack”, “BrainVision”, “CSV”, SET”, “GDF”
• :recording::String: e.g. equipment name
• :recording_date::String
• :recording_time::String
• :recording_notes::String
• :channel_type::Vector{String}: e.g. [“eeg”, “eog”, ‘emg’]
• :reference::String: e.g. “CAR”
• :labels::Vector{String}: e.g. [“Fp1”, “Fp2”]
• :transducers
• :units::Vector{String}: e.g. [“uV”]
• :prefiltering::Vector{String}
• :sampling_rate::Int64
• :gain::Vector{Float64}

For MEG objects, the recording dictionary contains the following keys:

• :data_type::String: “meg”
• :file_name::String
• :file_size_mb::Float64
• :file_type::String: “FIFF”
• :recording::String
• :recording_date::String
• :recording_time::String
• :recording_notes::String
• :channel_type::Vector{String}: e.g. [“mag”, “grad”]
• :reference::String
• :labels::Vector{String}: e.g. [“MEG1”, “MEG2”]
• :units::Vector{String}: e.g. [“fT”]
• :prefiltering::Vector{String}
• :sampling_rate::Int64
• :magnetometers::Vector{Int64}: list of channel of particular type
• :gradiometers::Vector{Int64}: list of channel of particular type
• :gradiometers_planar::Vector{Int64}: list of channel of particular type
• :gradiometers_axial::Vector{Int64}: list of channel of particular type
• :coils::Vector{Int64}

For NIRS objects, the recording dictionary contains the following keys:

• :data_type::String: “nirs”
• :file_name::String
• :file_size_mb::Float64
• :file_type::String: “NIRS”, NIRX” or “SNIRF”
• :recording::String: e.g. equipment name
• :recording_date::String
• :recording_time::String
• :recording_notes::String
• :wavelengths::Vector{Float64}
• :wavelength_index::Vector{Int64}: wavelength indices for nirs_int and nirs_od channels
• :channel_pairs::Matrix{Int64}: matrix of source-detector pairs
• :channel_type::Vector{String}
• :labels::Vector{String}: channel labels (sensor_detector wavelength), e.g. [“S1_D1 780”]
• :units::Vector{String}
• :optode_labels::Vector{String}: sensors and detector labels, e.g. [“nirs_int”, “nirs_od”, “nirs_hbo”]
• :sampling_rate::Int64

The experiment dictionary contains the following keys:

• :name
• :notes
• :design

For multichannel recordings, signal is stored in data as Array{Float64, 3} (channels × signals × epochs). If epochs are not defined, the whole signal is an epoch, i.e. there is always at least one epoch.

Higher NeuroAnalyzer functions (operating on NeuroAnalyzer.NEURO object) use named arguments for all arguments other than input object(s), e.g. delete_epoch!(my_eeg, ep=12).

Study object is stored in the NeuroAnalyzer.STUDY structure:

mutable struct STUDY
    header::Dict{Symbol, Any}
    objects::Vector{NeuroAnalyzer.NEURO}
    groups::Vector{Symbol}
end

Multiple dispatch mechanism is used wherever possible.

Most edit/process functions have a mutator variant (e.g. delete_epoch() and delete_epoch!()). Mutators modify the input NEURO object in-place, e.g. you may use delete_channel!(my_eeg, ch=1) instead of my_eeg = delete_channel(my_eeg, ch=1).