Load NIRS data:
n = import_nirs("test/files/fnirs-test-nirs.nirs")
info(n)Output:
Data type: NIRS
File format: NIRS
Source file: test/files/fnirs-test-nirs.nirs
File size [MB]: 0.72
Memory size [MB]: 0.35
Subject:
Recording:
Recording notes:
Recording date:
Recording time:
Sampling rate (Hz): 25
Signal length [samples]: 9015
Signal length [seconds]: 360.6
Number of channels: 4
Number of epochs: 1
Epoch length [samples]: 9015
Epoch length [seconds]: 360.6
Wavelength [nm]: [690.0, 830.0]
Labels: yes
Markers: no
Channel locations: yes
Components: no
Channels:
channel: 1 label: S1_D1 690 type: NIRS wavelength: 690.0 nm
channel: 2 label: S1_D2 690 type: NIRS wavelength: 690.0 nm
channel: 3 label: S1_D1 830 type: NIRS wavelength: 830.0 nm
channel: 4 label: S1_D2 830 type: NIRS wavelength: 830.0 nmLoad SNIRF data:
n = import_snirf("test/files/fnirs-test-snirf.snirf")
info(n)Output:
Data type: NIRS
File format: SNIRF
Source file: test/files/fnirs-test-snirf.snirf
File size [MB]: 1.91
Memory size [MB]: 0.29
Subject: default:
Recording:
Recording notes:
Recording date: 2022-03-03
Recording time: 12:03:48
Sampling rate (Hz): 50
Signal length [samples]: 500
Signal length [seconds]: 10.0
Number of channels: 72
Number of epochs: 1
Epoch length [samples]: 500
Epoch length [seconds]: 10.0
Wavelength [nm]: [760.0, 850.0]
Labels: yes
Markers: no
Channel locations: yes
Components: no
Channels:
channel: 1 label: S2_D1 760 type: DOD wavelength: 760.0
channel: 2 label: S4_D1 760 type: DOD wavelength: 760.0
channel: 3 label: S1_D1 760 type: DOD wavelength: 760.0
channel: 4 label: S4_D2 760 type: DOD wavelength: 760.0
channel: 5 label: S6_D2 760 type: DOD wavelength: 760.0
channel: 6 label: S3_D2 760 type: DOD wavelength: 760.0
channel: 7 label: S2_D3 760 type: DOD wavelength: 760.0
channel: 8 label: S4_D3 760 type: DOD wavelength: 760.0
channel: 9 label: S7_D3 760 type: DOD wavelength: 760.0
channel: 10 label: S5_D3 760 type: DOD wavelength: 760.0
channel: 11 label: S4_D4 760 type: DOD wavelength: 760.0
channel: 12 label: S6_D4 760 type: DOD wavelength: 760.0
channel: 13 label: S7_D4 760 type: DOD wavelength: 760.0
channel: 14 label: S8_D4 760 type: DOD wavelength: 760.0
channel: 15 label: S10_D5 760 type: DOD wavelength: 760.0
channel: 16 label: S9_D5 760 type: DOD wavelength: 760.0
channel: 17 label: S12_D6 760 type: DOD wavelength: 760.0
channel: 18 label: S14_D6 760 type: DOD wavelength: 760.0
channel: 19 label: S11_D6 760 type: DOD wavelength: 760.0
channel: 20 label: S10_D7 760 type: DOD wavelength: 760.0
channel: 21 label: S15_D7 760 type: DOD wavelength: 760.0
channel: 22 label: S13_D7 760 type: DOD wavelength: 760.0
channel: 23 label: S12_D8 760 type: DOD wavelength: 760.0
channel: 24 label: S14_D8 760 type: DOD wavelength: 760.0
channel: 25 label: S16_D8 760 type: DOD wavelength: 760.0
channel: 26 label: S17_D9 760 type: DOD wavelength: 760.0
channel: 27 label: S18_D9 760 type: DOD wavelength: 760.0
channel: 28 label: S21_D9 760 type: DOD wavelength: 760.0
channel: 29 label: S17_D10 760 type: DOD wavelength: 760.0
channel: 30 label: S18_D10 760 type: DOD wavelength: 760.0
channel: 31 label: S23_D10 760 type: DOD wavelength: 760.0
channel: 32 label: S19_D11 760 type: DOD wavelength: 760.0
channel: 33 label: S22_D11 760 type: DOD wavelength: 760.0
channel: 34 label: S19_D12 760 type: DOD wavelength: 760.0
channel: 35 label: S20_D12 760 type: DOD wavelength: 760.0
channel: 36 label: S24_D12 760 type: DOD wavelength: 760.0
channel: 37 label: S2_D1 850 type: DOD wavelength: 850.0
channel: 38 label: S4_D1 850 type: DOD wavelength: 850.0
channel: 39 label: S1_D1 850 type: DOD wavelength: 850.0
channel: 40 label: S4_D2 850 type: DOD wavelength: 850.0
channel: 41 label: S6_D2 850 type: DOD wavelength: 850.0
channel: 42 label: S3_D2 850 type: DOD wavelength: 850.0
channel: 43 label: S2_D3 850 type: DOD wavelength: 850.0
channel: 44 label: S4_D3 850 type: DOD wavelength: 850.0
channel: 45 label: S7_D3 850 type: DOD wavelength: 850.0
channel: 46 label: S5_D3 850 type: DOD wavelength: 850.0
channel: 47 label: S4_D4 850 type: DOD wavelength: 850.0
channel: 48 label: S6_D4 850 type: DOD wavelength: 850.0
channel: 49 label: S7_D4 850 type: DOD wavelength: 850.0
channel: 50 label: S8_D4 850 type: DOD wavelength: 850.0
channel: 51 label: S10_D5 850 type: DOD wavelength: 850.0
channel: 52 label: S9_D5 850 type: DOD wavelength: 850.0
channel: 53 label: S12_D6 850 type: DOD wavelength: 850.0
channel: 54 label: S14_D6 850 type: DOD wavelength: 850.0
channel: 55 label: S11_D6 850 type: DOD wavelength: 850.0
channel: 56 label: S10_D7 850 type: DOD wavelength: 850.0
channel: 57 label: S15_D7 850 type: DOD wavelength: 850.0
channel: 58 label: S13_D7 850 type: DOD wavelength: 850.0
channel: 59 label: S12_D8 850 type: DOD wavelength: 850.0
channel: 60 label: S14_D8 850 type: DOD wavelength: 850.0
channel: 61 label: S16_D8 850 type: DOD wavelength: 850.0
channel: 62 label: S17_D9 850 type: DOD wavelength: 850.0
channel: 63 label: S18_D9 850 type: DOD wavelength: 850.0
channel: 64 label: S21_D9 850 type: DOD wavelength: 850.0
channel: 65 label: S17_D10 850 type: DOD wavelength: 850.0
channel: 66 label: S18_D10 850 type: DOD wavelength: 850.0
channel: 67 label: S23_D10 850 type: DOD wavelength: 850.0
channel: 68 label: S19_D11 850 type: DOD wavelength: 850.0
channel: 69 label: S22_D11 850 type: DOD wavelength: 850.0
channel: 70 label: S19_D12 850 type: DOD wavelength: 850.0
channel: 71 label: S20_D12 850 type: DOD wavelength: 850.0
channel: 72 label: S24_D12 850 type: DOD wavelength: 850.0
View optode locations:
p = plot_locs(n, src_labels=false, det_labels=false, opt_labels=false, plot_size=600, head=false)
plot_save(p, file_name="nirs-locs.png")
(!) Red (or black in monochrome mode) optodes represent sources, green (white) optodes are detectors.
Get wavelengths:
n.header.recording[:wavelengths]Output:
2-element Vector{Float64}:
760.0
850.0Get channel of 760 or 850 nm wavelength:
ch760 = get_channel_bywl(n, wl=760)
ch850 = get_channel_bywl(n, wl=850)
d760 = n.data[ch760, :, :]
d850 = n.data[ch850, :, :]Convert RAW intensity to OD (optical density):
n = import_nirs("test/files/fnirs-test-nirs.nirs")
intensity2od!(n)(!) OD channels will be added to the object as nirs_od
channel type. OD channels will be placed after RAW (intensity channels)
and before other channels.
Convert OD (optical density) to hemoglobin concentration:
n = import_nirs("test/files/fnirs-test-nirs.nirs")
intensity2od!(n)
od2conc!(n)(!) For each channel three channels will be added:
nirs_hbo (oxygenated hemoglobin), nirs_hbr
(deoxgenated hemoglobin) and nirs_hbt (total hemoglobin).
The sequence of added channels is: ch1 HbO, ch1 HbR, ch1 HbT, ch2 HbO,
ch2 HbR, ch2 HbT etc.
(!) It is recommended to run a band-pass filter prior to calculating Hb concentration:
n = import_nirs("test/files/fnirs-test-nirs.nirs")
intensity2od!(n)
# OD of channel 1
ch1_od = n.data[5, :, :]
NeuroAnalyzer.filter!(n, fprototype=:fir, ftype=:bp, cutoff=(0.01, 0.5))
od2conc!(n)
# HbO, HbR, HbT of channel 1
n.header.recording[:channel_type][17:22]
ch1_od = n.data[17:22, :, :]
# do not plot AUX channels
p = NeuroAnalyzer.plot(n, seg=(1, signal_len(n)), ch=setdiff(1:22, 9:16))
plot_save(p, file_name="images/nirs1.png")
Plot Hb concentrations:
p1 = NeuroAnalyzer.plot(n, ch=[17, 20], type=:butterfly, seg=(1, signal_len(n)), title="HbO", ylabel="HbO [μM/mm]", xlabel="")
p2 = NeuroAnalyzer.plot(n, ch=[18, 21], type=:butterfly, seg=(1, signal_len(n)), title="HbR", ylabel="HbR [μM/mm]", xlabel="")
p3 = NeuroAnalyzer.plot(n, ch=[19, 22], type=:butterfly, seg=(1, signal_len(n)), title="HbT", ylabel="HbT [μM/mm]")
p = Plots.plot(p1, p2, p3, layout=(3,1), legend=:outertopright)
plot_save(p, file_name="images/nirs-hbo-hbr.png")