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hmrR_MotionCorrectSplineSG

Meryem Ayşe Yücel edited this page Jan 18, 2024 · 2 revisions

UI Name :
SplineSG_Motion_Correction

Syntax :
data_d = hmrR_MotionCorrectSplineSG(data_d, mlActAuto, p, FrameSize_sec, turnon)

Description :
The function first identifies the baseline shifts and spikes in the signal. The baseline shifts are corrected using a spline interpolation method. The remaining spikes are corrected by Savitzky-Golay filtering, which is a digital smoothing filter that substitutes each value of the signal series with a new value obtained by applying a cubic fitting to a subset of adjacent data points. The length of the subset is defined by the parameter FrameSize_sec. The method is described in the following paper. Citation: Jahani et al., Neurophotonics, 2018; doi: 10.1117/1.NPh.5.1.015003.

Inputs :

  • data_d: SNIRF object containing time course data.
  • mlActAuto:
  • p: Parameter p used in the spline interpolation. The value recommended in the literature is 0.99. Use -1 if you want to skip this motion correction.
  • FrameSize_sec:
  • turnon: Optional argument to enable/disable this function in a processing stream chain.

Outputs :

  • data_d: SNIRF object containing time course data after spline interpolation correction.

Usage Options :

  • SplineSG_Motion_Correction: dod = hmrR_MotionCorrectSplineSG(dod, mlActAuto, p, FrameSize_sec, turnon)

Default Parameters :

  • p=0.99
  • FrameSize_sec=10
  • turnon=1

Prerequisites :

  • Intensity_to_Delta_OD: dod = hmrR_Intensity2OD( intensity )
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