hmrR_MotionArtifact - BUNPC/Homer3 GitHub Wiki

UI Name :
Motion_Artifacts

Syntax :
tInc = hmrR_MotionArtifact(data, probe, mlActMan, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

Description :
Identifies motion artifacts in an input data matrix d. If any active data channel exhibits a signal change greater than std_thresh or amp_thresh, then a segment of data around that time point is marked as a motion artifact.

Inputs:

  • data: SNIRF data structure data, containing time course data.
  • probe: SNIRF data structure probe, containing probe source/detector geometry.
  • mlActMan: Cell array of vectors, one for each time base in data, specifying active/inactive channels with 1 meaning active, 0 meaning inactive.
  • tIncMan: Cell array of vectors corresponding to the number of time bases in data. tIncMan has been manually excluded. 0-excluded. 1-included. Vector same length as d.
  • tMotion: Check for signal change indicative of a motion artifact over time range tMotion. Units of seconds.Typical value ranges from 0.1 to 0.5.
  • tMask: Mark data over +/- tMask seconds around the identified motion artifact as a motion artifact. Units of seconds. Typical value ranges from 0.5 to 1.
  • STDEVthresh: If the signal d for any given active channel changes by more that stdev_thresh * stdev(d) over the time interval tMotion, then this time point is marked as a motion artifact. The standard deviation is determined for each channel independently. Typical value ranges from 5 to 20. Use a value of 100 or greater if you wish for this condition to not find motion artifacts.
  • AMPthresh: If the signal d for any given active channel changes by more that amp_thresh over the time interval tMotion, then this time point is marked as a motion artifact. Typical value ranges from 0.01 to 0.3 for optical density units. Use a value greater than 100 if you wish for this condition to not find motion artifacts.

Outputs:

  • tInc: A cell array of vectors corresponding to the number of time bases. Each array element is a vector of length time points with 1's indicating data included and 0's indicate motion artifact.

Usage Options :

  • Motion_Artifacts: tIncAuto = hmrR_MotionArtifact(dod, probe, mlActMan, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh)

Default Parameters :

  • tMotion: 0.5
  • tMask: 1.0
  • STDEVthresh: 50.0
  • AMPthresh: 5.0

Prerequisites :

  • Intensity_to_Delta_OD: dod = hmrR_Intensity2OD( intensity )
  • Alternative Option:
    • Prune_Channels: mlActAuto = hmrR_PruneChannels(data, probe, mlActMan, tIncMan, dRange, SNRthresh, SDrange, reset)

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