hmrR_MotionCorrectPCArecurse - BUNPC/Homer3 GitHub Wiki

UI Name :
Motion_Correct_PCA_Recurse

Syntax :
[data_dN, tInc, svs, nSV, tInc0] = hmrR_MotionCorrectPCArecurse(data_d, probe, mlActMan, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh, nSV, maxIter, turnon)

Description :
Identified motion artifacts in an input data matrix d. If any active data channel exhibits a signal change greater than STDEVthresh or AMPthresh, then a segment of data around that time point is marked as a motion artifact. Set turnon=0 to skip this function.

Inputs :

  • data_d: data matrix, timepoints x sd pairs.
  • sd: Source Detector Structure. The active data channels are indicated in SD.MeasListAct.
  • mlActMan: Cell array of vectors, one for each time base in data, specifying active/inactive channels with 1 meaning active, 0 meaning inactive.
  • tIncMan: Data that 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. Typically tMotion=0.5.
  • tMask: Mark data over +/- tMask seconds around the identified motion artifact as a motion artifact. Units of seconds. Typically tMask=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.
  • AMPthresh: If the signal d for any given active channel changes by more that AMPthresh over the time interval tMotion, then this time point is marked as a motion artifact.
  • nSV: This is the number of principal components to remove from the data. If this number is less than 1, then the filter removes the first n components of the data that removes a fraction of the variance up to nSV. Yucel et al uses nSV=0.97.
  • maxIter: Maximum number of iterations. Yucel et al uses maxIter=5.

Outputs :

  • data_dN: This is the motion corrected data.
  • tInc: a vector of length time points with 1's indicating data included and 0's indicate motion artifact AFTER correction of motion artifacts.
  • svs: the singular values of the PCA for each iteration in each column vector.
  • nSV: number of singular values removed from the data.
  • tInc0: a vector of length time points with 1's indicating data included and 0's indicate motion artifact BEFORE correction of motion artifacts.

Usage Options :

  • Motion_Correct_PCA_Recurse: [dod, tInc, svs, nSV, tInc0] = hmrR_MotionCorrectPCArecurse(dod, probe, mlActMan, tIncMan, tMotion, tMask, STDEVthresh, AMPthresh, nSV, maxIter, turnon)

Default Parameters :

  • tMotion: 0.5
  • tMask: 1.0
  • STDEVthresh: 20.0
  • AMPthresh: 5.00
  • nSV: 0.97
  • maxIter: 5
  • turnon: 1

Prerequisites :

  • Intensity_to_Delta_OD: dod = hmrR_Intensity2OD( intensity )

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