hmrR_MotionCorrectPCA - BUNPC/Homer3 GitHub Wiki

UI Name :
Motion_Correct_PCA

Syntax :
[data_d, svs, nSV] = hmrR_MotionCorrectPCA(data_d, mlActMan, tIncMan, nSV)

Description :
This function uses PCA to filter only the segments of data identified as a motion artifact. The motion artifacts are indicated in the tInc vector by the value of 0.

Inputs :

• data_d: SNIRF object containing data matrix, timepoints x sd pairs.
• mlActMan: Active data channels are indicated mlActMan.
• tIncMan: Cell array for each data block with vectors of length time points where 1's indicating data included and 0's indicating motion artifact.
• nSV: Cell array for each data block with the number of principal components to remove from each data block. 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. Percent variance you want to remove, or give an integer for number of components to remove.

Outputs :

• data_dN: SNIRF object containing the motion corrected data matrix.
• svs: Cell array for each data block with the singular values of the PCA.
• nSV: Cell array for each data block with the number of singular values removed from the data.

Usage Options :

• Motion_Correct_PCA: [dod, svs, nSV] = hmrR_MotionCorrectPCA(dod, mlActMan, tIncMan, nSV)

Default Parameters :

• nSV: 0.0

Prerequisites :

• Intensity_to_Delta_OD: dod = hmrR_Intensity2OD( intensity )