norm_BOLD {fMRItools}

Normalize BOLD data

Description

Center the data across space and/or time, detrend, and scale, in that order. For dual regression, row centering is required and column centering is not recommended. Scaling and detrending depend on the user preference.

Usage

norm_BOLD(
  BOLD,
  center_rows = TRUE,
  center_cols = FALSE,
  scale = c("local", "global", "none"),
  scale_sm_xifti = NULL,
  scale_sm_FWHM = 2,
  TR = NULL,
  hpf = 0.01
)

Arguments

BOLD

fMRI numeric data matrix (V \times T)

center_rows, center_cols

Center BOLD data across rows (each data location's time series) or columns (each time point's image)? Default: TRUE for row centering, and FALSE for column centering.

scale

"global" (default), "local", or "none". Global scaling will divide the entire data matrix by the mean image standard deviation (mean(sqrt(rowVars(BOLD)))). Local scaling will divide each data location's time series by its estimated standard deviation.

scale_sm_xifti, scale_sm_FWHM

Only applies if scale=="local" and BOLD represents CIFTI-format data. To smooth the standard deviation estimates used for local scaling, provide a "xifti" object with data locations in alignment with BOLD, as well as the smoothing FWHM (default: 2). If no "xifti" object is provided (default), do not smooth.

TR

The temporal resolution of the data, i.e. the time between volumes, in seconds. TR is required for detrending with hpf.

hpf

The frequency at which to apply a highpass filter to the data during pre-processing, in Hertz. Default: 0.01 Hertz. Set to 0 to disable the highpass filter.

The highpass filter serves to detrend the data, since low-frequency variance is associated with noise. Highpass filtering is accomplished by nuisance regression of discrete cosine transform (DCT) bases.

Note the TR argument is required for highpass filtering. If TR is not provided, hpf will be ignored.

Value

Normalized BOLD data matrix (V \times T)