Table 3.

Summary table of image quality metrics for functional (BOLD) MRI.

Spatial IQMs
EFC, FBER, FWHM, SNR, SSTATs (see Table 2)
IQMs measuring temporal variations
tSNR	A simplified interpretation of the original temporal SNR definition by Krüger et al.29. We report the median value of the tSNR map calculated as the average BOLD signal across time over the corresponding temporal s.d. map.
GCOR	Summary of time-series correlation as in30 using AFNI’s @compute_gcor
DVARS	The spatial standard deviation of the data after temporal differencing. Indexes the rate of change of BOLD signal across the entire brain at each frame of data. DVARS is calculated using Nipype, after head-motion correction
IQMs targeting specific artifacts
FD	Framewise Displacement - Proposed by Power et al.1 to regress out instantaneous head-motion in fMRI studies. MRIQC reports the average FD.
GSR	The Ghost to Signal Ratio31 estimates the mean signal in the areas of the image that are prone to N/2 ghosts on the phase encoding direction with respect to the mean signal within the brain mask10. Lower values are better.
DUMMY	The number of dummy scans - A number of volumes at the beginning of the fMRI time-series identified as nonsteady states.
IQMs from AFNI
AOR	AFNI’s outlier ratio - Mean fraction of outliers per fMRI volume as given by AFNI’s 3dToutcount
AQI	AFNI’s quality index - Mean quality index as computed by AFNI’s 3dTqual

MRIQC produces a vector of 64 image quality metrics (IQMs) per input BOLD scan.