The fmriqa package provides an implementation of the fMRI quality assurance (QA) analysis protocol detailed by Friedman and Glover (2006) http://dx.doi.org/10.1002/jmri.20583.
# load the package
library(fmriqa)
# get help on the options for run_fmriqa
?run_fmriqa
# run the analysis - a file chooser will appear when a data_file argument is not given
run_fmriqa()
library(fmriqa)## Warning: no DISPLAY variable so Tk is not available
fname <- system.file("extdata", "qa_data.nii.gz", package = "fmriqa")
res <- run_fmriqa(data_file = fname, gen_png = FALSE, gen_res_csv = FALSE, tr = 3)## Reading data : /home/runner/work/_temp/Library/fmriqa/extdata/qa_data.nii.gz
##
## Basic analysis parameters
## -------------------------
## X,Y matrix : 80x80
## Slices : 1
## X,Y,Z pix dims : 1x1x1mm
## TR : 3s
## Slice # : 1
## ROI width : 21
## Total vols : 200
## Analysis vols : 198
##
## QA metrics
## ----------
## Mean signal : 2561.3
## STD : 6.4
## Percent fluc : 0.25
## Drift : 2.06
## Drift fit : 1.42
## SNR : 141.3
## SFNR : 137
## RDC : 2.84
## TC outlier : 2.66
## Spec outlier : 5.12
## MBG percent : 0.74