Introduction to fmriqa

Overview

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.

Usage

# 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()

Real data example

library(fmriqa)
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  : /private/var/folders/nz/vv4_9tw56nv9k3tkvyszvwg80000gn/T/RtmpctsDVb/Rinst149a92b85ebb8/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