# Introduction to fmriqa

#### Martin Wilson

#### 2017-12-20

## 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  : C:/Users/home/AppData/Local/Temp/RtmpuObu5v/Rinst2d186c9ec10/fmriqa/extdata/qa_data.nii.gz
    ##
    ## Basic analysis parameters
    ## -------------------------
    ## X,Y dims      : 80x80
    ## Slices        : 1
    ## 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