run_fmriqa: Run fMRI quality assurance procedure on a NIfTI data file
In neuroconductor-releases/fmriqa: Functional MRI Quality Assurance Routines

Description Usage Arguments Value Examples

View source: R/run_fmriqa.R

Run fMRI quality assurance procedure on a NIfTI data file

run_fmriqa(data_file = NULL, roi_width = 21, slice_num = NULL,
  skip = 2, tr = NULL, pix_dim = NULL, poly_det_ord = 3,
  spike_detect = FALSE, x_pos = NULL, y_pos = NULL,
  plot_title = NULL, last_vol = NULL, gen_png = TRUE,
  gen_res_csv = TRUE, gen_pdf = FALSE, gen_spec_csv = FALSE,
  png_fname = NULL, res_fname = NULL, pdf_fname = NULL,
  spec_fname = NULL, verbose = TRUE, bg_smooth = 12,
  bg_shrink = 25)

`data_file`	input data in nifti format, a file chooser will open if not set
`roi_width`	roi analysis region in pixels (default=21)
`slice_num`	slice number for analysis (default=middle slice)
`skip`	number of initial volumes to exclude from the analysis (default=2)
`tr`	override the TR detected from data (seconds)
`pix_dim`	override the x,y,z pixel dimensions (mm) detected from data eg pixdim=c(3,3,3)
`poly_det_ord`	polynomial order used for detrending (default=3)
`spike_detect`	generate k-space spike-detection plot (default=FALSE)
`x_pos`	x position of ROI (default=center of gravity)
`y_pos`	y position of ROI (default=center of gravity)
`plot_title`	add a title to the png and pdf plots
`last_vol`	last volume number to use in the analysis
`gen_png`	output png plot (default=TRUE)
`gen_res_csv`	output csv results (default=TRUE)
`gen_pdf`	output pdf plot (default=FALSE)
`gen_spec_csv`	output csv of spectral points (default=FALSE)
`png_fname`	png plot filename
`res_fname`	csv results filename
`pdf_fname`	pdf plot filename
`spec_fname`	csv spectral data filename
`verbose`	provide text output while running (default=TRUE)
`bg_smooth`	amount to smooth background image before calculating the maximum BG percent metric (default=12mm)
`bg_shrink`	amount to shrink the BG image away from the object to avoid residual object signal in the maximum BG percent metric (default=25mm)

dataframe of QA metrics

1 2	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)