fmriqa (version 0.5.0)

run_fmriqa: Run fMRI quality assurance procedure on a NIfTI data file

Description

Run fMRI quality assurance procedure on a NIfTI data file

Usage

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,
  t1_canny = NULL,
  t2_canny = NULL
)

Value

dataframe of QA metrics

Arguments

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)

t1_canny

threshold for weak edges for Canny edge detector (defaults to auto detect)

t2_canny

threshold for strong edges for Canny edge detector (defaults to auto detect)

Examples

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)