Description Usage Arguments Value Examples
Run fMRI quality assurance procedure on a NIfTI data file
1 2 3 4 5 6 7 8 | 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)
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