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
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 : /home/runner/work/_temp/Library/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