| Type: | Package |
| Title: | Functional MRI Quality Assurance Routines |
| Version: | 0.3.0 |
| Date: | 2018-02-19 |
| Description: | Methods for performing fMRI quality assurance (QA) measurements of test objects. Heavily based on the fBIRN procedures detailed by Friedman and Glover (2006) <doi:10.1002/jmri.20583>. |
| BugReports: | https://github.com/martin3141/fmriqa/issues |
| License: | GPL-3 |
| LazyData: | true |
| RoxygenNote: | 6.0.1 |
| Imports: | viridisLite, RNifti, ggplot2, reshape2, gridExtra, grid, tidyr, optparse, tcltk, RcppEigen, imager, pracma |
| Encoding: | UTF-8 |
| Suggests: | testthat, covr, knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2018-02-19 12:33:39 UTC; wilsonmp |
| Author: | Martin Wilson [cre, aut] |
| Maintainer: | Martin Wilson <martin@pipegrep.co.uk> |
| Repository: | CRAN |
| Date/Publication: | 2018-02-19 15:59:01 UTC |
fmriqa: fMRI quality assurance routines
Description
The fmriqa package provides an implementation of the fMRI quality assurance analysis protocol detailed by Friedman and Glover (2006) <doi:10.1002/jmri.20583>.
Details
#' To learn more about fmriqa, start with the vignettes: 'browseVignettes(package = "fmriqa")'
For a full list of functions: 'help(package=fmriqa, help_type="html")'
Author(s)
Maintainer: Martin Wilson martin@pipegrep.co.uk
See Also
Useful links:
Report bugs at https://github.com/martin3141/fmriqa/issues
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)
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) |
Value
dataframe of QA metrics
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)