mr_data2bids: Create a BIDS file structure from a vector of data paths or...

In spant: MR Spectroscopy Analysis Tools

Create a BIDS file structure from a vector of data paths or list of mri/mrs data objects.

Description

Create a BIDS file structure from a vector of data paths or list of mri/mrs data objects.

Usage

mr_data2bids(
  mr_data,
  suffix,
  output_dir,
  sub = NULL,
  ses = NULL,
  task = NULL,
  acq = NULL,
  nuc = NULL,
  voi = NULL,
  rec = NULL,
  run = NULL,
  echo = NULL,
  inv = NULL,
  skip_existing = TRUE,
  mri_format = "nifti",
  deface_mri = FALSE
)

Arguments

mr_data	vector of data paths or list of mri/mrs objects.
suffix	vector of file suffixes, eg : c("svs", "mrsi", "T1w).
output_dir	the base directory to create the BIDS structure.
sub	optional vector of subject labels. If not specified, these will be automatically generated as a series of increasing zero-padded integer values corresponding to the mrs_data input indices.
ses	optional vector of session labels.
task	optional vector of task labels.
acq	optional vector of acquisition labels.
nuc	optional vector of nucleus labels.
voi	optional vector of volume of interest labels.
rec	optional vector of reconstruction labels.
run	optional vector of run indices.
echo	optional vector of echo time indices.
inv	optional vector of inversion indices.
skip_existing	skip any data files that have already been converted. Defaults to TRUE, set to FALSE to force an overwrite of any existing data files.
mri_format	defaults to "nifti", can also be "dicom" provided the divest packages is installed.
deface_mri	option to apply fsl_deface to the mri as a preprocessing step. Defaults to FALSE, requires the fslr package to be installed when TRUE.

spant documentation built on Nov. 5, 2025, 5:22 p.m.