mr_data2bids: 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.