Install data-sets from 'OpenNeuro' — install

Enjoy hundreds of open-access data sets from openneuro.org with a simple accession number.

Usage

install_openneuro(
  accession_number,
  subject_codes = NULL,
  tag = NULL,
  parent_folder = NULL
)

Arguments

accession_number: 'OpenNeuro' accession number
subject_codes: subject codes, with or without the prefix 'sub-', default is NULL to download the entire data repository
tag: version number; default is NULL to download the latest version
parent_folder: parent directory where the data will be downloaded into the data folder name is always the accession number

Value

The data folder name on the local disk.

Examples


if (FALSE) { # \dontrun{

# Download Hermes D, Miller KJ, Wandell BA, Winawer J (2015) dataset
# from https://openneuro.org/datasets/ds005953

install_openneuro('ds005953')

# Download subject sub-HUP070 used by Bernabei & Li et al.
# from https://openneuro.org/datasets/ds004100

install_openneuro('ds004100', subject_codes = "HUP070")

# access the downloaded data
bids_parent_root <- ravepipeline::raveio_getopt("bids_data_dir")

# ---- Example of visualizing electrodes on the fsaverage ----
# Load BIDS project
proj_ds004100 <- bidsr::bids_project(
  file.path(bids_parent_root, "ds004100"))

# BIDS-R Subject instance
sub_HUP070 <- bidsr::bids_subject(proj_ds004100, "HUP070")

# Find BIDS entities with electrodes as suffix
electrode <- bidsr::query_bids(sub_HUP070, list(
  data_types = "ieeg",
  suffixes = "electrodes",
  sidecars = TRUE
))

# resolve electrode table path
electrode_path <- bidsr::resolve_bids_path(
  x = proj_ds004100,
  format(electrode$parsed[[1]]))

# laod electrode coordinate
tabular <- bidsr::as_bids_tabular(electrode_path)

# Build RAVE electrode table
electrode_coordinates <- data.frame(
  Electrode = 1:nrow(tabular$content),
  x = tabular$content$x,
  y = tabular$content$y,
  z = tabular$content$z,
  Label = tabular$content$name,
  Radius = 2,
  BIDSSubject = "sub-HUP070"
)

# Load RAVE brain - fsaverage
template <- threeBrain::merge_brain(template_subject = "fsaverage")
fsaverage <- template$template_object

# This dataset uses surface RAS; see coordsys JSON
# tkrRAS: surface RAS
# scannerRAS: MRI RAS
fsaverage$set_electrodes(electrode_coordinates, coord_sys = "tkrRAS")

fsaverage$plot()



} # }