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The goal of ieegio is to provide integrated toolbox for common file formats used in intracranial Electroencephalography (iEEG) and deep-brain stimulation (DBS). Currently the package is under active development.

Installation

You can install the development version of ieegio from GitHub with:

# install.packages("pak")
pak::pak("dipterix/ieegio")

ieegio provides additional sample data. To download them:

# list all the sample data
sample_names <- ieegio::ieegio_sample_data()

lapply(sample_names, ieegio::ieegio_sample_data)

List 1: read formatted ephys data (examples)

The following formats have been (or will be) supported. Please feel free to make a wish-list by posting an issue in this repository.

Electrophysiology

Name Common Extensions Read Write
EDF(+)/BDF(+) (European Data Format) *.edf read_edf
BrainVision *.vhdr, *.vmrk, *.eeg, *.dat read_brainvis
BCI2000 *.dat read_bci2000
NEV/NSx (BlackRock neural-event/signal) *.nev, *.ns1, *.ns2, …, *.ns6 read_nsx
NWB (Neurodata Without Borders) *.nwb read_nwb *
MEF *.mef

* - NWB format only has low-level support due to its format nature. Please see examples with help(read_nwb)

List 2: read imaging data (examples)

Imaging

Name Common Extensions Read Write
NIfTI (Neuroimaging Informatics Technology Initiative) *.nii[.gz] read_volume (io_read_nii) write_volume (io_write_nii)
MGH/MGZ (Massachusetts General Hospital format) *.mgh, *.mgz read_volume (io_read_mgz) write_volume (io_write_mgz)
GIfTI (Geometry format under the NIfTI) *.gii[.gz] read_surface (io_read_gii) write_surface (io_write_gii)
FreeSurfer surface e.g. *h.pial, *h.white read_surface (io_read_fs(type="geometry")) write_surface(format="freesurfer", type="geometry")
FreeSurfer node values/weights e.g. *h.curv, *h.sulc read_surface (io_read_fs(type="measurements")) write_surface(format="freesurfer", type="measurements")
Surface annotation *.annot read_surface (io_read_fs(type="annotations")) write_surface(format="freesurfer", type="annotations")

List 3: common file formats used for meta data

Name Common Extensions Read Write
Matlab *.mat io_read_mat io_write_mat
HDF5 *.h5 io_read_h5 io_write_h5
YAML *.yml, *.yaml io_read_yaml io_write_yaml
JSON *.json io_read_json io_write_json
INI *.ini io_read_ini
FST *.fst io_read_fst io_write_fst