ieegio: IO toolbox for Intracranial Electroencephalography

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