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 |