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") |