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.
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)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 |
write_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)
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") |
TRK streamlines |
*.trk,
*.trk.gz |
read_streamlines
(io_read_trk) |
write_streamlines
(io_write_trk) |
TCK streamlines |
*.tck |
read_streamlines
(io_read_tck) |
write_streamlines
(io_write_tck) |
TT (DSI-Studio)
streamlines |
*.tt,
*.tt.gz |
read_streamlines
(io_read_tt) |
|
VTK poly-data (as
streamlines) |
*.vtk, *.vtp,
*.vtpb |
read_streamlines
(io_read_vtk_streamlines) |
read_streamlines
(io_write_vtk_streamlines) |
| 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 |