https://github.com/dipterix/ieegio
File input output for neuroscience study
https://github.com/dipterix/ieegio
bci2000 brain brainvision dbs edf electrophysiology ephys freesurfer ieeg neuroimaging neuroscience nifti nwb-format r
Last synced: about 2 months ago
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File input output for neuroscience study
- Host: GitHub
- URL: https://github.com/dipterix/ieegio
- Owner: dipterix
- License: other
- Created: 2024-09-08T17:08:47.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2025-03-19T03:05:30.000Z (2 months ago)
- Last Synced: 2025-03-19T04:20:31.287Z (2 months ago)
- Topics: bci2000, brain, brainvision, dbs, edf, electrophysiology, ephys, freesurfer, ieeg, neuroimaging, neuroscience, nifti, nwb-format, r
- Language: R
- Homepage: http://dipterix.org/ieegio/
- Size: 57.1 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
README
# `ieegio`: IO toolbox for Intracranial Electroencephalography
[](https://CRAN.R-project.org/package=ieegio)
[](https://dipterix.r-universe.dev/ieegio)
[](https://github.com/dipterix/ieegio/actions/workflows/R-CMD-check.yaml)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
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](https://github.com/) with:
``` r
# install.packages("pak")
pak::pak("dipterix/ieegio")
```
`ieegio` provides additional sample data. To download them:
``` r
# 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](https://dipterix.org/ieegio/articles/read-ephys.html))
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](https://dipterix.org/ieegio/articles/read-imaging-data.html))
**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` |