Intro to sovabids¶
sovabids is a python package for automating eeg2bids conversion.
- sovabids can be used through (click to see the examples):
Note
The advantage of the JSON-RPC way is that it can be used from other programming languages.
Limitation:
Do notice that at the moment the files have to be on the same computer that runs the server.
Warning
Currently meg2bids conversion is not supported, but this is a targeted feature.
Architecture¶
- The main elements of sovabids are:
A source path with the original dataset.
A bids path that will be the output path of the conversion.
A rules file that configures how the conversion is done from the general perspective.
A mapping file that encodes how the conversion is performed to each individual file of the dataset.
Internally sovabids uses MNE-Python and MNE-BIDS to perform the conversion. In a sense is a wrapper that allows to do conversions from the command line.
Installation¶
git clone https://github.com/yjmantilla/sovabids.git
cd sovabids
pip install -r requirements-user.txt
Installation for advanced usage¶
Run
git clone https://github.com/yjmantilla/sovabids.git
cd sovabids
pip install -r requirements-dev.txt
Notice that the requirements-dev.txt file already has the sovabids installation using editable mode.
Installation for developers¶
Fork this repo and run:
git clone https://github.com/<gh-username>/sovabids.git
cd sovabids
pip install -r requirements-dev.txt
Notice that the requirements-dev.txt file already has the sovabids installation using editable mode.
Basic Usage¶
The easiest way is to use sovabids through its CLI entry-points as follows:
sovapply¶
Use the sovapply entry-point to produce a mapping file from a source path, an output bids root path and a rules filepath.
sovapply source_path bids_path rules_path
By default the mapping file made will have the following filepath:
bids_path/code/sovabids/mappings.yml
sovaconvert¶
Use the sovaconvert entry-point to convert the dataset given its mapping file.
sovaconvert mapping_file
Funding¶
Acknowledgments¶
sovabids is developed with the help of the following entities:
What does sova means?¶
sova is a contraction of ‘eso va’ which mean ‘that goes’ in spanish.
Nevertheless the real usage by the original developers is just to convey the idea of :
we will make it happen, we dont know how, but we will