Intro to sovabids

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.

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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