BIDSme is a open-source python tool that converts ("bidsifies") source-level (raw) neuroimaging datasets to BIDS-conformed. Rather then depending on complex or ambiguous programmatic logic for the identification of imaging modalities, BIDSme uses a direct mapping approach to identify and convert the raw source data into BIDS data. The information sources that can be used to map the source data to BIDS are retrieved dynamically from source data headers (DICOM, BrainVision, nifti, etc.) and file structure (file and/or directory names, e.g. number of files).
The retrieved information can be modified/adjusted by a set of plugins. Plugins can also be used to complete the bidsified dataset, for example by parsing log files.
NB: BIDSme support variety of formats including nifty, dicom, BrainVision. Additional formats can be implemented.
The mapping information is stored as key-value pairs in human-readable, widely supported YAML files, generated from a template yaml-file.
Bidsme can be installed using pip:
python3 -m pip install git+https://github.com/CyclotronResearchCentre/bidsme.gitIt will automatically install packages from requirements.txt. When treating specific data formats, additional modules may be required:
- pydicom>=1.4.2 (for DICOM images)
- nibabel>=3.1.0 (for ECAT7 images)
- mne (for various EEG/MEG recordings)
It is recommended to use virtual environment when installing bidsme (more info here and here).
bidsme comes with an example/toy dataset, and the tutorial.
Additianl info are aviable in doc folder.