Description
bids is an agent skill for organising, querying, validating and converting datasets that follow the Brain Imaging Data Structure, known as BIDS. BIDS is a community standard for organising neuroscience and biomedical research data, with a consistent file naming convention, directory hierarchy and metadata schema, so that people and software can read a dataset straight away. The skill follows the specification, reviewed against version 1.11.2. BIDS began with MRI but now covers 11 modalities, including PET, microscopy, EEG, MEG, intracranial EEG, EMG, near-infrared spectroscopy, motion capture, behavioural data and MR spectroscopy. The Python tools it uses are PyBIDS for querying and indexing datasets, and the bids-validator for compliance checking. Conversion from DICOM is usually done with HeuDiConv, dcm2bids or BIDScoin. The skill also notes that repository submission rules differ by modality and archive, so you should check the target archive before preparing a deposit. Use it when you are organising or checking a neuroscience dataset. The skill is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars.…
Highlights
- Organises and validates BIDS datasets
- Queries datasets with PyBIDS
- Covers 11 modalities including MRI and EEG
- Converts DICOM with HeuDiConv, dcm2bids or BIDScoin
- Based on BIDS specification v1.11.2
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bids FAQ
What is BIDS?
The Brain Imaging Data Structure, a community standard for organising neuroscience and biomedical research datasets.
Which data types does it cover?
The skill says the specification covers 11 modalities, including MRI, PET, EEG, MEG, iEEG, EMG, NIRS and behavioural data.
How do I convert DICOM files?
The skill names HeuDiConv, dcm2bids and BIDScoin as the usual conversion tools.
What tools does it use to check a dataset?
PyBIDS for querying and indexing, and the bids-validator for compliance checking.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill bids.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best bids alternatives?
Popular alternatives to bids include neurokit2, neuropixels-analysis and batch-grill-me. See all bids alternatives