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Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.
Passed 22 of 23 test cases with the skill, and 17 of 23 without it.
and 2 more in the full report
5 fixed17 passed either way1 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 5 test cases the skill fixed. Same model, same prompt, with and without the skill.
I want to install the modern Deno-based reference BIDS validator via PyPI for command-line dataset validation. What is the exact PyPI package name to install using uv pip or pip?
| Checked | Without skill | With skill |
|---|---|---|
| Specifies bids-validator-deno as the package name. | Missed | Passed |
The instructions your model reads when the skill loads.
The Brain Imaging Data Structure (BIDS) is a community standard for organizing and describing neuroscience and biomedical research datasets. It defines a consistent file naming convention, directory hierarchy, and metadata schema so that datasets are immediately understandable by humans and software tools alike. BIDS is governed by the BIDS Specification (currently v1.11.x) and is maintained by the community via the BIDS-Standard GitHub organization.
While BIDS originated for MRI, it has grown well beyond neuroimaging. The specification now covers 11 modalities spanning imaging, electrophysiology, and behavioral data:
Active BEPs are extending BIDS further — notably BEP032 (microelectrode electrophysiology) will add support for extracellular recordings including Neuropixels probes, bringing BIDS to a prevalent methodology in animal neuroscience research (see also the neuropixels-analysis skill).
Adoption is required or strongly encouraged by major data repositories (OpenNeuro, DANDI), leading journals (NeuroImage, Human Brain Mapping, Scientific Data), and funding agencies (NIH, ERC).
The Python ecosystem for BIDS centers on PyBIDS (pybids) for querying and indexing BIDS datasets, and the bids-validator (Deno-based, available as PyPI package bids-validator-deno or via Deno directly) for compliance checking. Conversion from DICOM is typically done with HeuDiConv, dcm2bids, or BIDScoin.
Apply this skill when:
dataset_description.json for a new dataset.bidsignore to exclude files from validation# Core BIDS querying library
uv pip install pybids
# BIDS validator (Deno-based, installed via PyPI wrapper)
uv pip install bids-validator-deno
test cases passed, vs 17 / 23 without
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