| name | bids-neuroimaging |
| description | Plan and audit BIDS neuroimaging datasets, derivatives, validation, metadata, and reproducible preprocessing. Use when users mention BIDS, fMRI, MRI, EEG/MEG/iEEG, DICOM conversion, dataset_description.json, participants.tsv, or neuroimaging derivatives. |
| user-invocable | true |
| license | Apache-2.0 |
BIDS Neuroimaging
Source adaptation: BioRouter-original synthesis inspired by Scientific Agent Skills BIDS/neuroimaging patterns, rewritten under Apache-2.0.
When to Use
Use this skill when work touches the Brain Imaging Data Structure or neuroimaging dataset organization. Pair with biomedical-imaging-pathology for DICOM/PACS and image QC, and with neurophysiology-analysis for EEG/MEG/iEEG signal analysis.
Intake
Collect:
- Modality: MRI/fMRI/dMRI, PET, EEG, MEG, iEEG, or multimodal.
- Source data format and conversion path.
- Dataset scope: raw BIDS, derivatives, or both.
- Subject/session/task/run structure.
- Required metadata sidecars and privacy constraints.
- Intended pipeline: fMRIPrep, MRIQC, QSIPrep, MNE-BIDS, custom workflow, or archive deposit.
BIDS Audit
Check:
dataset_description.json, participants.tsv, README, CHANGES, and license files.- Subject/session folder naming.
- Modality-specific filenames and entities.
- JSON sidecars for acquisition parameters, task metadata, channels, electrodes, events, and coordinate systems.
- Derivative
dataset_description.json and source provenance.
- Defacing/de-identification and protected metadata removal.
Validation Workflow
- Run or plan
bids-validator before analysis.
- Separate warnings from errors and explain which affect inference.
- Preserve conversion logs and DICOM/source provenance.
- Check slice timing, phase encoding, intended-for fields, events timing, and channel metadata.
- Confirm derivatives do not overwrite raw data.
Quality Gates
Do not treat a dataset as analysis-ready unless:
- Validation status is reported.
- Known validator warnings are triaged.
- Subject/session/task/run counts match expectations.
- Metadata needed by the preprocessing tool is present.
- Privacy/de-identification status is explicit.
Output Shape
Return: dataset map, validation findings, required fixes, preprocessing route, and archive/readiness status.
