bids-validator

BIDS Validator Agent

Autonomously validate a BIDS dataset, interpret validation results, categorize errors by severity, and provide specific fixes for each issue.

Procedure

1. Locate Dataset

Find the BIDS dataset root (contains dataset_description.json):

find . -name "dataset_description.json" -maxdepth 2

2. Run BIDS Validator

# Try the CLI validator first
bids-validator /path/to/dataset --json 2>/dev/null

# Fallback: Python validator
python3 -c "from bids_validator import BIDSValidator; print('available')" 2>/dev/null

3. Parse Results

Categorize findings:

• Errors (must fix): Missing required files, invalid naming, schema violations
• Warnings (should fix): Missing recommended fields, deprecated practices
• Info (optional): Suggestions for improvement

4. Diagnose Common Issues

For each error, provide the specific fix:

MISSING_REQUIRED_FILE:

• Check which file is missing (dataset_description.json, participants.tsv, etc.)
• Generate the file with required fields

INVALID_FILE_NAME:

• Show correct naming pattern
• Provide rename command

SIDECAR_INVALID:

• Read the JSON sidecar
• Identify missing required fields
• Add them with appropriate values

EVENTS_TSV_MISSING:

• Check if events are in the data file
• Extract and create events.tsv

CHANNELS_TSV_MISSING:

• Read channel info from data file header
• Generate channels.tsv

5. Apply Fixes (with confirmation)

For each fixable issue:

1. Show what will be changed
2. Apply the fix
3. Re-validate to confirm

6. Generate Report

## BIDS Validation Report

Dataset: {path}
BIDS Version: {version from dataset_description.json}

### Summary
- Subjects: N
- Sessions: N
- Modalities: eeg, emg, anat
- Total errors: N
- Total warnings: N

### Errors Fixed
1. [FIXED] Missing dataset_description.json - created with required fields
2. [FIXED] sub-01_task-rest_eeg.json missing PowerLineFrequency - added 60

### Remaining Issues
1. [WARNING] Recommended field "InstitutionName" missing in 12 sidecars
2. [INFO] Consider adding a README file

### Ready for Submission: YES/NO