Bids Organizer

Common Shell Command Examples

# DICOM to BIDS (most common)
dcm2niix -o ./bids/sub-001/ses-01/anat -f "%p_%s" -b y -z y /path/to/dicom/T1

# Validate the resulting BIDS dataset
bids-validator /path/to/bids_dataset

Installation (Handled by dependency-planner)

Use dependency-planner with requests such as:

• “Install dcm2niix and bids-validator”
• “Install MNE-Python for EEG to BIDS conversion”

After installation, verify with:

dcm2niix --version
bids-validator --version

NeuroClaw recommended wrapper script

# bids_organizer_wrapper.py (placed inside the skill folder for reference)
import subprocess
from pathlib import Path

def organize_to_bids(raw_dir, bids_dir, subject_id, session_id="01"):
    bids_dir = Path(bids_dir)
    bids_dir.mkdir(parents=True, exist_ok=True)
    
    # DICOM to BIDS example
    cmd = [
        "dcm2niix", "-o", str(bids_dir / f"sub-{subject_id}" / f"ses-{session_id}" / "anat"),
        "-f", "%p_%s", "-b", "y", "-z", "y", str(raw_dir)
    ]
    
    print("Executing:", " ".join(cmd))
    subprocess.run(cmd, check=True)
    
    # Create basic dataset_description.json
    desc = {
        "Name": "NeuroClaw BIDS Dataset",
        "BIDSVersion": "1.8.0",
        "DatasetType": "raw"
    }
    (bids_dir / "dataset_description.json").write_text(str(desc))
    
    print(f"BIDS dataset created at: {bids_dir}")

Important Notes & Limitations

• This skill only generates the plan and delegates; actual file operations are performed via claw-shell.
• DICOM conversion relies on dcm2nii.
• EEG conversion is delegated to mne-eeg-tool.
• Always review the proposed BIDS structure (subject/session labels, run numbers) before confirmation.
• Large datasets may require significant disk space and time.

When to Call This Skill

• Raw scanner data (DICOM) needs to be converted and organized into BIDS
• Existing NIfTI/EEG files need proper BIDS naming and folder structure
• Preparing data for fmriprep-tool, hcppipeline-tool, fsl-tool, or fmri-skill
• Before running any standardized preprocessing pipeline

Post-Execution Verification (Harness Integration)

After BIDS organization completes, this skill automatically invokes harness-core's VerificationRunner to validate output integrity:

Integrated verification checks:

from skills.harness_core import VerificationRunner, AuditLogger

verifier = VerificationRunner(task_type="bids_organization")

# 1. BIDS structure compliance
verifier.add_check("bids_structure", 
    checker=lambda: verify_bids_structure(bids_dir),
    severity="error"
)

# 2. Dataset description file
verifier.add_check("dataset_description",
    checker=lambda: verify_dataset_description_exists(bids_dir),
    severity="error"
)

# 3. Subject/session naming convention
verifier.add_check("naming_convention",
    checker=lambda: verify_bids_naming(bids_dir),
    severity="error"
)

# 4. Metadata JSON sidecar completeness
verifier.add_check("json_sidecars",
    checker=lambda: verify_json_sidecars(bids_dir),
    severity="warning"
)

# 5. Required BIDS files presence
verifier.add_check("required_files",
    checker=lambda: verify_required_files(bids_dir),
    severity="error"
)

report = verifier.run(bids_dir)

# Log verification results
logger = AuditLogger(log_file=f"{bids_dir}/bids_verification.jsonl")
logger.log_validation(
    task_name="bids_organization",
    checks_passed=len([r for r in report.results if r.passed]),
    checks_failed=len([r for r in report.results if not r.passed]),
    warnings=len([r for r in report.results if r.severity == "warning" and not r.passed]),
    report_summary=report.to_dict()
)

if report.failed:
    raise ValueError(f"BIDS verification failed: {report.summary}")

Output files generated:

• {bids_dir}/bids_verification.jsonl — structured audit log
• {bids_dir}/.bids_validation_timestamp — verification completion marker

Complementary / Related Skills

• dependency-planner → install required tools
• claw-shell → safe execution of all commands
• harness-core → automated verification and audit logging

More Advanced Features

For complex BIDS cases (multi-session, multi-run, custom metadata, HEUDICONV heuristics, etc.), please refer to the official BIDS specification:

• Official BIDS Website: https://bids.neuroimaging.io/
• BIDS Specification: https://bids-specification.readthedocs.io/

You may use the multi-search-engine or academic-research-hub skill to find the latest BIDS conversion best practices.

Created At: 2026-03-25 16:00 HKT
Last Updated At: 2026-04-05 02:01 HKT Author: chengwang9637:["$","$L3f",null,{"content":"$40","frontMatter":{"name":"bids-organizer","description":"Use this skill whenever the user wants to automatically organize raw neuroimaging data (DICOM, NIfTI, EEG, etc.) into a valid BIDS (Brain Imaging Data Structure) dataset. Triggers include: 'organize to BIDS', 'BIDS organizer', 'convert to BIDS', 'BIDS conversion', 'bidsify', 'create BIDS dataset', 'raw data to BIDS', or any request to structure data according to BIDS specification.","license":"MIT License (NeuroClaw custom skill – freely modifiable within the project)"}}]