Ixi Skill

IXI Skill (Dataset-Orchestration Layer)

Overview

ixi-skill is the NeuroClaw orchestration skill for the IXI (Information eXtraction from Images) dataset.

It strictly follows the NeuroClaw hierarchical design principles:

• This skill only describes WHAT needs to be done and which tool skill to delegate to.
• It contains no implementation code or concrete commands.
• All concrete execution is delegated to existing base/tool skills via claw-shell.
• Companion scripts in scripts/ provide reference implementations for data reorganization, phenotype extraction, and QC.

Core workflow (never bypassed):

1. Identify input IXI data and target modalities.
2. Generate a numbered execution plan clearly stating WHAT needs to be done and which tool skill will handle each step.
3. Present the full plan, estimated runtime, resource requirements, and risks to the user and wait for explicit confirmation ("YES" / "execute" / "proceed").
4. On confirmation, delegate every step to the appropriate skill via claw-shell.
5. After execution, save all outputs in a clean directory structure (ixi_output/).

Research use only.

Quick Reference

Dataset Characteristics

• Cohort: ~600 healthy subjects
• Sites: 3 London hospitals with different scanners
  • Hammersmith Hospital (HH): Philips 3T
  • Guy's Hospital (Guy): Philips 1.5T
  • Institute of Psychiatry (IOP): GE 1.5T
• Modalities: T1w, T2w, MRA (some subjects also have PD and DTI)
• Format: NIfTI (.nii.gz)
• Access: https://brain-development.org/ixi-dataset/

Supported Modalities

Site-Specific Scanner Information

BIDS Preparation

Script: scripts/reorganize_ixi.py

Converts IXI native directory structure to BIDS-compliant layout.

python skills/ixi-skill/scripts/reorganize_ixi.py \
  --input /path/to/IXI/raw \
  --output /path/to/IXI/bids

Features:

• Subject ID normalization: IXI format (e.g., IXI002) to BIDS sub-IXI002
• Site detection from subject ID prefix
• Modality routing: T1w, T2w, MRA, PD, DTI
• Sidecar JSON generation with site-specific metadata
• dataset_description.json and participants.tsv generation
• Dry-run mode: --dry-run to preview without copying

Core Workflow (Never Bypassed)

1. Identify user target: full IXI processing, imaging subset, or BIDS staging only.
2. Generate a numbered plan with tools, outputs, runtime, storage, and risks.
3. Wait for explicit confirmation (YES / execute / proceed).
4. On confirmation, run download stage first (if needed).
5. After download success, run BIDS preparation using scripts/reorganize_ixi.py.
6. Delegate to smri-skill for structural MRI processing (T1w, T2w).
7. Process MRA if requested (vessel enhancement, angiography).
8. If QC summary is requested, run scripts/ixi_qc_summary.py.
9. Save outputs into ixi_output/.

Modality Processing Delegation

Standard Output Layout

ixi_output/
├── raw/                    # Downloaded original IXI files
├── bids/                   # BIDS-staged data
├── smri/                   # Structural MRI derivatives
├── mra/                    # MRA derivatives
├── qc/                     # QC summaries and exclusion lists
└── logs/                   # Processing logs

Benchmark Adapter Guidance

For benchmark-style prompts, do not force the full orchestration when the task only asks for local IXI data staging.

• If the task starts from raw IXI data already present on disk and only asks for BIDS-style staging:
  • Skip the mandatory download stage
  • Default to the narrow path local raw IXI discovery -> BIDS-style staging -> minimal metadata -> validation/report
• In benchmark mode, do not require explicit confirmation before presenting the direct staging solution.

Safety and Execution Policy

• No execution before explicit plan confirmation.
• All execution must be routed via claw-shell.
• Missing dependencies must be resolved by dependency-planner before running.

Important Notes and Limitations

• IXI is a multi-site dataset with different scanners; consider site effects in analysis.
• Site information can be inferred from subject ID prefix (HH, Guy, IOP).
• MRA data is unique to IXI; vessel analysis requires specialized tools.
• Some subjects may have missing modalities (PD, DTI).
• ixi-skill is orchestration-only; detailed preprocessing logic remains in modality skills.

When to Call This Skill

• User asks for end-to-end IXI workflow.
• User asks to download IXI and run structural MRI processing.
• User needs BIDS staging for IXI data.
• User asks for multi-site brain MRI analysis.
• User asks for MRA vessel analysis.

Complementary / Related Skills

• smri-skill → structural MRI preprocessing
• nibabel-skill → NIfTI I/O and MRA processing
• bids-organizer → BIDS validation and organization
• brain-visualization → visualization of derivatives
• dependency-planner → dependency resolution
• conda-env-manager → environment management
• claw-shell → command execution

Reference

• IXI Dataset: https://brain-development.org/ixi-dataset/
• Brain-development.org: https://brain-development.org/

Created At: 2026-05-06 13:31 HKT Last Updated At: 2026-05-06 13:31 HKT Author: chengwang96