ixi-skill

name	ixi-skill
description	Use this skill whenever the user wants an end-to-end workflow for the IXI (Information eXtraction from Images) dataset, including data download, BIDS organization, and multimodal processing of T1w, T2w, and MRA. Triggers include: 'IXI', 'IXI dataset', 'process IXI data', 'IXI MRI', or any request to run the IXI multimodal pipeline.
license	MIT License (NeuroClaw custom skill - freely modifiable within the project)
layer	subagent
skill_type	dataset
dependencies	["smri-skill","bids-organizer","claw-shell"]
complementary_skills	["nibabel-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

Task	What needs to be done	Delegate to	Expected output
Data download	Download IXI from brain-development.org	claw-shell	Raw IXI files
BIDS staging	Reorganize IXI native layout to BIDS	scripts/reorganize_ixi.py	BIDS-compliant dataset
sMRI processing	Brain extraction, tissue segmentation, cortical reconstruction	smri-skill	smri_output/ derivatives
MRA processing	Vessel enhancement, angiography analysis	nibabel-skill	MRA derivatives
QC summary	Per-subject quality control	scripts/ixi_qc_summary.py	QC summary + exclusion list

---

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

Modality	Description	Sites
T1w	High-resolution structural MRI	All 3 sites
T2w	T2-weighted structural MRI	All 3 sites
MRA	Magnetic Resonance Angiography	All 3 sites
PD	Proton Density (some subjects)	Selected sites
DTI	Diffusion Tensor Imaging (some subjects)	Selected sites

---

Site-Specific Scanner Information

Site	Scanner	Field Strength	Notes
Hammersmith Hospital (HH)	Philips	3T	Higher resolution, smaller voxel size
Guy's Hospital (Guy)	Philips	1.5T	Standard resolution
Institute of Psychiatry (IOP)	GE	1.5T	Standard resolution

---

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

Modality	Delegated skill	Typical tasks	Main outputs
sMRI (T1w/T2w)	smri-skill	brain extraction, tissue segmentation, cortical reconstruction	smri_output/ derivatives
MRA	nibabel-skill	vessel enhancement, angiography analysis	MRA derivatives
PD	smri-skill	proton density analysis	PD derivatives
DTI	smri-skill	diffusion tensor metrics	DTI derivatives

---

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