@brainpilot/skills 0.0.6 → 0.0.7

package/skills/06_fMRI_Neuroimaging/oasis-skill/SKILL.md

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+---
+name: oasis-skill
+description: "Use this skill whenever the user wants an end-to-end workflow for the OASIS (Open Access Series of Imaging Studies) dataset, including BIDS validation, multimodal processing of sMRI, and phenotype extraction for aging and Alzheimer's disease research. Triggers include: 'OASIS', 'OASIS-1', 'OASIS-2', 'OASIS-3', 'process OASIS data', 'Alzheimer', or any request to run the OASIS 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:
+  - fmri-skill
+  - asl-skill
+  - pet-skill
+  - brain-visualization
+---
+# OASIS Skill (Dataset-Orchestration Layer)
+
+## Overview
+
+`oasis-skill` is the NeuroClaw orchestration skill for the **OASIS (Open Access Series of Imaging Studies)** dataset, founded by the Knight Alzheimer Disease Research Center at Washington University.
+
+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 BIDS validation, phenotype extraction, and QC.
+
+**Core workflow (never bypassed):**
+1. Identify input OASIS 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 (`oasis_output/`).
+
+**Research use only.**
+
+---
+
+## Quick Reference
+
+| Task | What needs to be done | Delegate to | Expected output |
+|---|---|---|---|
+| BIDS validation | Validate OASIS BIDS structure | `scripts/validate_oasis.py` | Validation report |
+| sMRI processing | Brain extraction, tissue segmentation, cortical thickness | `smri-skill` | `smri_output/` derivatives |
+| Phenotype extraction | CDR, MMSE, demographic data | `scripts/extract_oasis_phenotype.py` | Merged phenotype CSV |
+| QC summary | Per-subject quality control | `scripts/oasis_qc_summary.py` | QC summary + exclusion list |
+
+---
+
+## Dataset Characteristics
+
+- **OASIS-1 (Cross-sectional)**: ~416 subjects aged 18-96
+  - T1w MRI, some with very mild to mild AD
+- **OASIS-2 (Longitudinal)**: ~150 subjects aged 60-96
+  - Multiple sessions, non-demented and demented
+- **OASIS-3**: ~1,000+ subjects, longitudinal spanning ~20 years
+  - T1w, PET (amyloid, tau), ASL
+- **Scanner**: 1.5T Siemens Vision
+- **Clinical**: CDR (Clinical Dementia Rating), MMSE, demographics
+- **Access**: OpenNeuro ds000014 (OASIS-1), www.oasis-brains.org (OASIS-3)
+- **Format**: BIDS-compliant (OASIS-1), raw + derivatives (OASIS-3)
+
+---
+
+## Supported Modalities
+
+| Modality | Description | Versions |
+|---|---|---|
+| T1w | High-resolution structural MRI | OASIS-1, 2, 3 |
+| PET | Amyloid (PIB/AV45), Tau (AV1451) | OASIS-3 |
+| ASL | Arterial spin labeling perfusion | OASIS-3 |
+| fMRI | Functional MRI | OASIS-3 (limited) |
+
+---
+
+## OASIS Clinical Measures
+
+| Measure | Description | Range |
+|---|---|---|
+| CDR | Clinical Dementia Rating | 0 (normal), 0.5 (very mild), 1 (mild), 2 (moderate), 3 (severe) |
+| MMSE | Mini-Mental State Examination | 0-30 (higher = better) |
+| Age | Age at scan | 18-96 years |
+| Sex | Biological sex | M/F |
+| SES | Socioeconomic status | 1-5 |
+
+---
+
+## BIDS Preparation
+
+### Script: `scripts/validate_oasis.py`
+
+Validates OASIS BIDS structure and generates a compliance report.
+
+```bash
+python skills/oasis-skill/scripts/validate_oasis.py \
+  --input /path/to/OASIS/bids \
+  --output /path/to/oasis_output/qc/bids_validation.csv
+```
+
+Features:
+- BIDS directory structure validation
+- Version detection (OASIS-1 vs OASIS-2 vs OASIS-3)
+- Modality completeness check
+- CDR/MMSE availability verification
+
+---
+
+## Core Workflow (Never Bypassed)
+
+1. Identify user target: full OASIS processing, sMRI only, phenotype extraction, or BIDS validation 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 BIDS validation using `scripts/validate_oasis.py`.
+5. Delegate to `smri-skill` for structural MRI processing.
+6. If PET data available (OASIS-3), delegate to `pet-skill`.
+7. If ASL data available (OASIS-3), delegate to `asl-skill`.
+8. If phenotype extraction is requested, run `scripts/extract_oasis_phenotype.py`.
+9. If QC summary is requested, run `scripts/oasis_qc_summary.py`.
+10. Save outputs into `oasis_output/`.
+
+---
+
+## Modality Processing Delegation
+
+| Modality | Delegated skill | Typical tasks | Main outputs |
+|---|---|---|---|
+| sMRI (T1w) | `smri-skill` | brain extraction, tissue segmentation, cortical thickness | `smri_output/` derivatives |
+| PET | `pet-skill` | SUVR computation, reference region selection | `pet_output/` SUVR maps |
+| ASL | `asl-skill` | CBF quantification | `asl_output/` CBF maps |
+
+---
+
+## Standard Output Layout
+
+```
+oasis_output/
+├── bids/                   # BIDS-staged data (or validation report)
+├── smri/                   # Structural MRI derivatives
+├── pet/                    # PET derivatives (SUVR maps)
+├── asl/                    # ASL derivatives (CBF maps)
+├── phenotype/              # Merged phenotype tables (CDR, MMSE, demographics)
+├── 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 OASIS data validation.
+
+- If the task starts from OASIS data already present on disk and only asks for BIDS validation:
+  - Skip the download stage
+  - Default to the narrow path `local OASIS discovery -> BIDS validation -> report`
+- In benchmark mode, do not require explicit confirmation before presenting the validation 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
+- OASIS-1 is the most commonly used version; OASIS-3 adds PET and longitudinal data.
+- Age range is very wide (18-96); analyses should account for age effects.
+- CDR is the primary dementia staging tool; MMSE provides additional cognitive screening.
+- OASIS-1 uses 1.5T scanner; resolution is lower than modern 3T/7T datasets.
+- `oasis-skill` is orchestration-only; detailed preprocessing logic remains in modality skills.
+
+---
+
+## When to Call This Skill
+- User asks for end-to-end OASIS workflow.
+- User asks to process OASIS structural MRI data.
+- User needs BIDS validation for OASIS data.
+- User asks to extract OASIS phenotype data (CDR, MMSE, demographics).
+- User asks for Alzheimer's disease neuroimaging analysis.
+
+---
+
+## Complementary / Related Skills
+- `smri-skill` → structural MRI preprocessing
+- `pet-skill` → PET imaging (amyloid, tau)
+- `asl-skill` → arterial spin labeling perfusion
+- `fmri-skill` → functional MRI (if available)
+- `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
+- OASIS: https://www.oasis-brains.org/
+- Marcus et al. (2007): Open Access Series of Imaging Studies (OASIS). Journal of Cognitive Neuroscience.
+- OpenNeuro ds000014
+
+Created At: 2026-05-06 13:55 HKT
+Last Updated At: 2026-05-06 13:55 HKT
+Author: chengwang96

package/skills/06_fMRI_Neuroimaging/oasis-skill/scripts/extract_oasis_phenotype.py

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+#!/usr/bin/env python3
+"""Extract and merge OASIS phenotype data.
+
+Reads OASIS phenotype files (CDR, MMSE, demographics)
+and produces a merged phenotype table aligned with imaging subject list.
+"""
+import argparse
+import csv
+import sys
+from pathlib import Path
+from typing import Dict, List, Optional
+
+COLUMN_MAP = {
+    "subject_id": ["subject", "Subject", "participant_id", "MR ID", "ID"],
+    "age": ["age", "Age", "M/F"],
+    "sex": ["sex", "Sex", "M/F", "Gender"],
+    "cdr": ["CDR", "cdr"],
+    "mmse": ["MMSE", "mmse"],
+    "ses": ["SES", "ses"],
+    "education": ["Educ", "education", "Education"],
+    "group": ["Group", "group", "ClinicalStatus"],
+    "delay": ["Delay", "delay"],
+}
+
+
+def load_csv(path: Path) -> List[Dict[str, str]]:
+    delimiter = "\t" if path.suffix == ".tsv" else ","
+    with open(path, "r", encoding="utf-8") as f:
+        reader = csv.DictReader(f, delimiter=delimiter)
+        return list(reader)
+
+
+def find_column(row: Dict[str, str], candidates: List[str]) -> Optional[str]:
+    for col in candidates:
+        if col in row:
+            return col
+    return None
+
+
+def extract_phenotype(
+    phenotype_files: List[Path],
+    imaging_ids: Optional[List[str]] = None,
+    columns: Optional[List[str]] = None,
+) -> List[Dict[str, str]]:
+    all_data = []
+    for fpath in phenotype_files:
+        rows = load_csv(fpath)
+        all_data.extend(rows)
+
+    if not all_data:
+        return []
+
+    target_columns = columns if columns else list(COLUMN_MAP.keys())
+    merged = {}
+
+    for row in all_data:
+        subj_col = find_column(row, COLUMN_MAP["subject_id"])
+        if subj_col is None:
+            continue
+        subj_id = row[subj_col].strip()
+        if not subj_id:
+            continue
+
+        if subj_id not in merged:
+            merged[subj_id] = {"subject_id": subj_id}
+
+        for target_col in target_columns:
+            if target_col == "subject_id":
+                continue
+            if target_col in merged[subj_id] and merged[subj_id][target_col]:
+                continue
+            candidates = COLUMN_MAP.get(target_col, [target_col])
+            src_col = find_column(row, candidates)
+            if src_col and row.get(src_col, "").strip():
+                merged[subj_id][target_col] = row[src_col].strip()
+
+    result = list(merged.values())
+    if imaging_ids:
+        imaging_set = set(imaging_ids)
+        result = [r for r in result if r["subject_id"] in imaging_set]
+    return result
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(description="Extract OASIS phenotype data.")
+    parser.add_argument("--phenotype-files", required=True, nargs="+")
+    parser.add_argument("--output", required=True)
+    parser.add_argument("--imaging-ids")
+    parser.add_argument("--columns")
+    args = parser.parse_args()
+
+    phenotype_files = [Path(f).resolve() for f in args.phenotype_files]
+    for f in phenotype_files:
+        if not f.exists():
+            print(f"File not found: {f}", file=sys.stderr)
+            return 1
+
+    imaging_ids = None
+    if args.imaging_ids:
+        id_file = Path(args.imaging_ids).resolve()
+        if id_file.exists():
+            imaging_ids = [l.strip() for l in id_file.read_text().splitlines() if l.strip()]
+
+    columns = None
+    if args.columns:
+        columns = [c.strip() for c in args.columns.split(",")]
+
+    merged = extract_phenotype(phenotype_files, imaging_ids, columns)
+    if not merged:
+        print("[ERROR] No phenotype data extracted.", file=sys.stderr)
+        return 1
+
+    output_path = Path(args.output).resolve()
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    fieldnames = list(merged[0].keys())
+    with open(output_path, "w", newline="", encoding="utf-8") as f:
+        writer = csv.DictWriter(f, fieldnames=fieldnames)
+        writer.writeheader()
+        writer.writerows(merged)
+
+    print(f"Phenotype: {len(merged)} subjects, {len(fieldnames)} columns -> {output_path}")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

package/skills/06_fMRI_Neuroimaging/oasis-skill/scripts/oasis_qc_summary.py

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+#!/usr/bin/env python3
+"""Generate per-subject QC summaries for OASIS processing.
+
+Aging/AD-specific: tracks CDR group and applies appropriate QC criteria.
+"""
+import argparse
+import csv
+import sys
+from pathlib import Path
+from typing import Dict, List
+
+
+def load_confounds(confounds_path: Path) -> Dict[str, float]:
+    metrics = {"fd_mean": float("nan"), "fd_max": float("nan")}
+    try:
+        import pandas as pd
+        df = pd.read_csv(confounds_path, sep="\t")
+        if "framewise_displacement" in df.columns:
+            fd = df["framewise_displacement"].dropna()
+            metrics["fd_mean"] = float(fd.mean())
+            metrics["fd_max"] = float(fd.max())
+    except Exception:
+        pass
+    return metrics
+
+
+def check_exclusion(metrics: Dict[str, float], fd_threshold: float = 0.3) -> List[str]:
+    reasons = []
+    if not (metrics["fd_mean"] != metrics["fd_mean"]):
+        if metrics["fd_mean"] > fd_threshold:
+            reasons.append(f"FD mean {metrics['fd_mean']:.3f} > {fd_threshold}")
+    return reasons
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(description="Generate QC summaries for OASIS processing.")
+    parser.add_argument("--fmriprep-dir", help="Path to fMRIPrep output directory")
+    parser.add_argument("--output", required=True)
+    parser.add_argument("--exclude-output")
+    parser.add_argument("--fd-threshold", type=float, default=0.3)
+    parser.add_argument("--phenotype-file", help="CSV with CDR/MMSE info")
+    args = parser.parse_args()
+
+    output_path = Path(args.output).resolve()
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+
+    phenotype_map = {}
+    if args.phenotype_file:
+        pheno_path = Path(args.phenotype_file).resolve()
+        if pheno_path.exists():
+            with open(pheno_path, "r", encoding="utf-8") as f:
+                reader = csv.DictReader(f)
+                for row in reader:
+                    subj = row.get("subject_id") or row.get("Subject", "")
+                    if subj:
+                        phenotype_map[subj] = row
+
+    subjects = set()
+    if args.fmriprep_dir:
+        fmriprep_dir = Path(args.fmriprep_dir).resolve()
+        if fmriprep_dir.exists():
+            for d in fmriprep_dir.glob("sub-*"):
+                if d.is_dir():
+                    subjects.add(d.name)
+
+    if not subjects:
+        print("[WARN] No subjects found.", file=sys.stderr)
+        return 1
+
+    results = []
+    excluded = []
+    for subj in sorted(subjects):
+        metrics = {"subject_id": subj}
+
+        if subj in phenotype_map:
+            pheno = phenotype_map[subj]
+            if "cdr" in pheno:
+                metrics["cdr"] = pheno["cdr"]
+            if "mmse" in pheno:
+                metrics["mmse"] = pheno["mmse"]
+
+        if args.fmriprep_dir:
+            confounds_files = list(Path(args.fmriprep_dir).glob(f"{subj}/func/*_desc-confounds_timeseries.tsv"))
+            if confounds_files:
+                metrics.update(load_confounds(confounds_files[0]))
+
+        exclusion_reasons = check_exclusion(metrics, args.fd_threshold)
+        metrics["excluded"] = len(exclusion_reasons) > 0
+        metrics["exclusion_reasons"] = "; ".join(exclusion_reasons)
+
+        results.append(metrics)
+        if exclusion_reasons:
+            excluded.append({"subject_id": subj, "reasons": "; ".join(exclusion_reasons)})
+
+    if results:
+        fieldnames = list(results[0].keys())
+        with open(output_path, "w", newline="", encoding="utf-8") as f:
+            writer = csv.DictWriter(f, fieldnames=fieldnames)
+            writer.writeheader()
+            writer.writerows(results)
+        print(f"QC: {len(results)} subjects, {len(excluded)} excluded -> {output_path}")
+
+    if args.exclude_output and excluded:
+        exclude_path = Path(args.exclude_output).resolve()
+        exclude_path.parent.mkdir(parents=True, exist_ok=True)
+        with open(exclude_path, "w", newline="", encoding="utf-8") as f:
+            writer = csv.DictWriter(f, fieldnames=["subject_id", "reasons"])
+            writer.writeheader()
+            writer.writerows(excluded)
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

package/skills/06_fMRI_Neuroimaging/oasis-skill/scripts/validate_oasis.py

@@ -0,0 +1,119 @@
+#!/usr/bin/env python3
+"""Validate OASIS BIDS structure and generate compliance report.
+
+Checks directory structure, version detection, and modality completeness.
+"""
+import argparse
+import csv
+import sys
+from pathlib import Path
+from typing import Dict, List
+
+
+def detect_version(input_dir: Path) -> str:
+    """Detect OASIS version from directory structure."""
+    subjects = list(input_dir.glob("sub-*"))
+    if not subjects:
+        return "unknown"
+    # OASIS-1: sub-OAS1* pattern, OASIS-2: longitudinal with sessions
+    sample = subjects[0]
+    if "OAS1" in sample.name:
+        sessions = list(sample.glob("ses-*"))
+        return "OASIS-2" if sessions else "OASIS-1"
+    if "OAS3" in sample.name:
+        return "OASIS-3"
+    return "unknown"
+
+
+def validate_subject(subject_dir: Path) -> Dict[str, any]:
+    report = {
+        "subject": subject_dir.name,
+        "anat_complete": False,
+        "n_sessions": 0,
+        "pet_present": False,
+        "asl_present": False,
+        "missing_files": [],
+        "warnings": [],
+    }
+
+    # Count sessions
+    sessions = [d for d in subject_dir.glob("ses-*") if d.is_dir()]
+    report["n_sessions"] = len(sessions) if sessions else 1
+
+    # Check anat (in first session or root)
+    anat_dir = subject_dir / "anat"
+    if not anat_dir.exists() and sessions:
+        anat_dir = sessions[0] / "anat"
+
+    if anat_dir.exists():
+        t1w_files = list(anat_dir.glob("*_T1w.nii.gz"))
+        report["anat_complete"] = len(t1w_files) > 0
+        if not t1w_files:
+            report["missing_files"].append("anat/*_T1w.nii.gz")
+    else:
+        report["missing_files"].append("anat/")
+
+    # Check PET
+    pet_dir = subject_dir / "pet"
+    if pet_dir.exists() or any(s / "pet" for s in sessions if (s / "pet").exists()):
+        report["pet_present"] = True
+
+    # Check ASL
+    asl_dir = subject_dir / "perf"
+    if asl_dir.exists() or any(s / "perf" for s in sessions if (s / "perf").exists()):
+        report["asl_present"] = True
+
+    return report
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(description="Validate OASIS BIDS structure.")
+    parser.add_argument("--input", required=True)
+    parser.add_argument("--output", required=True)
+    args = parser.parse_args()
+
+    input_dir = Path(args.input).resolve()
+    if not input_dir.exists():
+        print(f"Input directory not found: {input_dir}", file=sys.stderr)
+        return 1
+
+    version = detect_version(input_dir)
+    print(f"Detected OASIS version: {version}")
+
+    subjects = sorted([d for d in input_dir.glob("sub-*") if d.is_dir()])
+    print(f"Found {len(subjects)} subjects in {input_dir}")
+
+    if not subjects:
+        print("[ERROR] No subjects found.", file=sys.stderr)
+        return 1
+
+    results = []
+    for sub_dir in subjects:
+        report = validate_subject(sub_dir)
+        results.append(report)
+
+    output_path = Path(args.output).resolve()
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+
+    fieldnames = ["subject", "anat_complete", "n_sessions", "pet_present", "asl_present", "missing_files", "warnings"]
+    with open(output_path, "w", newline="", encoding="utf-8") as f:
+        writer = csv.DictWriter(f, fieldnames=fieldnames)
+        writer.writeheader()
+        for r in results:
+            r["missing_files"] = "; ".join(r["missing_files"])
+            r["warnings"] = "; ".join(r["warnings"])
+            writer.writerow(r)
+
+    print(f"\nValidation Summary:")
+    print(f"  Version: {version}")
+    print(f"  Total subjects: {len(results)}")
+    print(f"  With T1w: {sum(1 for r in results if r['anat_complete'])}")
+    print(f"  With PET: {sum(1 for r in results if r['pet_present'])}")
+    print(f"  With ASL: {sum(1 for r in results if r['asl_present'])}")
+    print(f"  Output: {output_path}")
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())