@brainpilot/skills 0.0.6 → 0.0.7

package/skills/06_fMRI_Neuroimaging/abcd-skill/scripts/abcd_qc_summary.py

@@ -0,0 +1,449 @@
+#!/usr/bin/env python3
+"""Generate per-subject QC summaries and exclusion lists for ABCD Study.
+
+Combines fMRIPrep confounds, FreeSurfer recon-all metrics, and ABCD native
+QC flags to produce a unified QC report with configurable exclusion criteria.
+"""
+import argparse
+import json
+import sys
+from pathlib import Path
+from typing import Dict, List, Optional, Set, Tuple
+
+try:
+    import pandas as pd
+except ImportError:
+    print("Error: pandas is required. Install with: pip install pandas", file=sys.stderr)
+    sys.exit(1)
+
+
+def detect_delimiter(file_path: Path) -> str:
+    """Detect whether file uses tab or comma delimiter."""
+    with open(file_path, "r", encoding="utf-8") as f:
+        first_line = f.readline()
+    if "\t" in first_line:
+        return "\t"
+    return ","
+
+
+def collect_fmriprep_qc(fmriprep_dir: Path) -> Dict[str, Dict[str, float]]:
+    """Collect QC metrics from fMRIPrep outputs.
+
+    Reads confounds TSV files to extract framewise displacement (FD) and DVARS.
+
+    Returns:
+        Dict mapping subject_id -> {mean_fd, max_fd, mean_dvars, n_volumes}
+    """
+    qc = {}
+
+    # Look for confounds files in fMRIPrep output structure
+    confounds_patterns = [
+        "**/desc-confounds_timeseries.tsv",
+        "**/*_desc-confounds_timeseries.tsv",
+        "**/confounds.tsv",
+    ]
+
+    confounds_files = []
+    for pattern in confounds_patterns:
+        confounds_files.extend(fmriprep_dir.rglob(pattern))
+
+    for confounds_file in confounds_files:
+        # Extract subject ID from path
+        subject_id = None
+        parts = confounds_file.parts
+        for part in parts:
+            if part.startswith("sub-"):
+                subject_id = part
+                break
+
+        if not subject_id:
+            continue
+
+        delimiter = detect_delimiter(confounds_file)
+        try:
+            df = pd.read_csv(confounds_file, sep=delimiter, low_memory=False)
+        except Exception as e:
+            print(f"[WARN] Failed to read {confounds_file}: {e}", file=sys.stderr)
+            continue
+
+        # Extract FD
+        fd_col = None
+        for col_name in ["framewise_displacement", "fd", "FD"]:
+            if col_name in df.columns:
+                fd_col = col_name
+                break
+
+        # Extract DVARS
+        dvars_col = None
+        for col_name in ["dvars", "DVARS", "std_dvars"]:
+            if col_name in df.columns:
+                dvars_col = col_name
+                break
+
+        metrics = {"n_volumes": len(df)}
+
+        if fd_col:
+            fd_values = pd.to_numeric(df[fd_col], errors="coerce").dropna()
+            if len(fd_values) > 0:
+                metrics["mean_fd"] = float(fd_values.mean())
+                metrics["max_fd"] = float(fd_values.max())
+                metrics["median_fd"] = float(fd_values.median())
+            else:
+                metrics["mean_fd"] = 0.0
+                metrics["max_fd"] = 0.0
+                metrics["median_fd"] = 0.0
+
+        if dvars_col:
+            dvars_values = pd.to_numeric(df[dvars_col], errors="coerce").dropna()
+            if len(dvars_values) > 0:
+                metrics["mean_dvars"] = float(dvars_values.mean())
+            else:
+                metrics["mean_dvars"] = 0.0
+
+        # Aggregate per-subject (take worst/best across runs)
+        if subject_id in qc:
+            existing = qc[subject_id]
+            existing["mean_fd"] = max(existing.get("mean_fd", 0), metrics.get("mean_fd", 0))
+            existing["max_fd"] = max(existing.get("max_fd", 0), metrics.get("max_fd", 0))
+            existing["n_volumes"] = existing.get("n_volumes", 0) + metrics.get("n_volumes", 0)
+        else:
+            qc[subject_id] = metrics
+
+    return qc
+
+
+def collect_freesurfer_qc(freesurfer_dir: Path) -> Dict[str, Dict[str, float]]:
+    """Collect QC metrics from FreeSurfer recon-all outputs.
+
+    Reads the scripts/recon-all.log to check for completion, and optionally
+    the aseg.stats for volume metrics.
+
+    Returns:
+        Dict mapping subject_id -> {completed, total_brain_volume, estimated_total_intracranial_volume}
+    """
+    qc = {}
+
+    # Check for recon-all completion
+    for subject_dir in sorted(freesurfer_dir.rglob("sub-*")):
+        if not subject_dir.is_dir():
+            continue
+
+        subject_id = subject_dir.name
+        if subject_id.startswith("sub-"):
+            pass
+        else:
+            # Check parent dirs
+            for part in subject_dir.parts:
+                if part.startswith("sub-"):
+                    subject_id = part
+                    break
+
+        # Check for recon-all log
+        recon_log = None
+        for candidate in [
+            subject_dir / "scripts" / "recon-all.log",
+            subject_dir / "ses-*" / "scripts" / "recon-all.log",
+        ]:
+            matches = list(freesurfer_dir.rglob(f"{subject_id}/**/recon-all.log"))
+            if matches:
+                recon_log = matches[0]
+                break
+
+        completed = False
+        if recon_log and recon_log.exists():
+            try:
+                with open(recon_log, "r", encoding="utf-8", errors="ignore") as f:
+                    content = f.read()
+                    completed = "finished without error" in content.lower() or "recon-all -done" in content.lower()
+            except Exception:
+                pass
+
+        # Try to read aseg.stats for volume metrics
+        aseg_matches = list(freesurfer_dir.rglob(f"{subject_id}**/aseg.stats"))
+        total_brain_vol = None
+        etiv = None
+
+        if aseg_matches:
+            aseg_file = aseg_matches[0]
+            try:
+                with open(aseg_file, "r", encoding="utf-8", errors="ignore") as f:
+                    for line in f:
+                        if "EstimatedTotalIntraCranialVol" in line:
+                            parts = line.split()
+                            if len(parts) >= 4:
+                                try:
+                                    etiv = float(parts[3])
+                                except ValueError:
+                                    pass
+                        elif "BrainSegVol" in line and "Not" not in line:
+                            parts = line.split()
+                            if len(parts) >= 4:
+                                try:
+                                    total_brain_vol = float(parts[3])
+                                except ValueError:
+                                    pass
+            except Exception:
+                pass
+
+        metrics = {"completed": completed}
+        if total_brain_vol is not None:
+            metrics["total_brain_volume"] = total_brain_vol
+        if etiv is not None:
+            metrics["estimated_total_intracranial_volume"] = etiv
+
+        qc[subject_id] = metrics
+
+    return qc
+
+
+def collect_abcd_native_qc(raw_qc_file: Path) -> Dict[str, Dict[str, float]]:
+    """Collect ABCD native QC flags (e.g., imgincl01).
+
+    Returns:
+        Dict mapping subject_id -> {include_t1, include_dti, include_rsfmri, etc.}
+    """
+    qc = {}
+    if not raw_qc_file.exists():
+        return qc
+
+    delimiter = detect_delimiter(raw_qc_file)
+    try:
+        df = pd.read_csv(raw_qc_file, sep=delimiter, low_memory=False)
+    except Exception as e:
+        print(f"[WARN] Failed to read {raw_qc_file}: {e}", file=sys.stderr)
+        return qc
+
+    # Standardize ID column
+    id_col = None
+    for col_name in ["src_subject_id", "SUBJECTKEY", "subject_id"]:
+        if col_name in df.columns:
+            id_col = col_name
+            break
+
+    if not id_col:
+        print(f"[WARN] No subject ID column found in {raw_qc_file}", file=sys.stderr)
+        return qc
+
+    # Look for include flags
+    include_cols = [c for c in df.columns if c.startswith("include_") or c.startswith("imgincl")]
+    event_col = "eventname" if "eventname" in df.columns else None
+
+    for _, row in df.iterrows():
+        sid = str(row[id_col]).strip()
+        event = str(row[event_col]).strip() if event_col else ""
+
+        # Use baseline by default
+        if event and "baseline" not in event.lower() and "1year" not in event.lower():
+            continue
+
+        metrics = {}
+        for col in include_cols:
+            val = row.get(col)
+            if pd.notna(val):
+                try:
+                    metrics[col] = int(val)
+                except (ValueError, TypeError):
+                    metrics[col] = val
+
+        if sid in qc:
+            # Update only if current entry is empty
+            if not qc[sid]:
+                qc[sid] = metrics
+        else:
+            qc[sid] = metrics
+
+    return qc
+
+
+def generate_qc_summary(
+    fmriprep_qc: Dict[str, Dict[str, float]],
+    freesurfer_qc: Dict[str, Dict[str, float]],
+    abcd_qc: Dict[str, Dict[str, float]],
+    fd_threshold: float = 0.3,
+    max_fd_threshold: float = 5.0,
+    coverage_threshold: float = 0.8,
+) -> Tuple["pd.DataFrame", List[str]]:
+    """Generate QC summary DataFrame and exclusion list.
+
+    Args:
+        fmriprep_qc: fMRIPrep QC metrics.
+        freesurfer_qc: FreeSurfer QC metrics.
+        abcd_qc: ABCD native QC flags.
+        fd_threshold: Mean FD threshold for exclusion.
+        max_fd_threshold: Max FD threshold for exclusion.
+        coverage_threshold: Minimum fraction of usable volumes.
+
+    Returns:
+        Tuple of (QC summary DataFrame, list of excluded subject IDs).
+    """
+    # Collect all unique subject IDs
+    all_subjects = set()
+    all_subjects.update(fmriprep_qc.keys())
+    all_subjects.update(freesurfer_qc.keys())
+    all_subjects.update(abcd_qc.keys())
+
+    rows = []
+    excluded = []
+
+    for sub_id in sorted(all_subjects):
+        row = {"subject_id": sub_id}
+        exclude_reasons = []
+
+        # fMRIPrep metrics
+        fp = fmriprep_qc.get(sub_id, {})
+        row["mean_fd"] = fp.get("mean_fd", None)
+        row["max_fd"] = fp.get("max_fd", None)
+        row["median_fd"] = fp.get("median_fd", None)
+        row["mean_dvars"] = fp.get("mean_dvars", None)
+        row["n_volumes"] = fp.get("n_volumes", None)
+
+        # FreeSurfer metrics
+        fs = freesurfer_qc.get(sub_id, {})
+        row["fs_completed"] = fs.get("completed", None)
+        row["total_brain_volume"] = fs.get("total_brain_volume", None)
+        row["etiv"] = fs.get("estimated_total_intracranial_volume", None)
+
+        # ABCD native QC
+        abcd = abcd_qc.get(sub_id, {})
+        for key, val in abcd.items():
+            row[f"abcd_{key}"] = val
+
+        # Apply exclusion criteria
+        if row["mean_fd"] is not None and row["mean_fd"] > fd_threshold:
+            exclude_reasons.append(f"mean_fd={row['mean_fd']:.3f}>{fd_threshold}")
+
+        if row["max_fd"] is not None and row["max_fd"] > max_fd_threshold:
+            exclude_reasons.append(f"max_fd={row['max_fd']:.3f}>{max_fd_threshold}")
+
+        if row["fs_completed"] is False:
+            exclude_reasons.append("FreeSurfer recon-all incomplete")
+
+        # Check ABCD include flags
+        for key in ["include_t1", "include_dti", "include_rsfmri", "include_tfmri"]:
+            abcd_key = f"abcd_{key}"
+            if abcd_key in row and row[abcd_key] == 0:
+                exclude_reasons.append(f"ABCD {key}=0")
+
+        row["exclude"] = len(exclude_reasons) > 0
+        row["exclude_reasons"] = "; ".join(exclude_reasons) if exclude_reasons else ""
+
+        if exclude_reasons:
+            excluded.append(sub_id)
+
+        rows.append(row)
+
+    df = pd.DataFrame(rows)
+    return df, excluded
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(
+        description="Generate per-subject QC summaries and exclusion lists for ABCD Study."
+    )
+    parser.add_argument(
+        "--fmriprep-dir",
+        help="Path to fMRIPrep output directory",
+    )
+    parser.add_argument(
+        "--freesurfer-dir",
+        help="Path to FreeSurfer output directory",
+    )
+    parser.add_argument(
+        "--raw-qc",
+        help="Path to ABCD native QC file (e.g., abcd_imgincl01.csv)",
+    )
+    parser.add_argument(
+        "--output",
+        required=True,
+        help="Output path for QC summary CSV",
+    )
+    parser.add_argument(
+        "--exclude-output",
+        help="Output path for exclusion list CSV",
+    )
+    parser.add_argument(
+        "--fd-threshold",
+        type=float,
+        default=0.3,
+        help="Mean framewise displacement threshold for exclusion (default: 0.3)",
+    )
+    parser.add_argument(
+        "--max-fd-threshold",
+        type=float,
+        default=5.0,
+        help="Maximum framewise displacement threshold for exclusion (default: 5.0)",
+    )
+    parser.add_argument(
+        "--coverage-threshold",
+        type=float,
+        default=0.8,
+        help="Minimum fraction of usable volumes (default: 0.8)",
+    )
+    args = parser.parse_args()
+
+    # Collect QC metrics
+    fmriprep_qc = {}
+    freesurfer_qc = {}
+    abcd_qc = {}
+
+    if args.fmriprep_dir:
+        fp_dir = Path(args.fmriprep_dir).resolve()
+        if fp_dir.exists():
+            print(f"Collecting fMRIPrep QC from {fp_dir}...")
+            fmriprep_qc = collect_fmriprep_qc(fp_dir)
+            print(f"  Found {len(fmriprep_qc)} subjects")
+        else:
+            print(f"[WARN] fMRIPrep directory not found: {fp_dir}")
+
+    if args.freesurfer_dir:
+        fs_dir = Path(args.freesurfer_dir).resolve()
+        if fs_dir.exists():
+            print(f"Collecting FreeSurfer QC from {fs_dir}...")
+            freesurfer_qc = collect_freesurfer_qc(fs_dir)
+            print(f"  Found {len(freesurfer_qc)} subjects")
+        else:
+            print(f"[WARN] FreeSurfer directory not found: {fs_dir}")
+
+    if args.raw_qc:
+        raw_qc_path = Path(args.raw_qc).resolve()
+        if raw_qc_path.exists():
+            print(f"Collecting ABCD native QC from {raw_qc_path}...")
+            abcd_qc = collect_abcd_native_qc(raw_qc_path)
+            print(f"  Found {len(abcd_qc)} subjects")
+        else:
+            print(f"[WARN] ABCD QC file not found: {raw_qc_path}")
+
+    if not fmriprep_qc and not freesurfer_qc and not abcd_qc:
+        print("[ERROR] No QC data collected. Check input paths.", file=sys.stderr)
+        return 1
+
+    # Generate summary
+    summary_df, excluded = generate_qc_summary(
+        fmriprep_qc=fmriprep_qc,
+        freesurfer_qc=freesurfer_qc,
+        abcd_qc=abcd_qc,
+        fd_threshold=args.fd_threshold,
+        max_fd_threshold=args.max_fd_threshold,
+        coverage_threshold=args.coverage_threshold,
+    )
+
+    # Write QC summary
+    output_path = Path(args.output).resolve()
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    summary_df.to_csv(output_path, index=False)
+    print(f"\nQC Summary: {len(summary_df)} subjects -> {output_path}")
+    print(f"  Excluded: {len(excluded)} / {len(summary_df)} ({100*len(excluded)/max(len(summary_df),1):.1f}%)")
+
+    # Write exclusion list
+    if args.exclude_output:
+        exclude_path = Path(args.exclude_output).resolve()
+        exclude_path.parent.mkdir(parents=True, exist_ok=True)
+        exclude_df = summary_df[summary_df["exclude"] == True][["subject_id", "exclude_reasons"]]
+        exclude_df.to_csv(exclude_path, index=False)
+        print(f"  Exclusion list: {exclude_path}")
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())