qsiprep-tool

name	qsiprep-tool
description	Use this skill whenever the user wants to run QSIPrep (BIDS App) for diffusion MRI (DWI) preprocessing with best-practice workflows (topup/eddy, denoising/unringing options, susceptibility/motion correction, coregistration/normalization, QC reports) on BIDS datasets. This skill is the NeuroClaw interface-layer wrapper for QSIPrep: it checks installation (Docker/Singularity/conda), generates an execution plan with exact commands and resource estimates, waits for explicit confirmation, then routes all execution through claw-shell.
license	MIT License (NeuroClaw custom skill – freely modifiable within the project)
layer	base
skill_type	tool
dependencies	["claw-shell","bids-organizer"]

QSIPrep Tool (Interface Layer)

Overview

QSIPrep is a BIDS-App pipeline for diffusion MRI (DWI) preprocessing that emphasizes:

• Robust distortion/motion/eddy-current correction
• Interoperable derivatives for downstream modeling (DTI/DKI/CSD, tractography, connectome, etc.)
• Strong QC reporting (HTML)

This skill is the NeuroClaw interface-layer wrapper for QSIPrep and strictly follows the NeuroClaw safety pattern:

1. Check whether QSIPrep is available (preferred: Docker/Singularity image; alternative: conda).
2. If missing → invoke dependency-planner to produce an installation plan.
3. Verify inputs (must be BIDS-compliant; detect DWI + fieldmaps/reverse-PE b0 if present).
4. Generate a clear numbered plan with exact commands, runtime/resource estimates, and risks.
5. Wait for explicit user confirmation (“YES” / “execute” / “proceed”).
6. On confirmation → delegate all commands to claw-shell.
7. Summarize outputs (derivatives paths + QC report location) and suggest next steps.

Research use only.

---

What QSIPrep Typically Does (High-Level)

• Validates BIDS layout (or skips if requested)
• Creates brain mask(s)
• Denoising (optional), Gibbs unringing (optional)
• Susceptibility distortion correction (e.g., reverse phase-encoded b0 via topup-style approach)
• Eddy-current + motion correction (FSL eddy family behavior within containerized workflow)
• Gradient/bvec handling (rotation after motion correction)
• Coregistration to anatomical (and optionally standard space outputs)
• Produces derivatives + QC HTML reports

---

Quick Reference

Task	Recommended Approach	Typical Output
Standard DWI preprocessing	QSIPrep BIDS-App participant	derivatives/qsiprep/sub-*/dwi/*preproc_dwi.nii.gz
Multi-subject run	--participant-label sub-001 sub-002 ...	per-subject derivatives
HPC / cluster	Singularity .sif execution	same derivatives
QC	Default QSIPrep reports	derivatives/qsiprep/sub-*/figures/*.html

Typical runtime (very data-dependent): ~0.5–4+ hours per subject.

---

Installation (Handled by dependency-planner)

Preferred: Docker (workstations) or Singularity/Apptainer (HPC).

Ask dependency-planner for one of:

• “Install Docker and pull latest QSIPrep image”
• “Install Apptainer/Singularity and pull QSIPrep .sif”
• “Install QSIPrep via conda (not recommended unless container is unavailable)”

Verification examples:

docker --version
docker image ls | grep -i qsiprep
# or
apptainer --version
apptainer exec qsiprep.sif qsiprep --version

FreeSurfer license: QSIPrep often requires a FreeSurfer license file.

• Usually passed with: --fs-license-file /path/to/license.txt
• This skill will request it if not provided.

---

Common Command Templates (Executed via claw-shell)

A) Docker (Recommended on workstations)

# Inputs:
BIDS_DIR=/data/bids
OUT_DIR=/data/derivatives
WORK_DIR=/data/work/qsiprep
FS_LICENSE=/data/license.txt

mkdir -p "$OUT_DIR" "$WORK_DIR"

docker run --rm -t \
  -v "$BIDS_DIR":/data:ro \
  -v "$OUT_DIR":/out \
  -v "$WORK_DIR":/work \
  -v "$FS_LICENSE":/opt/freesurfer/license.txt:ro \
  pennbbl/qsiprep:latest \
  /data /out participant \
  --participant-label sub-001 \
  --work-dir /work \
  --fs-license-file /opt/freesurfer/license.txt \
  --nthreads 16 --omp-nthreads 8 --mem-mb 64000

B) Singularity / Apptainer (Recommended on HPC)

BIDS_DIR=/data/bids
OUT_DIR=/data/derivatives
WORK_DIR=/data/work/qsiprep
FS_LICENSE=/data/license.txt
IMG=/images/qsiprep.sif

mkdir -p "$OUT_DIR" "$WORK_DIR"

apptainer run --cleanenv \
  -B "$BIDS_DIR":/data:ro \
  -B "$OUT_DIR":/out \
  -B "$WORK_DIR":/work \
  -B "$FS_LICENSE":/opt/freesurfer/license.txt:ro \
  "$IMG" \
  /data /out participant \
  --participant-label sub-001 \
  --work-dir /work \
  --fs-license-file /opt/freesurfer/license.txt \
  --nthreads 16 --omp-nthreads 8 --mem-mb 64000

Notes:

• Image name (pennbbl/qsiprep:latest) should be verified by dependency-planner against the latest official docs/releases.
• Some flags vary by QSIPrep version; this skill will always generate commands after checking installed version.

---

NeuroClaw recommended wrapper script (Reference): qsiprep_wrapper.py

This wrapper only builds and prints a plan; actual execution must be routed through claw-shell by the calling skill.

# qsiprep_wrapper.py (reference template)
import argparse
from pathlib import Path
from datetime import datetime

def build_qsiprep_cmd(engine, bids_dir, out_dir, work_dir, participant_labels, fs_license, img):
    labels = " ".join(participant_labels) if participant_labels else ""
    if engine == "docker":
        cmd = f"""
mkdir -p "{out_dir}" "{work_dir}"
docker run --rm -t \
  -v "{bids_dir}":/data:ro \
  -v "{out_dir}":/out \
  -v "{work_dir}":/work \
  -v "{fs_license}":/opt/freesurfer/license.txt:ro \
  {img} \
  /data /out participant \
  {"--participant-label " + labels if labels else ""} \
  --work-dir /work \
  --fs-license-file /opt/freesurfer/license.txt
""".strip()
    else:
        cmd = f"""
mkdir -p "{out_dir}" "{work_dir}"
apptainer run --cleanenv \
  -B "{bids_dir}":/data:ro \
  -B "{out_dir}":/out \
  -B "{work_dir}":/work \
  -B "{fs_license}":/opt/freesurfer/license.txt:ro \
  "{img}" \
  /data /out participant \
  {"--participant-label " + labels if labels else ""} \
  --work-dir /work \
  --fs-license-file /opt/freesurfer/license.txt
""".strip()
    return cmd

if __name__ == "__main__":
    p = argparse.ArgumentParser()
    p.add_argument("--engine", choices=["docker", "apptainer"], required=True)
    p.add_argument("--bids-dir", required=True)
    p.add_argument("--out-dir", required=True)
    p.add_argument("--work-dir", required=True)
    p.add_argument("--fs-license", required=True)
    p.add_argument("--img", required=True, help="Docker image (e.g., pennbbl/qsiprep:latest) or .sif path")
    p.add_argument("--participants", nargs="*", default=None)
    args = p.parse_args()

    cmd = build_qsiprep_cmd(
        engine=args.engine,
        bids_dir=Path(args.bids_dir).resolve(),
        out_dir=Path(args.out_dir).resolve(),
        work_dir=Path(args.work_dir).resolve(),
        participant_labels=args.participants,
        fs_license=Path(args.fs_license).resolve(),
        img=args.img
    )

    tag = f"qsiprep_{datetime.now().strftime('%Y%m%d_%H%M%S')}"
    print("Execution plan (delegate to claw-shell):")
    print(cmd)
    print("\nLog tag suggestion:", tag)

---

Important Notes & Limitations

• BIDS input is strongly recommended. If you only have raw NIfTI/DICOM, use bids-organizer (and dcm2nii) first.
• QSIPrep benefits a lot from having reverse phase-encoded b0 images (AP/PA) or valid fieldmaps; otherwise distortion correction may be limited.
• Ensure adequate resources:
  • RAM commonly 16–64 GB
  • Disk: work directory can be large (tens of GB)
• All execution must go through claw-shell due to long runtime and logging requirements.
• This skill does not replace downstream modeling (DTI/CSD/NODDI). After preprocessing, delegate to:
  • dipy-tool for Python-based metrics/ROI features
  • MRtrix/FSL-based workflows (future tool skills) for tractography/connectomes

---

When to Call This Skill

• User requests “run QSIPrep”, “preprocess DWI with QSIPrep”, “BIDS diffusion preprocessing”, “topup/eddy style pipeline with QC reports”.
• Before any quantitative diffusion features (FA/MD/tractometry/connectome) are extracted.

Post-Execution Verification (Harness Integration)

After QSIPrep completes, this skill automatically invokes harness-core's VerificationRunner to validate diffusion preprocessing outputs:

Integrated verification checks:

from skills.harness_core import VerificationRunner, AuditLogger
import nibabel as nib
import numpy as np
from pathlib import Path

verifier = VerificationRunner(task_type="qsiprep_diffusion_preprocessing")

# 1. Preprocessed DWI files exist
verifier.add_check("preprocessed_dwi_exists",
    checker=lambda: verify_preprocessed_dwi_files(output_dir),
    severity="error"
)

# 2. Brain mask generated
verifier.add_check("brain_mask_generated",
    checker=lambda: verify_brain_mask_exists(output_dir),
    severity="error"
)

# 3. DWI data shape consistent and reasonable
verifier.add_check("dwi_shape_consistency",
    checker=lambda: verify_dwi_shape(output_dir),
    severity="error"
)

# 4. No NaN/Inf in preprocessed DWI
verifier.add_check("dwi_data_integrity",
    checker=lambda: verify_dwi_no_nan_inf(output_dir),
    severity="error"
)

# 5. Gradient table preserved and reasonable
verifier.add_check("gradient_table",
    checker=lambda: verify_bval_bvec_files(output_dir),
    severity="warning"
)

# 6. Motion/susceptibility distortion corrections applied
verifier.add_check("preprocessing_applied",
    checker=lambda: verify_preprocessing_flags(output_dir),
    severity="warning"
)

# 7. Diffusion metrics (FA/MD) computable from output
verifier.add_check("diffusion_metric_bounds",
    checker=lambda: verify_fa_md_bounds(output_dir),
    severity="warning"
)

# 8. QC reports generated
verifier.add_check("qc_reports",
    checker=lambda: verify_qc_html_reports(output_dir),
    severity="warning"
)

report = verifier.run(output_dir)

# Log verification results
logger = AuditLogger(log_file=f"{output_dir}/qsiprep_verification.jsonl")
logger.log_validation(
    task_name="qsiprep_diffusion_preprocessing",
    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"QSIPrep verification failed: {report.summary}")

Output files generated:

• {output_dir}/qsiprep_verification.jsonl — structured audit log
• {output_dir}/.qsiprep_verification_timestamp — completion marker

Complementary / Related Skills

• dependency-planner → install Docker/Apptainer + QSIPrep image
• docker-env-manager → safe Docker operations (pull/run/prune) when needed
• claw-shell → mandatory safe execution layer
• harness-core → automated verification and audit logging

---

Reference

• QSIPrep documentation and BIDS App usage (official docs; version-dependent)
• NeuroClaw interface-layer pattern aligned with fmriprep-tool and hcppipeline-tool

Created At: 2026-03-26 00:45 HKT Last Updated At: 2026-04-05 02:01 HKT Author: chengwang96