qsiprep-tool

Plan and orchestrate QSIPrep diffusion MRI preprocessing on BIDS datasets.

78|3|Updated Mar 25, 2026
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroClaw --skill qsiprep-tool
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: qsiprep-tool
Source: https://github.com/CUHK-AIM-Group/NeuroClaw/tree/main/skills/qsiprep-tool
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroClaw --skill qsiprep-tool

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill provides a NeuroClaw interface-layer wrapper for QSIPrep to plan, validate inputs, manage dependencies, and route execution through claw-shell, delivering reproducible DWI preprocessing workflows on BIDS datasets.

Core Features & Use Cases

  • Interface-layer wrapper around QSIPrep that checks installation (Docker/Singularity/conda) and triggers dependency planning.
  • Generates a deterministic execution plan with exact commands, resource estimates, and potential risks; requires explicit user confirmation before execution.
  • Validates inputs (BIDS layout, presence of DWI and fieldmaps when available) and produces derivatives + QC HTML reports.
  • Executes via claw-shell with robust logging and post-run verification through the harness-core framework.
  • Use cases include single-subject or multi-subject diffusion datasets, HPC or workstation deployments, and reproducible preprocessing for downstream diffusion modeling (DTI, DKI, CSDE, tractography).

Quick Start

Run the QSIPrep tool on a BIDS dataset by generating an execution plan, validating inputs, and awaiting explicit confirmation to execute.

Frequently Asked Questions about qsiprep-tool

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I preprocess diffusion MRI data in BIDS format reproducibly?

Diffusion MRI preprocessing on BIDS datasets is handled by generating a deterministic execution plan, validating inputs, and executing containerized workflows to deliver reproducible derivatives and QC HTML reports.

Does QSIPrep require Docker or Singularity to run DWI preprocessing?

QSIPrep DWI preprocessing checks for Docker, Singularity, or conda environments during planning, managing dependencies automatically and routing execution through a shell wrapper to ensure reproducible processing.

Can I review the exact commands before running diffusion MRI preprocessing?

Yes, diffusion MRI preprocessing generates a deterministic execution plan with exact commands, resource estimates, and potential risks, requiring explicit user confirmation before any execution begins.

What do I need to validate before running BIDS diffusion preprocessing?

BIDS diffusion preprocessing validates the dataset layout and checks for the presence of DWI files and fieldmaps when available, ensuring inputs meet requirements before generating an execution plan.

Is there a way to automate multi-subject diffusion MRI preprocessing on a workstation?

Multi-subject diffusion MRI preprocessing is supported through containerized execution and dependency management, enabling scalable workflows on both HPC clusters and local workstations with robust logging.

Why does my DWI preprocessing workflow need fieldmap validation?

DWI preprocessing validates fieldmaps to correct for magnetic field inhomogeneities, and the planning phase explicitly flags missing fieldmaps as a potential risk before you confirm execution.