fmri-skill

fMRI Skill (Modality Layer)

Overview

fmri-skill is the NeuroClaw modality-layer interface skill responsible for all fMRI data processing and analysis tasks.

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: fmriprep-tool, hcppipeline-tool, conn-tool, fsl-tool, bids-organizer, and claw-shell.

Core workflow (never bypassed):

1. Identify input data (BIDS dataset or preprocessed BOLD files).
2. Generate a numbered execution plan that clearly states 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 (fmri_output/).

Benchmark-Facing Default Mainline

For benchmark-style prompts, choose the narrowest task-faithful fMRI route first and do not widen into unrelated branches just because multiple downstream tools are available.

• If the prompt is task fMRI or mentions events, contrasts, design matrices, conditions, first-level, second-level, FEAT, cope, or z-stat maps:
  • Default to BIDS -> fMRIPrep -> first-level GLM -> group-level GLM if requested.
  • Keep the answer on the GLM/statistical path.
  • Do not introduce resting-state connectivity, CONN, PPI, DCM, or EEG branches unless the prompt explicitly asks for them.
• If the prompt is resting-state or asks for ROI time series / connectivity:
  • Default to BIDS -> fMRIPrep -> XCP-D or ROI/connectivity extraction.
  • Do not introduce task-GLM steps unless the prompt explicitly asks for task analysis.
  • If the prompt is an ADNI-like or other raw-data resting-state benchmark, keep the answer on the narrow mainline raw data -> minimal BIDS organization -> fMRIPrep -> resting-state ROI/connectivity outputs.
  • Do not expand the primary solution into EEG branches, CONN, effective connectivity, or broad multimodal orchestration unless the prompt explicitly asks for those branches.
• If required task-fMRI inputs such as events.tsv, contrasts, or condition timing are missing:
  • State Missing required input explicitly.
  • Do not silently switch the task into a resting-state pipeline.
• Do not delegate to unrelated modality skills such as EEG for fMRI-only tasks.
• In benchmark mode, do not make environment creation, broad project scaffolding, or long installation/setup sections the center of the answer when the task is asking for the executable imaging mainline.