dmt-har-med-skill

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Use this skill whenever the user wants an end-to-end workflow for the DMT-HAR-MED dataset (ds006644), including download, BIDS organization, and processing of rs-fMRI data from a psychedelic intervention study. Triggers include: 'DMT-HAR-MED', 'DMT HAR MED', 'ds006644', 'process DMT data', 'psychedelic fMRI', or any request to run the DMT-HAR-MED pipeline. This is the NeuroClaw dataset-orchestration layer for DMT-HAR-MED.

BioTender-max By BioTender-max schedule Updated 5/30/2026
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name: dmt-har-med-skill description: "Use this skill whenever the user wants an end-to-end workflow for the DMT-HAR-MED dataset (ds006644), including download, BIDS organization, and processing of rs-fMRI data from a psychedelic intervention study. Triggers include: 'DMT-HAR-MED', 'DMT HAR MED', 'ds006644', 'process DMT data', 'psychedelic fMRI', or any request to run the DMT-HAR-MED pipeline. This is the NeuroClaw dataset-orchestration layer for DMT-HAR-MED." license: MIT License (NeuroClaw custom skill - freely modifiable within the project) layer: subagent skill_type: dataset dependencies: - fmri-skill - bids-organizer - claw-shell

DMT-HAR-MED Skill (Dataset-Orchestration Layer)

Overview

dmt-har-med-skill is the NeuroClaw orchestration skill for the DMT-HAR-MED dataset (OpenNeuro ds006644).

DMT-HAR-MED contains rs-fMRI data from 40 participants in a psychedelic intervention study investigating the effects of N,N-Dimethyltryptamine (DMT) on brain function. The dataset includes multiple experimental conditions (DMT, placebo) and behavioral/physiological measurements.

It coordinates a fixed three-phase workflow:

  1. Download DMT-HAR-MED data from OpenNeuro.
  2. Prepare and validate BIDS-style data organization.
  3. Delegate fMRI processing to fmri-skill.

It also provides phenotype extraction and QC integration paths:

  • Extract DMT-HAR-MED phenotype data (intervention conditions, behavioral measures).
  • Generate per-subject QC summaries with exclusion lists.

This skill follows NeuroClaw hierarchy:

  • Defines WHAT to do, not low-level implementation details.
  • Does not execute direct shell commands itself.
  • Delegates all execution via claw-shell to base/tool skills.

Research use only.

Download Stage (Mandatory First Step)

Source

DMT-HAR-MED data is available on OpenNeuro:

Supported DMT-HAR-MED Data Packages

  • Imaging data: rs-fMRI (NIfTI format)
  • Phenotype data: intervention conditions, behavioral and physiological measurements
  • Participants: 40 participants with psychedelic intervention

Delegation Rules for Download

  • Environment/setup checks: dependency-planner + conda-env-manager
  • OpenNeuro dataset download: claw-shell (via openneuro CLI or datalad)
  • Optional raw-data organization to BIDS-style staging: bids-organizer

Download Inputs to Confirm in Plan

  • Subject list scope (full or custom subset)
  • Destination directory with sufficient disk space

Core Workflow (Never Bypassed)

  1. Identify user target: download, BIDS staging, or full preprocessing.
  2. Generate a numbered plan with tools, outputs, runtime, storage, and risks.
  3. Wait for explicit confirmation (YES / execute / proceed).
  4. On confirmation, run download stage first (if needed).
  5. After download success, verify/prepare BIDS staging using scripts/reorganize_dmt_har_med.py.
  6. Delegate to fmri-skill for rs-fMRI processing.
  7. If phenotype extraction is requested, run scripts/extract_dmt_har_med_phenotype.py.
  8. If QC summary is requested, run scripts/dmt_har_med_qc_summary.py.
  9. Save outputs into a DMT-HAR-MED-centered structure under dmt_har_med_output/.

BIDS Preparation

Script: scripts/reorganize_dmt_har_med.py

Verifies and optionally reorganizes DMT-HAR-MED data to BIDS-compliant layout.

python skills/dmt-har-med-skill/scripts/reorganize_dmt_har_med.py \
  --input /path/to/dmt_har_med_raw \
  --output /path/to/dmt_har_med_bids

Features:

  • BIDS validation and verification
  • Subject ID normalization
  • Modality routing: rs-fMRI
  • dataset_description.json and participants.tsv generation
  • Dry-run mode: --dry-run to preview

Phenotype Extraction

Script: scripts/extract_dmt_har_med_phenotype.py

python skills/dmt-har-med-skill/scripts/extract_dmt_har_med_phenotype.py \
  --phenotype-dir /path/to/dmt_har_med_raw/phenotype \
  --output /path/to/dmt_har_med_output/phenotype/merged_phenotype.csv \
  --imaging-ids /path/to/dmt_har_med_output/bids/participants.tsv

QC Integration

Script: scripts/dmt_har_med_qc_summary.py

python skills/dmt-har-med-skill/scripts/dmt_har_med_qc_summary.py \
  --fmriprep-dir /path/to/dmt_har_med_output/fmriprep \
  --output /path/to/dmt_har_med_output/qc/qc_summary.csv \
  --exclude-output /path/to/dmt_har_med_output/qc/exclude_list.csv \
  --fd-threshold 0.3

Recommended Output Layout

All assets should be organized under ./dmt_har_med_output/:

  • dmt_har_med_output/raw/ (downloaded original files)
  • dmt_har_med_output/bids/ (BIDS data)
  • dmt_har_med_output/fmri/ (links or copies from fmri_output/)
  • dmt_har_med_output/phenotype/ (merged phenotype tables)
  • dmt_har_med_output/qc/ (QC summaries and exclusion lists)
  • dmt_har_med_output/logs/ (download + orchestration logs)

Benchmark Adapter Guidance

For benchmark-style prompts, do not force the full download -> staging -> multimodal processing orchestration when the task is only asking for local DMT-HAR-MED data staging or organization.

  • If the task starts from raw DMT-HAR-MED data already present on disk and only asks for BIDS-style staging / validation:
    • skip the mandatory download stage
    • default to the narrow path local raw DMT-HAR-MED discovery -> BIDS validation -> minimal metadata -> report
  • In benchmark mode, do not require explicit confirmation before presenting the direct staging 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

  • DMT-HAR-MED is a specialized psychedelic intervention dataset; analysis requires domain expertise.
  • DMT-HAR-MED data from OpenNeuro is already in BIDS format; re-staging may not be needed.
  • The dataset includes multiple experimental conditions; event files define condition timing.
  • DMT-HAR-MED includes only rs-fMRI; no structural (T1w) or diffusion data is available.
  • dmt-har-med-skill is orchestration-only; detailed preprocessing logic remains in fmri-skill.

When to Call This Skill

  • User asks for end-to-end DMT-HAR-MED workflow.
  • User asks to download DMT-HAR-MED data and then run rs-fMRI processing.
  • User needs BIDS validation for DMT-HAR-MED data.
  • User asks to extract DMT-HAR-MED phenotype data.
  • User needs DMT-HAR-MED-specific QC summaries.

Complementary / Related Skills

  • fmri-skill
  • bids-organizer
  • fmriprep-tool
  • dependency-planner
  • conda-env-manager
  • claw-shell

Reference

Created At: 2026-05-06 01:56 HKT Last Updated At: 2026-05-06 01:56 HKT Author: chengwang96

Install via CLI
npx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill dmt-har-med-skill
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