dmt-har-med-skill

Orchestrates download, BIDS staging, and rs-fMRI processing for the DMT-HAR-MED dataset.

89|5|Updated Mar 25, 2026
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill dmt-har-med-skill-cuhk-aim-group
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: dmt-har-med-skill
Source: https://github.com/CUHK-AIM-Group/NeuroDiscovery/tree/main/skills/dmt-har-med-skill
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill dmt-har-med-skill-cuhk-aim-group

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, and includes scripts (resource) components.

What problem does it solve? Working with the DMT-HAR-MED psychedelic intervention dataset (OpenNeuro ds006644) requires coordinating dataset download, BIDS validation, phenotype extraction, and fMRI preprocessing across multiple tools, which is error-prone when done manually. ## Core Features & Use Cases - End-to-End Dataset Orchestration: Coordinates a fixed three-phase workflow of OpenNeuro download, BIDS organization, and delegation of rs-fMRI processing to fmri-skill. - Phenotype Extraction: Merges intervention condition, behavioral, and physiological phenotype files into a single CSV aligned with imaging subject IDs. - QC Summaries: Generates per-subject quality control reports and exclusion lists from fMRIPrep confounds using framewise displacement thresholds. - Use Case: A researcher studying DMT effects on brain function can request the full pipeline and receive BIDS-validated data, preprocessed rs-fMRI outputs, merged phenotype tables, and QC exclusion lists under one output directory. ## Quick Start Download the DMT-HAR-MED dataset from OpenNeuro, organize it into BIDS format, and run rs-fMRI preprocessing with QC summaries.

Frequently Asked Questions about dmt-har-med-skill

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

FAQPage Schema
How do I download and process the DMT-HAR-MED dataset from OpenNeuro?

Request the DMT-HAR-MED workflow and the skill coordinates download via the openneuro CLI or datalad, then validates BIDS structure and delegates rs-fMRI processing to fmri-skill. You confirm a numbered plan before any execution begins.

How to extract phenotype data from ds006644 for analysis?

Run the extract_dmt_har_med_phenotype.py script with the phenotype directory and an output CSV path. It merges CSV/TSV phenotype files, normalizes condition labels like DMT and placebo, and optionally filters rows against BIDS participants.tsv subject IDs.

Does DMT-HAR-MED include structural or diffusion MRI data?

No, DMT-HAR-MED contains only resting-state fMRI data from 40 participants. There is no T1w structural or diffusion imaging, so analyses requiring anatomical scans need external data sources.

How is subject exclusion decided in fMRI quality control?

The QC script reads fMRIPrep confounds files and computes mean and maximum framewise displacement per subject. Subjects exceeding the mean FD threshold of 0.3 or max FD of 5.0 are flagged with reasons in an exclusion list CSV.

Can I skip the download step if DMT-HAR-MED data is already local?

Yes, when raw data already exists on disk and only BIDS staging is needed, the skill skips the download phase and runs local discovery, BIDS validation, and minimal metadata reporting directly.