One-click install
npx skills add https://github.com/HaoxuanLiTHUAI/awesome_cognitive_and_neuroscience_skills --skill fmri-glm-analysis-guide
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: fMRI GLM Analysis Guide
Source: https://github.com/HaoxuanLiTHUAI/awesome_cognitive_and_neuroscience_skills/tree/main/skills/fmri-glm-analysis-guide
Command: npx skills add https://github.com/HaoxuanLiTHUAI/awesome_cognitive_and_neuroscience_skills --skill fmri-glm-analysis-guide

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This guide provides domain-specific knowledge for designing and executing fMRI GLMs, helping researchers avoid common misspecifications and ensure robust statistical inference.

Core Features & Use Cases

  • HRF model selection: canonical, derivatives, and FIR options for various designs and populations.
  • Design matrix construction: block, event-related, and mixed designs with timing, covariates, and HRF convolution.
  • Confound handling and autocorrelation: strategies for motion regressors, high-pass filtering, and prewhitening.
  • Second-level analysis and multiple comparison corrections: planning, reporting, and ROI considerations.
  • Use case: plan a first-level model for a task fMRI study and a group-level analysis with proper controls.

Quick Start

Follow the step-by-step guide to draft your first-level GLM configuration and plan the subsequent group analysis.

Frequently Asked Questions about fMRI GLM Analysis Guide

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

FAQPage Schema
How do I construct a design matrix for task-based fMRI GLM analysis?

To construct a design matrix for fMRI GLM, define your block or event-related timing, add covariates, and model the hemodynamic response function. This ensures robust statistical inference by properly separating neural signals from noise.

What HRF model should I use for my fMRI study?

HRF model selection for fMRI depends on your design and population, choosing among canonical, derivative, and FIR options. This guides you in specifying the correct hemodynamic response to avoid common model misspecifications.

How do I handle motion regressors and high-pass filtering in fMRI GLM?

Handling motion regressors and high-pass filtering in fMRI GLM involves adding nuisance regressors and applying temporal filtering to confounds. This strategy mitigates autocorrelation and physiological noise during prewhitening.

What is the best way to plan second-level analysis and multiple comparison corrections for fMRI?

The best way to plan second-level fMRI analysis is to define group-level contrasts and apply multiple comparison corrections. This ensures valid statistical inference across participants and experiments for reproducible workflows.

Does this fMRI GLM guide support mixed designs with both block and event-related timing?

Yes, the fMRI GLM guide supports mixed designs with both block and event-related timing. It helps you document timing, convolve with the HRF, and configure covariates within a single robust statistical model.