fmridesign

Design Matrix Construction for fMRI Analysis

Overview

fmridesign provides tools for constructing design matrices for functional magnetic resonance imaging (fMRI) analyses. It includes facilities for creating event models with flexible hemodynamic response functions (HRFs), baseline models for nuisance regression, and utilities for handling experimental designs.

This package focuses on the design aspect of fMRI analysis and is intended to be used with analysis packages like fmrireg.

Installation

# Install development version from GitHub
# install.packages("devtools")
# devtools::install_github("bbuchsbaum/fmridesign")
install.packages("fmridesign", repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org'))

Key Features

• Event Models: Create experimental design matrices with flexible HRF specifications
• Baseline Models: Build nuisance regressors for drift, motion, and other confounds
• Flexible HRFs: Support for various hemodynamic response functions via the fmrihrf package
• Block Designs: Handle multi-run/session fMRI experiments

Basic Usage

library(fmridesign)

# Create event data
event_data <- data.frame(
  condition = factor(c("A", "B", "A", "B")),
  onsets = c(1, 10, 20, 80),
  run = c(1, 1, 1, 1)
)

# Define sampling frame
sframe <- sampling_frame(blocklens = 100, TR = 2)

# Create event model
ev_model <- event_model(
  onsets ~ hrf(condition),
  data = event_data,
  block = ~run,
  sampling_frame = sframe
)

# Create baseline model
base_model <- baseline_model(
  basis = "bs",
  degree = 3,
  sframe = sframe
)

# Extract design matrices
event_dm <- design_matrix(ev_model)
baseline_dm <- design_matrix(base_model)

Related Packages

• fmrireg: Analysis and fitting of fMRI models
• fmrihrf: Hemodynamic response functions
• fmridataset: fMRI dataset structures

Documentation & Vignettes

• Online site (pkgdown): https://bbuchsbaum.github.io/fmridesign/
• Articles index: https://bbuchsbaum.github.io/fmridesign/articles/

From R, you can also open installed vignettes:

vignette("a_01_introduction", package = "fmridesign")
vignette("a_03_baseline_model", package = "fmridesign")
vignette("a_04_event_models", package = "fmridesign")
vignette("a_05_contrasts", package = "fmridesign")

License

MIT

Albers theme

This package uses the albersdown theme. Existing vignette theme hooks are replaced so albers.css and local albers.js render consistently on CRAN and GitHub Pages. The defaults are configured via params$family and params$preset (family = 'lapis', preset = 'adobe'). The pkgdown site uses template: { package: albersdown }.