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neuroim2 - Data Structures for Brain Imaging Data

A collection of data structures and methods for handling volumetric brain imaging data, with a focus on functional magnetic resonance imaging (fMRI). Provides efficient representations for three-dimensional and four-dimensional neuroimaging data through sparse and dense array implementations, memory-mapped file access for large datasets, and spatial transformation capabilities. Implements methods for image resampling, spatial filtering, region of interest analysis, and connected component labeling. General introduction to fMRI analysis can be found in Poldrack et al. (2024, "Handbook of functional MRI data analysis", <ISBN:9781108795760>).

Last updated

fmrineuroimagingzlibcppopenmp

9.73 score 3 stars 9 dependents 334 scripts 524 downloads

fmrihrf - Hemodynamic Response Functions for fMRI Data Analysis

Creates, manipulates, and evaluates hemodynamic response functions and event-related regressors for functional magnetic resonance imaging data analysis. Supports multiple basis sets including Canonical, Gamma, Gaussian, B-spline, and Fourier bases. Features decorators for time-shifting and blocking, and efficient convolution algorithms for regressor construction. Methods are based on standard fMRI analysis techniques as described in Jezzard et al. (2001, ISBN:9780192630711).

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openblascppopenmp

7.78 score 4 dependents 78 scripts 480 downloads

fmrireg - Regression Analysis of Functional Magnetic Resonance Imaging Data

Provides tools for the analysis of functional magnetic resonance imaging (fMRI) data. Facilities are included to construct flexible hemodynamic response functions, experimental regressors, and conduct univariate fMRI regression analyses.

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openblascppopenmp

7.77 score 7 stars 1 dependents 97 scripts

bidser - Work with 'BIDS' (Brain Imaging Data Structure) Projects

Tools for working with 'BIDS' (Brain Imaging Data Structure) formatted neuroimaging datasets. The package provides functionality for reading and querying 'BIDS'-compliant projects, creating mock 'BIDS' datasets for testing, and extracting preprocessed data from 'fMRIPrep' derivatives. It supports searching and filtering 'BIDS' files by various entities such as subject, session, task, and run to streamline neuroimaging data workflows. See Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44> for the 'BIDS' specification.

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7.48 score 6 stars 66 scripts 402 downloads

fmridesign - Design Matrix Construction for fMRI Analysis

Constructs and inspects design matrices for functional magnetic resonance imaging (fMRI) analyses. Provides a formula interface for specifying event-related designs with flexible hemodynamic response function (HRF) bases, parametric modulators, and trialwise models. Includes facilities for baseline/nuisance regressors, contrast specification, and utilities for naming, validation, and visualization. Intended to support the model-building stage prior to statistical fitting. Implements methods described in Friston et al. (1995) <doi:10.1006/nimg.1995.1007> and Lindquist (2008) <doi:10.1214/09-STS282>.

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6.70 score 2 dependents 104 scripts

neuroatlas - Neuroimaging Atlases and Parcellations

Provides a unified interface to access and work with various neuroimaging atlases and parcellations including Schaefer, Brainnetome, Glasser, HCPex, FreeSurfer ASEG, and Olsen MTL atlases. Integrates with TemplateFlow for standardized template access and supports interactive brain surface visualisation via triangle-mesh rendering with 'ggplot2' and 'ggiraph'.

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atlasneuroimagingparcellation

6.54 score 5 stars 22 scripts

amatrix - Backend-Agnostic Matrix Extensions

Matrix-compatible S4 classes with backend-dispatch hooks for accelerated execution and predictable CPU fallback.

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openblas

6.32 score 4 dependents 166 scripts

delarr - Lazy Delayed Arrays with Fused Execution

Provides a lightweight delayed array abstraction for lazy, fused evaluation of multi-dimensional numeric data. Compared with Bioconductor's 'DelayedArray', it offers a small S3 API with tidy-friendly verbs, chunked materialisation, and optional backends for HDF5, memory mapping, and shared-memory parallelism. Expression trees are optimised before streaming evaluation, and results can be written directly to disk without fully materialising arrays in memory.

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6.12 score 4 dependents 6 scripts 353 downloads

fmridataset - Spatially Typed Annotated fMRI Datasets

Provides spatially typed, annotated observation-by-feature containers for functional magnetic resonance imaging (fMRI) data. The package aligns lazy numerical assays with observation metadata, feature metadata, experimental entities, and explicit neuroimaging spaces while retaining compatibility with NIfTI, HDF5, BIDS, and in-memory sources.

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6.07 score 3 dependents 30 scripts

fmrigds - Lazy, Format-Agnostic Group Analysis for fMRI

Provides lazy, spatially typed group-analysis plans for observation-by-feature functional magnetic resonance imaging (fMRI) frames together with compatibility workflows for first-level statistical outputs represented as sample by subject by contrast Group Data Sets (GDS). Supports bounded feature-block reducers, tabular, 'NIfTI', 'HDF5', and 'fmristore' inputs, space-aware transformations, provenance tracking, and reproducible export.

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openblascppopenmp

5.81 score 2 dependents 22 scripts

shard - Deterministic, Zero-Copy Parallel Execution for R

Provides a parallel execution runtime for R that emphasizes deterministic memory behavior and efficient handling of large shared inputs. 'shard' enables zero-copy parallel reads via shared/memory-mapped segments, encourages explicit output buffers to avoid large result aggregation, and supervises worker processes to mitigate memory drift via controlled recycling. Diagnostics report peak memory usage, end-of-run memory return, and hidden copy/materialization events to support reproducible performance benchmarking.

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openblas

5.76 score 5 stars 23 scripts 255 downloads

fmriAR - Fast AR and ARMA Noise Whitening for Functional MRI (fMRI) Design and Data

Lightweight utilities to estimate autoregressive (AR) and autoregressive moving average (ARMA) noise models from residuals and apply matched generalized least squares to whiten functional magnetic resonance imaging (fMRI) design and data matrices. The ARMA estimator follows a classic 1982 approach <doi:10.1093/biomet/69.1.81>, and a restricted AR family mirrors workflows described by Cox (2012) <doi:10.1016/j.neuroimage.2011.08.056>.

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openblascppopenmp

5.73 score 3 dependents 9 scripts 461 downloads

neurocluster - Spatially Constrained Clustering for Neuroimaging Data

Provides multiple algorithms for spatially constrained clustering of 3D and 4D neuroimaging data. Methods include supervoxels, SNIC (Simple Non-Iterative Clustering), SLIC (Simple Linear Iterative Clustering), slice-based minimum spanning forest, FLASH-3D with DCT compression, and adaptive correlation superclustering (ACSC). All methods balance feature similarity and spatial proximity to produce coherent brain parcellations. A unified 'cluster4d' interface standardizes access to all algorithms.

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cppopenmp

5.67 score 59 scripts

mixeff - Mixed-Effects Models via the 'mixeff-rs' Rust Crate

Fits linear and generalized linear mixed-effects models from 'lme4'-style formulas, with optimization by the bundled 'mixeff-rs' Rust crate. A fitted model stores the compiled model specification, the optimizer certificate, and per-coefficient inference metadata (method, status, reliability) as data, so a result can be inspected, saved, and reloaded without a live handle to the compiled engine. When an inference method is unavailable for a fit, the affected value is either withheld with a stable reason code or reported under the name of the method actually used, never silently swapped. Vignettes cover migration from 'lme4' and the meaning of random-effects formula syntax.

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rustcargo

5.44 score 77 scripts

fmrilatent - Latent Space Representations of fMRI Data

Provides S4 classes and methods for representing neuroimaging data in latent spaces. The LatentNeuroVec class offers a memory-efficient representation using matrix factorization (basis x loadings plus a per-voxel offset), enabling compact storage and efficient computation for PCA, temporal bases, graph and wavelet dictionaries, Slepian bases, HRBF atoms, and related fMRI decompositions. Integrates with the neuroim2 package for standard neuroimaging data structures.

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cppopenmp

5.40 score 1 dependents 17 scripts

neurosurf - Data Structures and Visualization for Surface-Based Neuroimaging Data

A comprehensive toolkit for working with surface-based neuroimaging data represented as triangle meshes. The package provides classes and methods for creating, manipulating, and visualizing 3D surface geometries (e.g., cortical surfaces), with support for various file formats including FreeSurfer and GIFTI. Key features include: surface smoothing, curvature computation, neighborhood graph construction, geodesic distance calculations, searchlight analysis for surface-based machine learning, and interactive 3D visualization via HTMLWidgets. The package facilitates advanced surface-based analyses through specialized data structures for representing surface geometry and associated functional data.

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cpp

5.08 score 1 stars 35 scripts

albersdown - Minimalist Theme and Vignette Kit for 'pkgdown' and R Markdown

Provides a minimalist 'ggplot2' theme, colour scales, and 'pkgdown' template built around a curated colour palette system inspired by Josef Albers' colour theory (Albers (1963, ISBN:978-0-300-17935-4) "Interaction of Color"). Includes helpers to apply consistent theming to 'ggplot2' plots, 'gt' tables, and 'bslib' Bootstrap 5 sites, along with one-command setup functions for adopting the style across an R package.

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5.04 score 1 stars 487 downloads

niflowr - Spec-Driven Neuroimaging Command-Line Tool Wrappers

A lightweight, declarative framework for wrapping neuroimaging command-line tools (FSL, AFNI, ANTs, FreeSurfer) in R. Tool interfaces are defined as JSON specifications that describe inputs, outputs, CLI rendering rules, and validation constraints. The package builds safe argument vectors (never shell strings), executes via 'processx', captures provenance, and integrates with 'targets' for pipeline orchestration.

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4.48 score 8 scripts

fmristore - Efficient Storage of fMRI Data

Provides efficient storage and retrieval of functional magnetic resonance imaging (fMRI) data using HDF5 format. The package offers S4 classes and methods for working with dense and sparse representations of 4D neuroimaging data, latent space decompositions, and spatially clustered voxel time series. It includes memory-efficient access patterns for large datasets and integrates with the neuroim2 package for standard neuroimaging data structures.

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4.39 score 33 scripts

neurotransform - Geometric Transforms for Neuroimaging Data

A self-contained, dependency-light library for geometric transforms in neuroimaging. Provides affine and nonlinear (warp) mappings between coordinate systems, plus volume-to-surface mapping primitives. Emphasizes correctness, elegance, and composability with a category-theoretic flavor.

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openblascpp

4.00 score 7 scripts

fmrilss - Least Squares Separate (LSS) Analysis for fMRI Data

Implements efficient least squares separate (LSS) analysis for functional magnetic resonance imaging (fMRI) data, following Mumford et al. (2012) <doi:10.1016/j.neuroimage.2011.08.076>. LSS estimates trial-by-trial activation patterns in event-related designs. The package provides reference R implementations, optimized C++ backends, prewhitening, and methods for voxel-specific haemodynamic response functions, including a fast implementation of GLMsingle (Prince et al., 2022) <doi:10.7554/eLife.77599>.

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openblascppopenmp

3.97 score 1 stars 2 dependents 31 scripts

templateflow - Client for the 'TemplateFlow' Archive

R client for querying and fetching resources from the TemplateFlow archive using a local cache backed by the public TemplateFlow S3 bucket. Provides functions to list template assets, download missing files, read template metadata, and retrieve citations.

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brain-templatesmedical-imagingneuroimagingtemplateflow

3.88 score 1 dependents 3 scripts

xnatR - Interface with XNAT Systems

An R package for interacting with XNAT systems via the REST API. Provides functions to authenticate, list projects/subjects/experiments/scans, search, and download data from XNAT neuroimaging archives.

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3.78 score

openneuroR - Programmatic Access to OpenNeuro Datasets

Search, explore, and download datasets from 'OpenNeuro' <https://openneuro.org>, the largest open neuroimaging data repository. Queries the 'OpenNeuro' GraphQL API to discover datasets by modality, diagnosis, or keyword; inspect snapshots, files, and subject lists; and download full datasets or selected subsets via HTTPS, Amazon S3, or 'DataLad'. Downloaded data are cached locally so subsequent requests skip already-fetched files.

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3.70 score

amatrix.opencl - OpenCL and CLBlast Backend for 'amatrix'

Cross-platform GPU backend for the 'amatrix' package using 'OpenCL' with 'CLBlast' for dense float32 linear algebra. Both libraries are located at run time (never linked), so the package builds and installs on any platform, including Windows; when no OpenCL runtime or 'CLBlast' is present the backend reports itself unavailable and 'amatrix' falls back to CPU execution. See amatrix_install_clblast() for a guided 'CLBlast' setup.

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3.50 score 91 scripts

dipca - Dynamic Inner Principal Component Analysis

Methods for dynamic inner principal component analysis (DiPCA), dynamic inner canonical correlation analysis (DiCCA), and dynamic inner partial least squares (DiPLS) for multivariate time series. These methods extract latent components that follow autoregressive models, enabling temporal prediction and reconstruction. Based on Dong and Qin (2018) <doi:10.1016/j.jprocont.2017.05.002>, Dong and Qin (2018) <doi:10.1016/j.ifacol.2018.09.379>, and Dong and Qin (2018) <doi:10.1016/j.jprocont.2018.04.006>. Integrates with the 'multivarious' package for consistent preprocessing and projection interfaces.

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cpp

3.48 score 4 scripts

fmrireport - PDF Reporting for fMRI GLM Fits

Generates publication-oriented PDF reports for fitted fMRI GLM models from 'fmrireg'. Reports include model/design summaries, HRF plots, coefficient summaries, contrast brain maps, and peak coordinate tables.

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3.30 score

amatrix.mlx - MLX Backend for 'amatrix' on Apple Silicon

GPU-accelerated backend for the 'amatrix' package using Apple 'MLX' via the 'mlx-c' C API. Registers dense float32 matrix products, factorizations, and resident (GPU-memory) execution on Apple Silicon; builds a mock bridge and reports itself unavailable when 'mlx-c' is absent, so installation is safe on any platform.

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2.54 score 9 scripts

amatrix.metal - Metal Sparse Backend for 'amatrix' on macOS

Experimental sparse-first GPU backend for the 'amatrix' package using Apple 'Metal'. Provides a direct Objective-C++ bridge for sparse matrix times dense matrix products on macOS; on other platforms (or without the 'Metal' frameworks) it builds a mock bridge and reports itself unavailable, so installation is safe anywhere.

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cpp

2.54 score 1 scripts

amatrix.arrayfire - ArrayFire Backend for 'amatrix'

Portable GPU backend for the 'amatrix' package using the 'ArrayFire' C API for dense float32 linear algebra. Builds with or without the 'ArrayFire' runtime present; without it the backend reports itself unavailable and 'amatrix' falls back to CPU execution.

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openblascpp

2.54 score 5 scripts

ciftier - Read and Write CIFTI-2 Neuroimaging Files

Pure R implementation of CIFTI-2 format I/O for grayordinate neuroimaging data. Reads and writes dense timeseries (.dtseries.nii), dense scalars (.dscalar.nii), and dense labels (.dlabel.nii) files without requiring external tools such as Connectome Workbench. Provides S4 classes mirroring the CIFTI-2 XML schema, user-friendly axis abstractions, and optional integration with 'neuroim2' and 'neurosurf' for spatially-aware brain imaging objects.

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2.00 score