Package: fmridesign 0.6.0

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>.

Authors:Bradley Buchsbaum [aut, cre, cph]

fmridesign_0.6.0.tar.gz
fmridesign_0.6.0.zip(r-4.7-any)fmridesign_0.6.0.zip(r-4.6-any)fmridesign_0.6.0.zip(r-4.5-any)
fmridesign_0.6.0.tgz(r-4.6-any)fmridesign_0.6.0.tgz(r-4.5-any)
fmridesign_0.6.0.tar.gz(r-4.7-any)fmridesign_0.6.0.tar.gz(r-4.6-any)
fmridesign_0.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fmridesign/json (API)

# Install 'fmridesign' in R:
install.packages('fmridesign', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bbuchsbaum/fmridesign/issues

Pkgdown/docs site:https://bbuchsbaum.github.io

On CRAN:

Conda:

6.37 score 2 packages 103 scripts 102 exports 71 dependencies

Last updated from:1486585573. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK213
source / vignettesOK231
linux-release-x86_64OK218
macos-release-arm64OK146
macos-oldrel-arm64OK128
windows-develOK173
windows-releaseOK178
windows-oldrelOK158
wasm-releaseOK138

Exports:as_hrfbaselinebaseline_modelbaseline_termsbasis_suffixblockblockidsblocklensboxcar_hrf_genBSplinecellscheck_collinearitycheck_nuisanceclean_nuisancecolumn_contrastcolumnscondition_basis_listcondition_mapconditionsconstructcontrastcontrast_from_maskcontrast_maskcontrast_setcontrast_weightscontrastsconvolveconvolve_designcorrelation_mapcovariatedesign_colmapdesign_mapdesign_matrixdesign_metaduration_hrf_gendurationselementsevaluateevent_basisevent_conditionsevent_factorevent_matrixevent_modelevent_tableevent_termevent_termsevent_variableeventsFcontrastsfeature_suffixgen_hrfget_all_external_hrf_functionsget_basis_entryget_external_hrfspec_functionsget_external_hrfspec_infoglobal_onsetshrfHRFhrf_spmg1Identinteraction_contrastis_categoricalis_continuousis_external_hrfspeclist_external_hrfspecslist_registered_baseslongnamesnbasisnuisanceone_against_all_contrastoneway_contrastonsetspair_contrastpairwise_contrastsplot_contrastsPolypoly_contrastregister_basisregister_hrfspec_extensionregressorregressorsrequires_external_processingresidualizeRobustScalesamplessampling_framesanitizeScaleScaleWithinshortnamessliding_window_contrastssplit_by_blocksplit_onsetsStandardizedsub_basisterm_indicesterm_matricesterm_namestrialwiseunit_contrastvalidate_contrastsweighted_hrf_gen

Dependencies:askpassassertthatbase64encbslibcachemclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfmrihrffontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemimenumDerivopensslotelpillarpkgconfigplotlypracmapromisespurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownS7sassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Building Event Models
Introduction: Modeling Task Effects | Quick HRF Primer | Timing and Sampling | A Simple Single-Factor Design (Single Run) | Visualizing the Event Model | Design with Multiple Runs | Two-Factor Design | Amplitude Modulation (Parametric Regressors) | Interaction Between Factors and Amplitude Modulation | Specifying Different HRFs | Per-Onset HRF Specification with hrf_fun | Advanced: Parametric Modulator with FIR HRF and Windowed F-contrast | Trialwise Models for Beta-Series Analysis | Covariates (Non-convolved Regressors) | Accessing Model Components | Visualizing the Design Matrix and Correlations | Contrasts Quickstart | Combining Event and Baseline Designs
Rendered froma_04_event_models.Rmdusingknitr::rmarkdown

Last update: 2026-03-29
Started: 2025-08-14

Contrasts in fmridesign
Introduction to Contrasts | Types of Contrasts | Defining Contrasts in Event Models | Quick Validation | Advanced Contrast Specifications | Pairwise Contrasts | Polynomial Contrasts | Factorial Design Contrasts | Main Effects and Interactions | Parametric Modulators: Do You Need a Contrast? | F-contrasts for Omnibus Tests | Working with Contrast Weights | Extracting and Manipulating Weights | Contrast Validation | Contrasts for Multi-Run Designs | Contrast Specification Best Practices | 2. Scaling and Normalization | Advanced Topics | Custom Contrast Functions | Troubleshooting Common Issues | 1. Rank-Deficient Contrasts | 2. Multicollinearity in Contrasts | Summary
Rendered froma_05_contrasts.Rmdusingknitr::rmarkdown

Last update: 2026-03-29
Started: 2025-09-11

Introduction to fmridesign
Overview | The fMRI Design Matrix | Package Architecture | Quick Start: Complete Workflow | Understanding the Components | Sampling Frame | Event Specification | Common Use Cases | 1. Block Design | 2. Rapid Event-Related Design | 3. Parametric Modulation | Integration with fMRI Analysis | Best Practices | Next Steps | Getting Help
Rendered froma_01_introduction.Rmdusingknitr::rmarkdown

Last update: 2026-03-29
Started: 2025-09-11

Modeling Baseline and Nuisance Effects
The Purpose of a Baseline Model | Modeling Drift with Basis Functions | Visualizing Baseline Regressors | Intercept Control | Adding Arbitrary Nuisance Regressors | Combining Basis Sets and Nuisance Regressors | Accessing the Design Matrix
Rendered froma_03_baseline_model.Rmdusingknitr::rmarkdown

Last update: 2026-03-29
Started: 2025-08-14

Readme and manuals

Help Manual

Help pageTopics
Create a Baseline Specificationbaseline
Construct a Baseline Modelbaseline_model
Extract baseline termsbaseline_terms baseline_terms.baseline_model
Create Basis Function Suffixbasis_suffix
Create a Block Variableblock
Create duration-based boxcar HRF generatorboxcar_hrf_gen
B-spline basisBSpline
Extract cells from a design objectcells cells.baseline_model cells.covariate_convolved_term cells.event cells.event_term
Check design matrix for multicollinearitycheck_collinearity
Check nuisance regressors for rank and column problemscheck_nuisance
Clean nuisance regressors by dropping rank-useless columnsclean_nuisance
Column Contrast Specificationcolumn_contrast
Extract columnscolumns columns.RobustScale columns.Scale columns.ScaleWithin
Convert an 'event_term' to a per-condition basis listcondition_basis_list
Map Display and Canonical Condition Namescondition_map
Extract conditions from a design objectconditions conditions.event_term
Construct methodconstruct construct.baselinespec construct.covariatespec
Contrast Specificationcontrast
Package a base mask into a 'contrast' objectcontrast_from_mask
Build a base contrast maskcontrast_mask
Create a Set of Contrastscontrast_set
Unit Contrast Weightscontrast_weights contrast_weights.column_contrast_spec contrast_weights.contrast_diff_spec contrast_weights.contrast_formula_spec contrast_weights.contrast_set contrast_weights.convolved_term contrast_weights.event_model contrast_weights.interaction_contrast_spec contrast_weights.oneway_contrast_spec contrast_weights.pair_contrast_spec contrast_weights.poly_contrast_spec contrast_weights.unit_contrast_spec
Extract contrastscontrasts
Retrieve contrast definitions for an event modelcontrasts.event_model
Retrieve contrast definitions for an event termcontrasts.event_term
Retrieve contrast specifications from an hrfspeccontrasts.hrfspec
Convolve events with a hemodynamic response functionconvolve convolve.event_term
Convolve HRF with Design Matrix.convolve_design
Compute correlation mapcorrelation_map
correlation_map.baseline_modelcorrelation_map.baseline_model
Visualize Regressor Correlationscorrelation_map.event_model
Construct a Covariate Termcovariate
Column Metadata Mapdesign_colmap
Column metadata for a design matrixdesign_colmap.event_model
Compute design mapdesign_map
Heatmap visualization of the baseline_model design matrixdesign_map.baseline_model
Visualize Event Model Design Matrixdesign_map.event_model
Extract or construct a design matrixdesign_matrix design_matrix.baseline_model design_matrix.baseline_term design_matrix.event_model design_matrix.event_term
Accessor: column metadata for a design matrixdesign_meta
Create duration-aware normalized HRF generatorduration_hrf_gen
Extract elements from an objectelements elements.event elements.event_term
Create an event set from a ParametricBasis object.event_basis
Retrieve per-event condition assignmentsevent_conditions
Create a categorical event sequence from a factor.event_factor
Create a continuous event set from a matrix.event_matrix
Generic functions for fmridesign packageevent_model
Extract event tableevent_table
Create an event model term from a named list of variables.event_term
Extract event termsevent_terms
Create a continuous event sequence from a numeric vector.event_variable
Retrieve canonical event informationevents
Compute F-contrastsFcontrasts Fcontrasts.convolved_term Fcontrasts.event_model
Create Feature Suffixfeature_suffix
Get All External HRF Function Namesget_all_external_hrf_functions
Look Up a Registered Basis Entryget_basis_entry
Get the HRF Function Name for External Specificationsget_external_hrfspec_functions
Get Information About a Registered External HRF Specificationget_external_hrfspec_info
hemodynamic regressor specification function for model formulas.hrf
IdentIdent
Interaction Contrastinteraction_contrast
Check if categoricalis_categorical is_categorical.event
Check if continuousis_continuous is_continuous.event
Check if a Class is a Registered External HRF Specificationis_external_hrfspec
Get Formatted Labels for a Single Eventlabels.event
Extract Levels from fmrireg Objectscolumns.event levels.event levels.RobustScale levels.Scale levels.ScaleWithin
List All Registered External HRF Specificationslist_external_hrfspecs
List Registered Parametric Basis Classeslist_registered_bases
Extract longnameslongnames
Get number of basis functions from hrfspecnbasis.hrfspec
Create a Nuisance Specificationnuisance
One Against All Contrastone_against_all_contrast
One-way Contrastoneway_contrast
Pair Contrastpair_contrast
Pairwise Contrastspairwise_contrasts
plot_contrastsplot_contrasts
plot_contrasts.event_modelplot_contrasts.event_model
Plot Event Modelplot.event_model
Polynomial basisPoly
Polynomial Contrastpoly_contrast
Predict from a ParametricBasis objectpredict.BSpline predict.Ident predict.ParametricBasis predict.Poly predict.RobustScale predict.Scale predict.ScaleWithin predict.Standardized
Print a Baseline Modelprint.baseline_model print.contrast print.contrast_diff_spec print.contrast_set print.contrast_spec print.convolved_term print.event print.event_model print.event_term print.fmri_term print.poly_contrast_spec
Print and Plot for sampling_frameplot.sampling_frame print.sampling_frame
Register a Parametric Basis Classregister_basis
Register an External HRF Specification Typeregister_hrfspec_extension
Extract regressorsregressors regressors.event_term
Check if an Object Requires External Processingrequires_external_processing
Residualize Data Against a Designresidualize
Residualize methodsresidualize-methods residualize.baseline_model residualize.event_model residualize.matrix
Robust Scaling (Median/MAD)RobustScale
Sanitize Strings for Use in R Namessanitize
Z-score (global) basisScale
Z-score within groupsScaleWithin
Extract shortnamesshortnames
Sliding-Window Contrasts (Disjoint)sliding_window_contrasts
Split by blocksplit_by_block split_by_block.event_model
Split onsetssplit_onsets split_onsets.event_term
Standardized basisStandardized
sub_basissub_basis sub_basis.RobustScale sub_basis.Scale sub_basis.ScaleWithin
Extract term indicesterm_indices term_indices.default
Extract term matricesterm_matrices
Extract term namesterm_names
trialwisetrialwise
Unit Contrastunit_contrast
Validate contrast weights against a design matrix or event modelvalidate_contrasts
Create weighted HRF generator from list columnsweighted_hrf_gen