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) | Continuous Features | 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
Package: fmridesign 0.6.1.9000
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:
fmridesign_0.6.1.9000.tar.gz
fmridesign_0.6.1.9000.zip(r-4.7-any)fmridesign_0.6.1.9000.zip(r-4.6-any)fmridesign_0.6.1.9000.zip(r-4.5-any)
fmridesign_0.6.1.9000.tgz(r-4.6-any)fmridesign_0.6.1.9000.tgz(r-4.5-any)
fmridesign_0.6.1.9000.tar.gz(r-4.7-any)fmridesign_0.6.1.9000.tar.gz(r-4.6-any)
fmridesign_0.6.1.9000.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
Last updated from:de70e2e025. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 204 | ||
| source / vignettes | OK | 343 | ||
| linux-release | OK | 165 | ||
| macos-release | OK | 189 | ||
| macos-oldrel | OK | 182 | ||
| windows-devel | OK | 183 | ||
| windows-release | OK | 171 | ||
| windows-oldrel | OK | 188 | ||
| wasm-release | OK | 124 |
Exports:as_hrfbaselinebaseline_modelbaseline_termsbasis_suffixblockblockidsblocklensboxcar_hrf_genBSplinecellscheck_collinearitycheck_estimabilitycheck_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_variableeventsFcontrastsfeaturefeature_regressorfeature_suffixfmridesign_palettegen_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_namestheme_fmridesigntrialwiseunit_contrastvalidate_contrastsweighted_hrf_gen
Dependencies:assertthatcachemclicpp11dplyrfarverfastmapfmrihrfgenericsggplot2gluegtableisobandjsonlitelabelinglatticelifecyclemagrittrMatrixmemoisenumDerivpillarpkgconfigpracmapurrrR6RColorBrewerRcppRcppArmadillorlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Building Event Models
Last update: 2026-09-25
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
Last update: 2026-08-09
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
Last update: 2026-08-09
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
Last update: 2026-08-09
Started: 2025-08-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create a Baseline Specification | baseline |
| Construct a Baseline Model | baseline_model |
| Extract baseline terms | baseline_terms baseline_terms.baseline_model |
| Create Basis Function Suffix | basis_suffix |
| Create a Block Variable | block |
| Run (block) ids of an event model's events | blockids.event_model |
| Create duration-based boxcar HRF generator | boxcar_hrf_gen |
| B-spline basis | BSpline |
| Extract cells from a design object | cells cells.baseline_model cells.covariate_convolved_term cells.event cells.event_model cells.event_term cells.feature_term |
| Check design matrix for multicollinearity | check_collinearity |
| Check full-design estimability and contrast precision | check_estimability print.estimability_check |
| Check nuisance regressors for rank and column problems | check_nuisance |
| Clean nuisance regressors by dropping rank-useless columns | clean_nuisance |
| Column Contrast Specification | column_contrast |
| Extract columns | columns columns.event_model columns.RobustScale columns.Scale columns.ScaleWithin |
| Convert an 'event_term' to a per-condition basis list | condition_basis_list |
| Map Display and Canonical Condition Names | condition_map condition_map.covariate_convolved_term condition_map.covariate_term condition_map.feature_term |
| Extract conditions from a design object | conditions conditions.baseline_model conditions.convolved_term conditions.covariate_convolved_term conditions.covariate_term conditions.event_term conditions.feature_term |
| Construct method | construct construct.baselinespec construct.covariatespec construct.featurespec |
| Contrast Specification | contrast |
| Package a base mask into a 'contrast' object | contrast_from_mask |
| Build a base contrast mask | contrast_mask |
| Create a Set of Contrasts | contrast_set |
| Unit Contrast Weights | contrast_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 contrasts | contrasts contrasts.feature_term |
| Retrieve contrast definitions for an event model | contrasts.event_model |
| Retrieve contrast definitions for an event term | contrasts.event_term |
| Retrieve contrast specifications from an hrfspec | contrasts.hrfspec |
| Convolve events with a hemodynamic response function | convolve convolve.event_term |
| Convolve HRF with Design Matrix. | convolve_design |
| Compute correlation map | correlation_map |
| Regressor correlation heatmap | correlation_map.baseline_model correlation_map.event_model |
| Construct a Covariate Term | covariate |
| Column Metadata Map | design_colmap |
| Column metadata for a design matrix | design_colmap.event_model |
| Compute design map | design_map |
| Design matrix heatmap | design_map.baseline_model design_map.event_model |
| Extract or construct a design matrix | design_matrix design_matrix.baseline_model design_matrix.baseline_term design_matrix.convolved_term design_matrix.event_model design_matrix.event_term |
| Accessor: column metadata for a design matrix | design_meta |
| Create duration-aware normalized HRF generator | duration_hrf_gen |
| Extract elements from an object | elements elements.event elements.event_term |
| Create an event set from a ParametricBasis object. | event_basis |
| Retrieve per-event condition assignments | event_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 package | event_model |
| Extract event table | event_table event_table.convolved_term event_table.feature_term |
| Create an event model term from a named list of variables. | event_term |
| Extract event terms | event_terms |
| Create a continuous event sequence from a numeric vector. | event_variable |
| Retrieve canonical event information | events events.feature_term |
| Compute F-contrasts | Fcontrasts Fcontrasts.convolved_term Fcontrasts.event_model Fcontrasts.feature_term |
| Continuous Feature Term | feature |
| Create Feature Suffix | feature_suffix |
| Colour palettes used by fmridesign plots | fmridesign_palette |
| fmrihrf reexports | fmrihrf-reexports |
| Get All External HRF Function Names | get_all_external_hrf_functions |
| Look Up a Registered Basis Entry | get_basis_entry |
| Get the HRF Function Name for External Specifications | get_external_hrfspec_functions |
| Get Information About a Registered External HRF Specification | get_external_hrfspec_info |
| hemodynamic regressor specification function for model formulas. | hrf |
| Ident | Ident |
| Interaction Contrast | interaction_contrast |
| Check if categorical | is_categorical is_categorical.event |
| Check if continuous | is_continuous is_continuous.event |
| Check if a Class is a Registered External HRF Specification | is_external_hrfspec |
| Get Formatted Labels for a Single Event | labels.event |
| Extract Levels from fmrireg Objects | columns.event levels.event levels.RobustScale levels.Scale levels.ScaleWithin |
| List All Registered External HRF Specifications | list_external_hrfspecs |
| List Registered Parametric Basis Classes | list_registered_bases |
| Extract longnames | longnames longnames.convolved_term longnames.covariate_convolved_term longnames.covariate_term longnames.event_model longnames.event_seq longnames.feature_term |
| Accessor generics shared with fmrihrf | fmrihrf-generics nbasis.convolved_term nbasis.covariate_convolved_term nbasis.feature_term |
| Get number of basis functions from hrfspec | nbasis.hrfspec |
| Create a Nuisance Specification | nuisance |
| One Against All Contrast | one_against_all_contrast |
| One-way Contrast | oneway_contrast |
| Pair Contrast | pair_contrast |
| Pairwise Contrasts | pairwise_contrasts |
| plot_contrasts | plot_contrasts |
| Contrast weight heatmap | plot_contrasts.event_model |
| Plot a Baseline Model | plot.baseline_model |
| Plot Event Model | plot.event_model |
| Plot a sampling_frame | plot.sampling_frame |
| Polynomial basis | Poly |
| Polynomial Contrast | poly_contrast |
| Predict from a ParametricBasis object | predict.BSpline predict.Ident predict.ParametricBasis predict.Poly predict.RobustScale predict.Scale predict.ScaleWithin predict.Standardized |
| Print a Baseline Model | print.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.feature_term print.fmri_term print.poly_contrast_spec |
| Register a Parametric Basis Class | register_basis |
| Register an External HRF Specification Type | register_hrfspec_extension |
| Extract regressors | regressors regressors.event_term |
| Check if an Object Requires External Processing | requires_external_processing |
| Residualize Data Against a Design | residualize |
| Residualize methods | residualize-methods residualize.baseline_model residualize.event_model residualize.matrix |
| Robust Scaling (Median/MAD) | RobustScale |
| Sanitize Strings for Use in R Names | sanitize |
| Z-score (global) basis | Scale |
| Z-score within groups | ScaleWithin |
| Extract shortnames | shortnames shortnames.convolved_term shortnames.covariate_convolved_term shortnames.covariate_term shortnames.event_model shortnames.event_seq shortnames.feature_term |
| Sliding-Window Contrasts (Disjoint) | sliding_window_contrasts |
| Split by block | split_by_block split_by_block.event_model |
| Split onsets | split_onsets split_onsets.event_term |
| Standardized basis | Standardized |
| sub_basis | sub_basis sub_basis.RobustScale sub_basis.Scale sub_basis.ScaleWithin |
| Extract term indices | term_indices term_indices.default |
| Extract term matrices | term_matrices |
| Extract term names | term_names |
| ggplot2 theme for fmridesign plots | theme_fmridesign |
| trialwise | trialwise |
| Unit Contrast | unit_contrast |
| Validate contrast weights against a design matrix or event model | validate_contrasts |
| Create weighted HRF generator from list columns | weighted_hrf_gen |