Package: fmrireg 0.2.0

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.

Authors:Bradley Buchsbaum [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
fmrireg/json (API)

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

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

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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

openblascppopenmp

5.74 score 8 stars 1 packages 86 scripts 197 exports 126 dependencies

Last updated from:1b034e7bd1. Checks:8 WARNING, 2 OK, 3 ERROR. Indexed: yes.

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Exports:.resample_paramapply_soft_projectionar_parametersas_hrfas_manifestas.matrix_datasetbaselinebaseline_modelbaseline_specbaseline_termsbatch_errorsbatch_valuesblockblockidsblocklensBSplinebuild_modelcellscoef_imagecoef_imagescoef_namescollect_resultscolumn_contrastcolumnscompute_dvarscompute_lm_contrastscompute_lm_contrasts_from_suffstatscondition_basis_listconditionsconstructcontrastcontrast_setcontrast_weightsconvolveconvolve_designcorrelation_mapcovariatecreate_3d_blockscreate_design_matrix_from_benchmarkcreate_fmri_modeldata_chunksdataset_specdesign_mapdesign_matrixdesign_plotdurationsdvars_to_weightselementsengine_specengine_specsestimateestimate_betasestimate_hrfevaluateevaluate_method_performanceevent_basisevent_factorevent_matrixevent_modelevent_tableevent_termevent_termsevent_variableexport_jobsextract_csv_dataextract_nuisance_timeseriesFcontrastsfit_contrastsfit_glm_from_suffstatsfit_glm_on_transformed_seriesfit_glm_with_configfitted_hrfflip_signfmri_datasetfmri_jobfmri_latent_lmfmri_lmfmri_lm_controlfmri_mem_datasetfmri_metafmri_meta_fitfmri_meta_fit_contrastsfmri_meta_fit_covfmri_meta_fit_extendedfmri_modelfmri_ols_fitfmri_rlmfmri_templatefmri_ttestfmrireg_clifrom_bidsgen_hrfgenerate_interaction_contrastgenerate_main_effect_contrastget_benchmark_summaryget_contrastsget_covariatesget_dataget_data_matrixget_formulaget_maskget_roisget_subjectsglm_lssglm_olsglobal_onsetsgroup_datagroup_data_from_csvgroup_data_from_fmrilmgroup_data_from_h5group_data_from_niftihrfHRFhrf_smoothing_kernelhrf_spmg1Identinstall_cliinstantiateinteraction_contrastis_categoricalis_continuouslatent_datasetlist_benchmark_datasetsload_benchmark_datasetlongnameslowrank_controlmatrix_datasetmeta_effective_nmeta_fit_vcov_cppmixed_solve_cppn_subjectsnbasisnuisanceols_t_cppols_t_vcov_cppone_against_all_contrastoneway_contrastonsetsp_valuespair_contrastpaired_diff_blockplot_contrastsPolypoly_contrastpreflightpvaluesr_to_zread_fmri_configread_h5_fullread_jobsread_nifti_fullrealize_datasetreduce_betasreduce_contrastsreduce_identityreduce_write_resultsregister_basisregister_engineregister_run_backendregressorresolve_basisRobustScalerun_backendsrun_jobrun_jobssamplessampling_frameScaleScaleWithinseshortnamessimulate_bold_signalsimulate_fmri_matrixsimulate_noise_vectorsimulate_simple_datasetsoft_projectionsoft_subspace_optionsspatial_fdrstandard_errorStandardizedstatssub_basist_to_beta_set_to_dterm_indicesterm_matricestidytidy_fitted_hrftrialwiseunit_contrastvalidate_jobvalidate_templatevolume_weightswelch_t_cppwrite_resultsz_to_rzscores

Dependencies:askpassassertthatbase64encBHbigassertrbigmemorybigmemory.sribigparallelrbigstatsrbitbit64bslibcachemclicodetoolscowplotcpp11crayoncrosstalkcurldata.tabledbscandeflistdelarrDEoptimRdigestdoParalleldplyrevaluatefarverfastmapffflockfmriARfmridatasetfmridesignfmrigdsfmrihrffmrilssfontawesomeforeachfsfurrrfuturefuture.applygenericsggplot2glmnetglobalsgluegtablehdf5rhighrhmshtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelistenvmagrittrMASSMatrixmatrixStatsmemoisemimemmapneuroim2numDerivopensslotelparallellypatchworkpillarpkgconfigplotlypracmaprettyunitsprogresspromisespspurrrR6RANNrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRhpcBLASctlrlangrmarkdownrmioRNiftiRNiftyRegrobustbaseroptimRSpectraS7sassscalesshapestringistringrsurvivalsystibbletidyrtidyselecttinytexutf8uuidvctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Plugin registration and helpers for fmrireg.fmrireg_engine_registry
Resample parameter vector with specified distribution.resample_param
Apply Soft Projection to Data and Designapply_soft_projection
Extract Estimated AR Parameters from fmri_lm Fitar_parameters ar_parameters.fmri_lm
Coerce bindings to an fmri_manifestas_manifest
Coerce NeuroVec to base arrayas.array.NeuroVec
Autoplot method for Reg objectsautoplot.Reg
Baseline specification (subject-invariant)baseline_spec
Extract per-job errors from a batch resultbatch_errors
Extract successful values from a batch resultbatch_values
Block IDs for event_modelblockids.event_model
Assemble the full fMRI model for a jobbuild_model
Extract Image/Volume for Coefficientcoef_image coef_image.fmri_lm
Extract Coefficient Image from fmri_ttest_fitcoef_image.fmri_ttest_fit
Extract Images/Volumes for Multiple Coefficientscoef_images coef_images.fmri_lm
Get Available Coefficient Namescoef_names coef_names.fmri_lm
Extract Coefficients from Meta-Analysiscoef.fmri_meta
Collect per-subject result maps into a group_data objectcollect_results
Extract Column Names or Identifierscolumns columns.event_model
Compute DVARS (Temporal Derivative of Timecourses)compute_dvars
Compute linear model contrast statistics (public API)compute_lm_contrasts
Compute contrast statistics from sufficient statistics (public API)compute_lm_contrasts_from_suffstats
Visualize the entire design matrix as a heatmapconditions.convolved_term
Contrast genericcontrast
Create a contrast setcontrast_set
Apply Contrast to Meta-Analysis Resultscontrast.fmri_meta
correlation_mapcorrelation_map correlation_map.baseline_model
correlation_map.fmri_modelcorrelation_map.fmri_model
Create 3D Blocks for Voxelwise Analysiscreate_3d_blocks
Create Design Matrix from Benchmark Datasetcreate_design_matrix_from_benchmark
Describe how to (re)construct a subject's datasetdataset_spec
Heatmap visualization of the combined fmri_model design matrixdesign_map.fmri_model
Design Matrix for Convolved Termsdesign_matrix.convolved_term
Design Matrix Method for fmri_lm Objectsdesign_matrix.fmri_lm
Design Matrix for fMRI Modelsdesign_matrix.fmri_model
Design Plot for fMRI Modeldesign_plot
Convert DVARS to Volume Weightsdvars_to_weights
Inspect a Registered Engine Specificationengine_spec
List Registered Engine Specificationsengine_specs
Deprecated helper: estimate()estimate
Estimate Beta Coefficients for fMRI Dataestimate_betas estimate_betas.latent_dataset
Estimate betas using various regression methodsestimate_betas.fmri_dataset
Estimate betas for a matrix datasetestimate_betas.matrix_dataset
Estimate hemodynamic response function (HRF) using Generalized Additive Models (GAMs)estimate_hrf
Evaluate Method Performance on Benchmark Datasetevaluate_method_performance
Extract event table from convolved termevent_table.convolved_term
Export jobs for external / array executionexport_jobs
Extract Data for Meta-Analysis from CSVextract_csv_data
Extract Nuisance Timeseries from Maskextract_nuisance_timeseries
Fit Contrastsfit_contrasts
Fit Contrasts for Linear Model (Default Method)fit_contrasts.default
Fit Contrasts for fMRI Linear Model Objectsfit_contrasts.fmri_lm
Fit GLM from sufficient statisticsfit_glm_from_suffstats
Fit the core GLM on a transformed time-series matrixfit_glm_on_transformed_series
Fit GLM with full config (AR/robust) on a transformed seriesfit_glm_with_config
fitted_hrffitted_hrf
Compute Fitted Hemodynamic Response Functions for an fmri_lm Objectfitted_hrf.fmri_lm
Flip Sign of Coefficientsflip_sign
Benchmark fMRI datasetsfmri_benchmark_datasets
Construct a per-subject job recipefmri_job
Fast fMRI Regression Model Estimation from a Latent Component Datasetfmri_latent_lm
Fit a Linear Regression Model for fMRI Data Analysisfmri_lm fmri_lm.fmri_model fmri_lm.formula
Configuration for fmri_lm fittingfmri_lm_control
Fit Group-Level Meta-Analysisfmri_meta
Fit Meta-Analysis Modelsfmri_meta_fit
Fit Meta-Analysis Models with Exact Contrastsfmri_meta_fit_contrasts
Fit Meta-Analysis and return packed covariance per voxelfmri_meta_fit_cov
Extended Meta-Analysis Fit with Voxelwise Covariatefmri_meta_fit_extended
Construct an fMRI Regression Modelfmri_model
OLS Fit with Optional Voxelwise Covariatefmri_ols_fit
Fit a Robust Linear Model for fMRI Data Analysisfmri_rlm
Define a subject-invariant model templatefmri_template
fmrireg t-tests for Group Analysisfmri_ttest
Run the fmrireg command line interfacefmrireg_cli
Build a manifest from a BIDS projectfrom_bids
Fast factorial contrast generatorsgenerate_interaction_contrast generate_main_effect_contrast
Get Benchmark Dataset Summaryget_benchmark_summary
Get Available Contrastsget_contrasts
Get Covariatesget_covariates
Get Available ROIsget_rois
Get Subject IDsget_subjects
GLM LSS Estimation Convenience Function (Single Trial Estimation)glm_lss
GLM OLS Estimation Convenience Functionglm_ols
Create Group Dataset for Meta-Analysisgroup_data
Create Group Dataset from CSV File or Data Framegroup_data_from_csv
Create Group Dataset from fmri_lm Objectsgroup_data_from_fmrilm
Create Group Dataset from HDF5 Filesgroup_data_from_h5
Create Group Dataset from NIfTI Filesgroup_data_from_nifti
Compute an HRF smoothing kernelhrf_smoothing_kernel
Install the fmrireg command wrapperinstall_cli
Instantiate a template into per-subject jobsinstantiate
List Available Benchmark Datasetslist_benchmark_datasets
Load fMRI Benchmark Datasetsload_benchmark_dataset
Extract Long Names of Variable Levelslongnames longnames.convolved_term longnames.event_model longnames.event_seq longnames.event_term
Low-rank / sketch controls for fast GLMlowrank_control
Compute Effective Sample Size for Meta-Analysismeta_effective_n
Meta-regression with ONE voxelwise covariatemeta_fit_vcov_cpp
Mixed Model Solver using Rcpp and roptimmixed_solve_cpp
Extract Number of Subjectsn_subjects
OLS t-test / ANCOVA across featuresols_t_cpp
OLS with ONE voxelwise covariateols_t_vcov_cpp
Extract P-values from a Model Fitp_values p_values.fmri_lm
Helper Functions for fmri_ttestpaired_diff_block
Preflight-check jobs before fan-outpreflight
Print Meta-Analysis Resultsprint.fmri_meta
Print an fmri_lm_result objectprint.fmri_lm print.fmri_model print.fmri_rlm
Print method for fmri_ttest_fitprint.fmri_ttest_fit
Print Group Data Objectprint.group_data
Print Spatial FDR Resultsprint.spatial_fdr_result
Compute P-values from Meta-Analysispvalues
Convert Correlation to Fisher's Zr_to_z
Read All Data from HDF5 Filesread_h5_full
Read jobs exported by export_jobs()read_jobs
Read All Data from NIfTI Filesread_nifti_full
Realize the dataset described by a jobrealize_dataset
Reducer: tidy beta-estimate tablereduce_betas
Reducer: tidy contrast tablereduce_contrasts
Reducer: return the fitted model unchangedreduce_identity
Reducer: write per-subject results to disk (BIDS-keyed)reduce_write_results
Register an HRF/basis constructorregister_basis
Register a plugin engine for 'fmri_lm'register_engine
Register an execution backend for run_jobs()register_run_backend
Resolve a registered basis function by nameresolve_basis
List registered execution backendsrun_backends
Run a single jobrun_job
Run a batch of jobsrun_jobs
Extract Standard Errors from Meta-Analysisse
Short Namesshortnames shortnames.event_model shortnames.event_term
Simulate fMRI Time Seriessimulate_bold_signal
Simulate fMRI Time Courses, Return Shared Onsets + Column-Specific Amplitudes/Durationssimulate_fmri_matrix
Simulate fMRI Noisesimulate_noise_vector
Simulate Complete fMRI Datasetsimulate_simple_dataset
Create Soft Projection Operatorsoft_projection
Soft Subspace Control Optionssoft_subspace_options
Soft Subspace Projection for Nuisance Removalsoft_subspace_projection
Spatially-Aware Multiple Comparisons Correctionspatial_fdr
Extract Standard Errors from a Model Fitstandard_error standard_error.fmri_latent_lm standard_error.fmri_lm
Extract Test Statistics from a Model Fitstats stats.fmri_lm
Summary of Meta-Analysis Resultssummary.fmri_meta
Summary method for fmri_ttest_fitsummary.fmri_ttest_fit
Summary of Group Data Objectsummary.group_data
Summary of Spatial FDR Resultssummary.spatial_fdr_result
Convert t-statistics to Effect Sizest_to_beta_se
Convert T-statistics to Effect Sizes and Variancest_to_d
Extract term matrices from fmri_modelterm_matrices.fmri_model
Tidy generictidy
Tidy fitted HRF curves from an fmri_lm fittidy_fitted_hrf
Tidy Meta-Analysis Resultstidy.fmri_meta
Validate an fmri_jobvalidate_job
Validate an fmri_templatevalidate_template
Volume Quality Metrics and Temporal Weightingvolume_quality
Compute Volume Quality Weights from Datavolume_weights
Welch two-sample t-test across featureswelch_t_cpp
Write Results from fMRI Analysiswrite_results
Write Results from fMRI Linear Modelwrite_results.fmri_lm
Write Meta-Analysis Resultswrite_results.fmri_meta
Back-transform Fisher's Z to Correlationz_to_r
Compute Z-scores from Meta-Analysiszscores