bbuchsbaum/fmrireg
R package for the anlysis of fmri data

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Search the bbuchsbaum/fmrireg package
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Functions
781
Source code
157
Man pages
151
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bbuchsbaum/fmrireg: R package for the anlysis of fmri data
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API

API for bbuchsbaum/fmrireg
R package for the anlysis of fmri data

Global functions
.calculate_mask_weights Source code
.checkEVArgs Source code
.condnames Source code
.correlation_map_common Source code
.ensure_benchmark_data_loaded Source code
.estimate_ar Source code
.event_set Source code
.fast_F_contrast Source code
.fast_lm_matrix Source code Source code
.fast_preproject Source code Source code
.fast_t_contrast Source code
.label_component Source code
.level_vector Source code
.lm_basic_stats Source code
.load_and_reconstruct_raw_dataset Source code
.make_decon_command_str Source code
.nz Source code
.onLoad Source code
.process_hrf_params Source code
.reconstruct_hrf_object Source code
.resample_param Man page Source code
.safe_cor Source code
.sanitizeName Source code
.trial_factor Man page Source code
.vector_of_labels Source code
AFNI_BLOCK Source code
AFNI_CSPLIN Source code
AFNI_GAM Source code
AFNI_HRF Man page Source code
AFNI_POLY Source code
AFNI_SIN Source code
AFNI_SPMG1 Source code
AFNI_SPMG2 Source code
AFNI_SPMG3 Source code
AFNI_TENT Source code
AFNI_WAV Source code
AFNI_dmBLOCK Source code
BSpline Man page Source code
Fcontrasts Man page Source code
Fcontrasts.convolved_term Man page Source code
Fcontrasts.event_model Source code
Fcontrasts.event_term Source code
HRF Man page
Ident Man page Source code
Poly Man page Source code
ReorderFactor Source code
RobustScale Man page Source code
Scale Man page Source code
ScaleWithin Man page Source code
Standardized Man page Source code
`%||%` Source code Source code Source code Source code
`-.contrast_spec` Source code
add_basis Source code
adjust_stats_for_effective_df Source code
afni_baseline_matrix Source code
afni_command_switch Source code
afni_command_switch.afni_stim_file Source code
afni_command_switch.afni_stim_im_times Source code
afni_command_switch.afni_stim_times Source code
afni_hrf Man page Source code
afni_lm Man page Source code
afni_stim_file Source code
afni_stim_im_times Source code
afni_stim_times Source code
afni_trialwise Man page Source code
amplitudes Man page Source code
ar_parameters Man page Source code
ar_parameters.fmri_lm Man page Source code
ar_whiten_inplace Man page Source code
ar_whiten_transform Source code
as.character.AFNI_HRF Source code
as.matrix_dataset Man page
as_hrf Man page
as_vectors Source code
autoplot.Reg Man page Source code
baseline Man page Source code
baseline_model Man page Source code
baseline_term Source code
baseline_terms Man page Source code
baseline_terms.fmri_model Source code
basis_suffix Man page Source code
beta_stats Source code
beta_stats_matrix Source code
beta_stats_matrix_voxelwise Source code
block Man page Source code
blockids Man page
blockids.convolved_term Source code
blockids.event_model Source code
blockids.event_term Source code
blocklens Man page
blocklens.event_model Source code
blocklens.fmri_model Source code
bootstrap_case Source code
bootstrap_glm_inference Source code
bootstrap_hypothesis_test Source code
bootstrap_residual Source code
bootstrap_wild Source code
build_afni_stims Man page Source code Source code
build_afni_stims.afni_hrf_convolved_term Source code
build_afni_stims.afni_trialwise_convolved_term Source code
build_afni_stims.convolved_term Source code
build_afni_stims.event_term Man page Source code
build_baseline_stims Source code
build_decon_command Source code
build_design_data Source code
build_event_model_design_matrix Source code
calculate_effective_df Source code
calculate_sandwich_variance Source code
cells Man page Source code
cells.baseline_model Man page Source code
cells.convolved_term Source code
cells.covariate_convolved_term Man page Source code
cells.event Man page Source code
cells.event_term Man page Source code
cells.fmri_model Source code
chunkwise_lm Source code
chunkwise_lm.fmri_dataset Man page Source code
chunkwise_lm.fmri_dataset_old Man page Source code
chunkwise_lm.latent_dataset Source code
chunkwise_lm_fast Source code
chunkwise_lm_slow Source code
coef.fmri_latent_lm Source code
coef.fmri_lm Source code Source code
column_contrast Man page Source code
columns Man page Source code
columns.BSpline Source code
columns.Ident Source code
columns.Poly Source code
columns.RobustScale Man page
columns.Scale Man page Source code
columns.ScaleWithin Man page Source code
columns.Standardized Source code
columns.event Man page
compute_ar_effective_df Source code
compute_bca_ci Source code
compute_contrast Source code
compute_effective_df Source code
compute_effective_df_ar Source code
compute_effective_df_ar_robust Source code
compute_effective_df_robust Source code
compute_f_statistic Source code
compute_residuals_cpp Source code
compute_robust_effective_df Source code
compute_sandwich_variance Source code
compute_standard_errors Source code
compute_voxelwise_contrasts Source code
condition_basis_list Man page Source code
conditions Man page Source code
conditions.afni_hrf_convolved_term Man page Source code
conditions.afni_trialwise_convolved_term Man page Source code
conditions.baseline_model Source code
conditions.baseline_term Source code
conditions.convolved_term Man page Source code
conditions.event_model Source code
conditions.event_term Man page Source code
conditions.fmri_model Source code
construct Source code
construct.afni_hrfspec Man page Source code
construct.afni_trialwise_hrfspec Man page Source code
construct.baselinespec Source code
construct.blockspec Source code
construct.covariatespec Source code
construct.hrfspec Source code
construct.nuisancespec Source code
construct_block_term Source code
construct_contrast_matrix Source code
construct_event_term Source code
continuous_token Source code
contrast Man page Source code
contrast_set Man page Source code
contrast_weights Man page Source code
contrast_weights.column_contrast_spec Man page Source code
contrast_weights.contrast_diff_spec Man page Source code
contrast_weights.contrast_formula_spec Man page Source code
contrast_weights.contrast_set Man page Source code
contrast_weights.convolved_term Man page Source code
contrast_weights.event_model Man page Source code
contrast_weights.fmri_model Man page Source code Source code
contrast_weights.interaction_contrast_spec Man page Source code
contrast_weights.oneway_contrast_spec Man page Source code
contrast_weights.pair_contrast_spec Man page Source code
contrast_weights.poly_contrast_spec Man page Source code
contrast_weights.unit_contrast_spec Man page Source code
convolve Man page Source code
convolve.event_term Man page Source code
convolve_design Man page Source code
correlation_map Man page Source code
correlation_map.baseline_model Man page Source code
correlation_map.fmri_model Man page Source code
covariate Man page Source code
covariate_term Source code
create_bootstrap_blocks Source code
create_design_matrix_from_benchmark Man page Source code
create_fmri_model Man page Source code Source code Source code
create_full_contrast_matrix Source code
create_full_contrast_vector Source code
data_chunks Man page
dctbasis Source code
design_env Source code
design_env.fmri_model Source code
design_kernel Source code
design_map Man page Source code
design_map.baseline_model Man page Source code
design_map.fmri_model Man page Source code
design_matrix Man page Source code
design_matrix.afni_hrf_convolved_term Man page Source code
design_matrix.baseline_model Man page Source code
design_matrix.baseline_term Man page Source code
design_matrix.convolved_term Man page Source code
design_matrix.event_model Man page Source code
design_matrix.event_term Man page Source code
design_matrix.fmri_model Man page Source code
design_plot Man page Source code
do_fixef Source code
durations Man page Source code
elements Man page Source code
elements.event Man page Source code
elements.event_term Man page Source code
estcon Source code
estcon.contrast Source code
estimate_ar_parameters Source code
estimate_betas Man page Source code
estimate_betas.fmri_dataset Man page Source code
estimate_betas.latent_dataset Man page Source code
estimate_betas.matrix_dataset Man page Source code
estimate_contrast Source code
estimate_contrast.Fcontrast Source code
estimate_contrast.contrast Source code
estimate_hrf Man page Source code
evaluate Man page
evaluate.hrfspec Source code
evaluate_method_performance Man page Source code
evaluate_regressor_convolution Source code
evaluate_regressor_cpp Source code
evaluate_regressor_fast Source code
event Source code
event_basis Man page Source code
event_factor Man page Source code
event_matrix Man page Source code
event_model Man page Source code Source code
event_table Man page Source code
event_table.convolved_term Man page Source code
event_table.covariate_convolved_term Source code
event_table.event_term Source code
event_term Man page Source code
event_terms Man page Source code
event_terms.fmri_model Source code
event_variable Man page Source code
extract_colind Source code
fast_rlm_run Source code
feature_suffix Man page Source code
find_and_eval_hrf_calls Source code
fit_Fcontrasts Source code
fit_Ftests Source code
fit_contrasts Man page Source code
fit_contrasts.default Man page Source code
fit_contrasts.fmri_lm Man page Source code
fit_lm_contrasts Man page Source code
fit_lm_contrasts_fast Source code
fit_lm_contrasts_voxelwise Source code
fit_lm_contrasts_voxelwise_chunked Source code
fit_lm_contrasts_voxelwise_qr Source code
fitted_hrf Man page Source code
fitted_hrf.fmri_lm Man page Source code Source code
fmri_benchmark_datasets Man page
fmri_dataset Man page
fmri_latent_lm Man page Source code
fmri_lm Man page Source code
fmri_lm_config Source code
fmri_lm_control Man page Source code
fmri_lm_fit Man page Source code
fmri_mem_dataset Man page
fmri_model Man page Source code
fmri_rlm Man page Source code
fmrireg Man page
fmrireg-package Man page
format_contrast_results Source code
formula.event_term Source code
gen_afni_lm Man page Source code
gen_afni_lm.fmri_config Source code
gen_beta_design Source code
gen_hrf Man page
generate_interaction_contrast Man page Source code
generate_main_effect_contrast Man page Source code
get_AFNI_HRF Source code
get_benchmark_summary Man page Source code
get_col_inds Source code
get_data Man page
get_data_matrix Man page
get_formula Source code
get_formula.fmri_model Man page Source code Source code
get_mask Man page
get_methods Source code
glm_context Source code
glm_lss Man page Source code
glm_ols Man page Source code
global_onsets Man page
hrf Man page Source code
hrf_from_coefficients Man page Source code
hrf_smoothing_kernel Man page Source code
hrf_spmg1 Man page
hrfspec Source code
initialize_contrast_storage Source code
inject_basis Source code
instantaneous_correlation_rcpp Source code
interaction_contrast Man page Source code
is.formula Source code Source code
is.glm_context Source code
is_categorical Man page Source code
is_categorical.event Man page Source code
is_categorical.event_term Source code
is_continuous Man page Source code
is_continuous.event Man page Source code
is_continuous.event_term Source code
iterative_ar_solve Source code
kenward_roger_df Source code
labels.event Man page Source code
latent_dataset Man page
level_token Source code
levels.BSpline Source code
levels.Ident Source code
levels.Poly Source code
levels.RobustScale Man page Source code
levels.Scale Man page Source code
levels.ScaleWithin Man page Source code
levels.Standardized Source code
levels.event Man page Source code
list_benchmark_datasets Man page Source code
load_benchmark_dataset Man page Source code
longnames Man page Source code Source code
longnames.afni_hrf_convolved_term Man page Source code
longnames.afni_trialwise_convolved_term Man page Source code
longnames.convolved_term Man page Source code Source code
longnames.event_seq Man page Source code
longnames.event_term Man page Source code
lss_compute_cpp Source code
lss_compute_r Source code
lss_fast Source code
make_column_names Source code
make_cond_tag Source code
make_hrf Source code
make_nuisance_term Source code
make_term_tag Source code
make_unique_tags Source code
map_voxels Source code
masked_vectors Source code
matrix_dataset Man page
meta_Fcontrasts Source code
meta_betas Source code Source code
meta_contrasts Source code Source code
meta_fixef Source code
meta_stouffer Source code
mixed_betas Source code
mixed_betas_cpp Source code
mixed_solve_cpp Man page Source code
mixed_solve_internal Source code
multiresponse_bootstrap_lm Man page Source code
multiresponse_lm Man page Source code
multiresponse_rlm Source code
n_events Source code
n_events.ParametricBasis Source code
n_events.default Source code
n_events.matrix Source code
nbasis Man page Man page Source code
nbasis.BSpline Man page Source code
nbasis.Ident Man page Source code
nbasis.Poly Man page Source code
nbasis.RobustScale Man page Source code
nbasis.Scale Man page Source code
nbasis.ScaleWithin Man page Source code
nbasis.Standardized Man page Source code
nbasis.convolved_term Man page Source code
nbasis.covariate_convolved_term Man page Source code
nbasis.hrfspec Source code
neural_input Man page Source code
neural_input_rcpp Source code
next_dir_name Source code
nuisance Man page Source code
ols_betas Source code
one_against_all_contrast Man page Source code
oneway_contrast Man page Source code
onsets Man page Source code
onsets.convolved_term Source code
onsets.event_term Source code
p_values Man page Source code
package_fcontrast_result Source code
package_tcontrast_result Source code
pair_contrast Man page Source code
pairwise_contrasts Man page Source code
parent_terms Source code
parent_terms.event_term Source code
parse_event_formula Source code
parse_event_model Source code
parse_term Source code
penalty_matrix Man page Source code
plot.baseline_model Man page Source code
plot.fmri_model Source code
plot_contrasts Man page Source code
plot_contrasts.event_model Man page Source code
pls_betas Source code
pls_global_betas Source code
poly_contrast Man page Source code
pool_run_results Source code
pool_runwise_results Source code
predict.BSpline Man page Source code
predict.Ident Man page Source code
predict.ParametricBasis Man page Source code
predict.Poly Man page Source code
predict.RobustScale Man page Source code
predict.Scale Man page Source code
predict.ScaleWithin Man page Source code
predict.Standardized Man page Source code
prediction_matrix Source code
prepare_chunkwise_matrices Source code
print.afni_hrf_convolved_term Man page
print.afni_lm_spec Man page Source code
print.baseline_model Man page Source code
print.contrast Man page Source code
print.contrast_diff_spec Man page Source code
print.contrast_set Man page Source code
print.contrast_spec Man page Source code
print.convolved_term Man page Source code
print.event Man page Source code
print.event_model Man page Source code
print.event_term Man page
print.fmri_lm Man page Source code Source code
print.fmri_lm_config Source code
print.fmri_model Man page Source code
print.fmri_rlm Man page Source code
print.fmri_term Man page Source code
print.poly_contrast_spec Man page Source code
process_chunk Source code
process_f_contrasts Source code
process_run_ar_robust Source code
process_run_integrated Source code
process_run_robust Source code
process_run_standard Source code
process_t_contrasts Source code
pull_stat Source code Source code
pull_stat_revised Man page Source code Source code
read_fmri_config Man page
realise_event_terms Source code
reconstruction_matrix Man page Source code
recycle_or_error Source code
reexports Man page
regressor Man page
regressors Man page Source code
regressors.event_term Man page Source code
reshape_coef Man page Source code Source code
residual_effective_df Source code
ridge_betas Source code
robust_iterative_fitter Source code
run Source code
run.afni_lm_spec Man page Source code
run_estimate_betas Source code
runwise_lm Man page Source code Source code
runwise_lm_fast Source code
runwise_lm_slow Source code
runwise_lm_voxelwise Source code
samples Man page
sampling_frame Man page
sandwich_variance Man page
sanitize Man page Source code
satterthwaite_df Source code
shift Man page Source code
shortnames Man page Source code
shortnames.event_model Man page Source code
shortnames.event_term Man page Source code
simulate_bold_signal Man page Source code
simulate_fmri_matrix Source code
simulate_noise_vector Man page Source code
simulate_simple_dataset Man page Source code
slm_betas Source code
solve_ar_pipeline Source code
solve_ar_robust_pipeline Source code
solve_glm_core Source code
solve_integrated_glm Source code
solve_ols_pipeline Source code
solve_robust_pipeline Source code
split_by_block Man page Source code
split_onsets Man page Source code
split_onsets.event_term Man page Source code
standard_error Man page Source code
standard_error.fmri_latent_lm Man page Source code
standard_error.fmri_lm Man page Source code Source code
stats Man page Source code
stats.fmri_latent_lm Source code
stats.fmri_lm Man page Source code Source code
store_voxel_contrasts Source code
sub_basis Man page Source code
sub_basis.BSpline Source code
sub_basis.Ident Source code
sub_basis.Poly Source code
sub_basis.RobustScale Man page
sub_basis.Scale Man page Source code
sub_basis.ScaleWithin Man page Source code
sub_basis.Standardized Source code
term_indices Man page Source code
term_indices.event_model Source code
term_matrices Man page Source code
term_matrices.fmri_model Man page Source code Source code
term_names Source code
term_names.baseline_model Source code
term_names.event_model Source code
terms.baseline_model Source code
terms.event_model Source code
terms.fmri_model Source code
tibble_to_neurovec Source code
to_glt Man page Source code
to_glt.contrast Man page Source code Source code
translate_legacy_pattern Man page Source code
trialwise Man page Source code
unit_contrast Man page Source code
unpack_chunkwise Source code
whiten_glm_context Source code
with_package Source code
write_afni_stim Source code
write_afni_stim.afni_stim_file Source code
write_afni_stim.afni_stim_times Source code
write_baseline_mat Source code
write_baseline_mats Source code
write_censor_file Source code
write_glt Man page Source code
write_glt.glt_contrast Man page Source code
write_glts Source code
write_stim_files Source code
zeropad Source code
bbuchsbaum/fmrireg documentation built on June 10, 2025, 8:18 p.m.

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