Hemodynamic Response Functions for fMRI Data Analysis

Documentation for package ‘fmrihrf’ version 0.4.0

Help Pages

-- A --

acquisition_onsets	Get fMRI Acquisition Onset Times
acquisition_onsets.sampling_frame	Get fMRI Acquisition Onset Times
amplitudes	Get amplitudes from an object
amplitudes.Reg	Get amplitudes from an object

-- B --

blockids	Get block identifiers
blockids.sampling_frame	Get block identifiers
blocklens	Get block lengths
blocklens.sampling_frame	Get block lengths
block_hrf	Create a Blocked HRF Object

-- D --

deriv	Compute derivatives of HRF functions
deriv.HRF	Default derivative method for HRF objects
deriv.SPMG1_HRF	Default derivative method for HRF objects
deriv.SPMG2_HRF	Default derivative method for HRF objects
deriv.SPMG3_HRF	Default derivative method for HRF objects
durations	Get durations of an object
durations.Reg	Get durations of an object

-- E --

evaluate	Evaluate a regressor object over a time grid
evaluate.HRF	Evaluate an HRF Object
evaluate.Reg	Evaluate a regressor object over a time grid
evaluate.RegSet	Construct a Regressor Set

-- F --

feature_regressor	Construct a Feature Regressor from a Sampled Time Series
fmrihrf_cli	Command line entrypoint for fmrihrf

-- G --

gen_hrf	Construct an HRF Instance using Decorators
gen_hrf_blocked	Generate a Blocked HRF Function
gen_hrf_lagged	Generate a Lagged HRF Function
getHRF	Get HRF by Name
global_onsets	Convert onsets to global timing
global_onsets.sampling_frame	Convert onsets to global timing

-- H --

HRF	HRF Constructor Function
hrf_basis_lwu	LWU HRF Basis for Taylor Expansion
hrf_blocked	Generate a Blocked HRF Function
hrf_boxcar	Boxcar HRF (No Hemodynamic Delay)
HRF_BSPLINE	Pre-defined Hemodynamic Response Function Objects
hrf_bspline	B-spline HRF (hemodynamic response function)
hrf_bspline_generator	Create B-spline HRF Basis Set
hrf_daguerre_generator	Create Daguerre HRF Basis Set
HRF_FIR	Pre-defined Hemodynamic Response Function Objects
hrf_fir_generator	Create FIR HRF Basis Set
hrf_fourier	Fourier basis for HRF modeling
hrf_fourier_generator	Create Fourier HRF Basis Set
hrf_from_coefficients	Combine HRF Basis with Coefficients
hrf_from_coefficients.HRF	Combine HRF Basis with Coefficients
HRF_GAMMA	Pre-defined Hemodynamic Response Function Objects
hrf_gamma	Gamma HRF (hemodynamic response function)
HRF_GAUSSIAN	Pre-defined Hemodynamic Response Function Objects
hrf_gaussian	Gaussian HRF (hemodynamic response function)
hrf_half_cosine	Half-cosine HRF
hrf_inv_logit	hrf_inv_logit
hrf_lagged	Generate a Lagged HRF Function
hrf_lwu	Lag-Width-Undershoot (LWU) HRF
hrf_mexhat	Mexican Hat HRF (hemodynamic response function)
HRF_objects	Pre-defined Hemodynamic Response Function Objects
hrf_palette	Colour palettes for HRF and regressor plots
hrf_sine	hrf_sine
HRF_SPMG1	Pre-defined Hemodynamic Response Function Objects
hrf_spmg1	hrf_spmg1
HRF_SPMG2	Pre-defined Hemodynamic Response Function Objects
HRF_SPMG3	Pre-defined Hemodynamic Response Function Objects
hrf_tent_generator	Create Tent HRF Basis Set
hrf_time	HRF (hemodynamic response function) as a linear function of time
hrf_toeplitz	HRF Toeplitz Matrix
hrf_weighted	Weighted HRF (No Hemodynamic Delay)

-- I --

install_cli

Install fmrihrf command line wrappers

-- L --

lag_hrf	Lag an HRF Object
list_available_hrfs	List all available hemodynamic response functions (HRFs)

-- M --

make_hrf

Create an HRF from a basis specification

-- N --

nbasis	Number of basis functions
nbasis.HRF	Number of basis functions
nbasis.Reg	Number of basis functions
neural_input	Generate Neural Input Function from Event Timing
neural_input.Reg	Generate Neural Input Function from Event Timing
normalise_hrf	Normalise Each Basis of an HRF to Unit Peak
normalize_hrf	Normalize an HRF Object with a Fixed Scale

-- O --

onsets	Get event onsets from an object
onsets.Reg	Get event onsets from an object

-- P --

penalty_matrix	Generate penalty matrix for regularization
penalty_matrix.BSpline_HRF	Generate penalty matrix for regularization
penalty_matrix.Daguerre_HRF	Generate penalty matrix for regularization
penalty_matrix.FIR_HRF	Generate penalty matrix for regularization
penalty_matrix.Fourier_HRF	Generate penalty matrix for regularization
penalty_matrix.HRF	Generate penalty matrix for regularization
penalty_matrix.SPMG2_HRF	Generate penalty matrix for regularization
penalty_matrix.SPMG3_HRF	Generate penalty matrix for regularization
penalty_matrix.Tent_HRF	Generate penalty matrix for regularization
plot.FeatureReg	Plot a Feature Regressor
plot.HRF	Plot an HRF Object
plot.Reg	Plot a Regressor Object
plot_hrfs	Compare Multiple HRF Functions
plot_regressors	Compare Multiple Regressor Objects
print.HRF	Print an HRF Object
print.Reg	Print method for Reg objects
print.sampling_frame	Print method for Reg objects

-- R --

reconstruction_matrix	Combine HRF Basis with Coefficients
reconstruction_matrix.HRF	Combine HRF Basis with Coefficients
regressor	Construct a Regressor Object
regressor_design	Build a Design Matrix from Block-wise Onsets
regressor_set	Construct a Regressor Set

-- S --

samples	Get sample acquisition times
samples.sampling_frame	Get sample acquisition times
sampling_frame	A 'sampling_frame' describes the block structure and temporal sampling of an fMRI paradigm.
scale_color_hrf	ggplot2 colour scales matching fmrihrf plots
scale_colour_hrf	ggplot2 colour scales matching fmrihrf plots
scale_fill_hrf	ggplot2 colour scales matching fmrihrf plots
shift	Shift a time series object
shift.FeatureReg	Shift a time series object
shift.Reg	Shift a time series object
single_trial_regressor	Create a single trial regressor