HRF Generators

Why Generators?

Most pre-defined HRFs in fmrihrf (like HRF_SPMG1 or HRF_GAUSSIAN) are ready-to-use objects. However, some HRFs are actually generators. A generator is a function that creates a new HRF object when you call it. This allows you to specify the number of basis functions (nbasis) and the time span (span) at creation time.

The library provides generators for flexible basis sets such as B-splines and finite impulse response (FIR) models. They are available through the internal HRF_REGISTRY and are also returned by list_available_hrfs() with type “generator”.

list_available_hrfs(details = TRUE) %>%
  dplyr::filter(type == "generator")
#>       name      type nbasis_default is_alias                description
#> 1  bspline generator              5    FALSE   bspline HRF (generator) 
#> 2     tent generator              5    FALSE      tent HRF (generator) 
#> 3  fourier generator              5    FALSE   fourier HRF (generator) 
#> 4 daguerre generator              3    FALSE  daguerre HRF (generator) 
#> 5      fir generator             12    FALSE       fir HRF (generator) 
#> 6      lwu generator       variable    FALSE       lwu HRF (generator) 
#> 7       bs generator              5     TRUE bs HRF (generator) (alias)

Creating a Basis with a Generator

To obtain an actual HRF object from a generator, simply call the generator function with your desired parameters. For example, to create a B-spline basis with 8 functions spanning 32 seconds:

# Create a B-spline basis using gen_hrf
bs8 <- gen_hrf(hrf_bspline, N = 8, span = 32)
print(bs8)
#> function (t) 
#> hrf(t, ...)
#> <bytecode: 0x127e322e8>
#> <environment: 0x123e9a950>
#> attr(,"class")
#> [1] "HRF"      "function"
#> attr(,"name")
#> [1] "hrf_bspline"
#> attr(,"nbasis")
#> [1] 8
#> attr(,"span")
#> [1] 32
#> attr(,"params")
#> list()

The returned value is a standard HRF object, so you can evaluate it or use it in model formulas like any other HRF.

times <- seq(0, 32, by = 0.5)
mat <- bs8(times)
head(mat)
#>              1          2            3 4 5 6 7 8
#> [1,] 0.0000000 0.00000000 0.0000000000 0 0 0 0 0
#> [2,] 0.3081055 0.02164714 0.0003255208 0 0 0 0 0
#> [3,] 0.4960938 0.07942708 0.0026041667 0 0 0 0 0
#> [4,] 0.5844727 0.16259766 0.0087890625 0 0 0 0 0
#> [5,] 0.5937500 0.26041667 0.0208333333 0 0 0 0 0
#> [6,] 0.5444336 0.36214193 0.0406901042 0 0 0 0 0

Visualising FIR Basis Functions

Here is a quick look at an FIR basis generated with 10 bins over a 20 second window:

# Use the pre-defined FIR basis or create one with gen_hrf
fir10 <- HRF_FIR  # Pre-defined FIR with 12 basis functions
resp <- fir10(times)

fir_df <- data.frame(Time = times, resp)
fir_long <- tidyr::pivot_longer(fir_df, -Time)

ggplot(fir_long, aes(Time, value, colour = name)) +
  geom_line(linewidth = 1) +
  labs(title = "Finite Impulse Response Basis",
       x = "Time (s)", y = "Response") +
  theme_minimal() +
  theme(legend.position = "none")

HRF Generators

Bradley R. Buchsbaum

2025-09-11

Why Generators?

Creating a Basis with a Generator

Visualising FIR Basis Functions

Summary