make_design: Make design matrix
In hrf: Hemodynamic Response Function

make_design

R Documentation

Make design matrix

Description

Make the design matrix for the GLM, from the task information.

Usage

make_design(
  EVs,
  nTime,
  TR,
  dHRF = 0,
  upsample = 100,
  onset = NULL,
  offset = NULL,
  scale_design = TRUE,
  onsets_sep = FALSE,
  offsets_sep = FALSE,
  verbose = TRUE,
  ...
)

Arguments

`EVs`	The explanatory variables i.e. the task stimulus information, from which a design matrix will be constructed. This is a list where each entry represents a task as a matrix of onsets (first column) and durations (second column) for each stimuli (each row) of the task, in seconds. List names should be the task names. `nTime` and `TR` are required. An example of a properly-formatted `EVs` is: `on_s1 <- list(taskA=cbind(on=c(1,9,17), dr=rep(1,3)), taskB=cbind(on=c(3,27), dr=rep(5,2)))`. In this example, there are two tasks: the first has three 1s-long stimuli, while the second has two 5s-long stimuli.
`nTime`	the number of timepoints (volumes) in the task fMRI data.
`TR`	the temporal resolution of the data, in seconds.
`dHRF`	Controls the extent of HRF derivatives modeling. Set to `0` to only model the main HRF regressor (default), and not include its derivatives; set to `1` to model the temporal derivative too; or, set to `2` to model both the temporal and dispersion derivatives. If `dHRF==0`, there is one design column (field) per task. If `dHRF==1`, there are two fields per task. And if `dHRF==2`, there are three fields per task. If there are several tasks and `dHRF>0`, the total number of design matrix columns may exceed five, which may require large computation times with INLA. The analysis can be adjusted by modeling the derivatives as nuisance signals rather than as fields. To do so, move the corresponding columns from the design matrix to the `nuisance` argument for `BayesGLM`.
`upsample`	Upsample factor for convolving stimulus boxcar or stick function with canonical HRF. Default: `100`.
`onset`, `offset`	Add task regressors indicating the onset and/or offset of each event block? Provide the names of the tasks as a character vector. All onsets (or offsets) across the specified tasks will be represented by one additional column in the design matrix. The task names must match the names of `EVs`. Can also be `"all"` to use all tasks. Onsets/offset modeling is only compatible with a block design experiment. An error will be raised if the events in `EVs` do not have duration greater than one second.
`scale_design`	Scale the columns of the design matrix? Default: `TRUE`.
`onsets_sep`, `offsets_sep`	Model the onsets (`onsets_sep`) or offsets (`offsets_sep`) separately for each task? Default: `FALSE`, to model all onsets together, or all offsets together, as a single field in the design.
`verbose`	Print diagnostic messages? Default: `TRUE`.
`...`	Additional arguments to `HRF_calc`.

Value

A "BfMRI_design" object: a list with elements

design: The volumes by fields design matrix. Column names are field names.
field_names: The name of each task from the provided onsets.
dHRF: The input dHRF parameter.
HRF_info: Additional HRF modeling results.

Examples

EVs <- list(taskA=cbind(on=c(1,9,17), dr=rep(1,3)), taskB=cbind(on=c(3,27), dr=rep(5,2)))
TR <- .72
nTime <- ceiling(65/TR)
make_design(EVs, nTime, TR)

hrf documentation built on April 3, 2025, 10:36 p.m.