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Add motion confound set shortcuts #32

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Merged
michaelhallquist merged 1 commit into from
Aug 5, 2025
Merged

Add motion confound set shortcuts #32

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42 changes: 40 additions & 2 deletions R/postprocess_confounds.R
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Original file line number Diff line number Diff line change
Expand Up @@ -183,6 +183,9 @@ postprocess_confounds <- function(proc_files, cfg, processing_sequence,
#' `motion_param_<1,25>` expands to `motion_param_1` and
#' `motion_param_25`. Patterns without angle brackets are treated as
#' regular expressions evaluated against the available column names.
#' In addition, common motion-confound sets can be requested using the
#' shortcuts `"6p"`, `"12p"`, `"24p"`, and `"36p"` which expand to the
#' corresponding standard collections of parameters.
#'
#' @param patterns Character vector of column patterns.
#' @param available Character vector of available column names.
Expand All @@ -198,8 +201,43 @@ postprocess_confounds <- function(proc_files, cfg, processing_sequence,
expand_confound_columns <- function(patterns = NULL, available) {
if (is.null(patterns) || length(patterns) == 0 || all(is.na(patterns))) return(NULL) # nothing to expand
checkmate::assert_character(patterns, all.missing = FALSE)
patterns <- na.omit(patterns) # just in case
checkmate::assert_character(available)
patterns <- na.omit(patterns) # just in case
checkmate::assert_character(available)

# expand standard motion/confound sets if present
shortcuts <- list(
"6p" = c("rot_x", "rot_y", "rot_z", "trans_x", "trans_y", "trans_z"),
"12p" = c(
"rot_x", "rot_x_derivative1", "rot_y", "rot_y_derivative1",
"rot_z", "rot_z_derivative1", "trans_x", "trans_x_derivative1",
"trans_y", "trans_y_derivative1", "trans_z", "trans_z_derivative1"
),
"24p" = c(
"rot_x", "rot_x_derivative1", "rot_x_derivative1_power2", "rot_x_power2",
"rot_y", "rot_y_derivative1", "rot_y_derivative1_power2", "rot_y_power2",
"rot_z", "rot_z_derivative1", "rot_z_derivative1_power2", "rot_z_power2",
"trans_x", "trans_x_derivative1", "trans_x_derivative1_power2", "trans_x_power2",
"trans_y", "trans_y_derivative1", "trans_y_derivative1_power2", "trans_y_power2",
"trans_z", "trans_z_derivative1", "trans_z_derivative1_power2", "trans_z_power2"
),
"36p" = c(
"csf", "csf_derivative1", "csf_derivative1_power2", "csf_power2",
"global_signal", "global_signal_derivative1", "global_signal_derivative1_power2",
"global_signal_power2",
"rot_x", "rot_x_derivative1", "rot_x_derivative1_power2", "rot_x_power2",
"rot_y", "rot_y_derivative1", "rot_y_derivative1_power2", "rot_y_power2",
"rot_z", "rot_z_derivative1", "rot_z_derivative1_power2", "rot_z_power2",
"trans_x", "trans_x_derivative1", "trans_x_derivative1_power2", "trans_x_power2",
"trans_y", "trans_y_derivative1", "trans_y_derivative1_power2", "trans_y_power2",
"trans_z", "trans_z_derivative1", "trans_z_derivative1_power2", "trans_z_power2",
"white_matter", "white_matter_derivative1", "white_matter_derivative1_power2",
"white_matter_power2"
)
)
if (any(patterns %in% names(shortcuts))) {
expanded <- unlist(shortcuts[patterns[patterns %in% names(shortcuts)]], use.names = FALSE)
patterns <- c(setdiff(patterns, names(shortcuts)), expanded)
}

res <- unlist(lapply(patterns, function(pat) {
if (is.na(pat) || pat == "") return(character())
Expand Down
47 changes: 47 additions & 0 deletions tests/testthat/test-expand_confound_columns.R
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Expand Up @@ -29,3 +29,50 @@ test_that("expand_confound_columns expands regex and angle brackets", {
# ensure that bad regexs return nothing
expect_null(expand_confound_columns("csfsdflkj", available))
})

test_that("expand_confound_columns expands motion/confound shortcuts", {
available <- c(
"csf", "csf_derivative1", "csf_derivative1_power2", "csf_power2",
"global_signal", "global_signal_derivative1", "global_signal_derivative1_power2",
"global_signal_power2",
"rot_x", "rot_x_derivative1", "rot_x_derivative1_power2", "rot_x_power2",
"rot_y", "rot_y_derivative1", "rot_y_derivative1_power2", "rot_y_power2",
"rot_z", "rot_z_derivative1", "rot_z_derivative1_power2", "rot_z_power2",
"trans_x", "trans_x_derivative1", "trans_x_derivative1_power2", "trans_x_power2",
"trans_y", "trans_y_derivative1", "trans_y_derivative1_power2", "trans_y_power2",
"trans_z", "trans_z_derivative1", "trans_z_derivative1_power2", "trans_z_power2",
"white_matter", "white_matter_derivative1", "white_matter_derivative1_power2",
"white_matter_power2"
)

expect_setequal(
expand_confound_columns("6p", available),
c("rot_x", "rot_y", "rot_z", "trans_x", "trans_y", "trans_z")
)

expect_setequal(
expand_confound_columns("12p", available),
c(
"rot_x", "rot_x_derivative1", "rot_y", "rot_y_derivative1",
"rot_z", "rot_z_derivative1", "trans_x", "trans_x_derivative1",
"trans_y", "trans_y_derivative1", "trans_z", "trans_z_derivative1"
)
)

expect_setequal(
expand_confound_columns("24p", available),
c(
"rot_x", "rot_x_derivative1", "rot_x_derivative1_power2", "rot_x_power2",
"rot_y", "rot_y_derivative1", "rot_y_derivative1_power2", "rot_y_power2",
"rot_z", "rot_z_derivative1", "rot_z_derivative1_power2", "rot_z_power2",
"trans_x", "trans_x_derivative1", "trans_x_derivative1_power2", "trans_x_power2",
"trans_y", "trans_y_derivative1", "trans_y_derivative1_power2", "trans_y_power2",
"trans_z", "trans_z_derivative1", "trans_z_derivative1_power2", "trans_z_power2"
)
)

expect_setequal(
expand_confound_columns("36p", available),
available
)
})
4 changes: 4 additions & 0 deletions vignettes/postprocessing.Rmd
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Expand Up @@ -196,6 +196,10 @@ or numeric ranges inside angle brackets. For example
pattern like `^trans_` will match all six motion parameters. This expansion
is implemented in `expand_confound_columns()`.【F:R/postprocess_functions.R†L996-L1036】

Standard motion-confound bundles can also be selected using shortcuts such as
`"6p"`, `"12p"`, `"24p"`, or `"36p"` to request common sets of motion
parameters and their derivatives/squared terms.

Filtered confounds (listed in `columns`) undergo the same temporal
filtering as the BOLD data, while unfiltered confounds (listed in
`noproc_columns`) are appended without processing. Typical unfiltered
Expand Down
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