More judicious tests of missing confound columns when confound calculate/regress enabled

Author: michaelhallquist

R/postprocess_confounds.R

@@ -87,6 +87,7 @@ postprocess_confounds <- function(proc_files, cfg, processing_sequence,
     stop("Cannot handle overlaps in noproc_columns and columns for confounds")
   }
 
+  confounds_to_filt <- NULL
   if (isTRUE(cfg$scrubbing$enable)) {
     to_log(lg, "info", "Computing spike regressors using expression: {paste(cfg$scrubbing$expression, collapse=', ')}")
     spike_mat <- compute_spike_regressors(confounds, cfg$scrubbing$expression, lg = lg)
@@ -108,6 +109,17 @@ postprocess_confounds <- function(proc_files, cfg, processing_sequence,
   has_confounds <- !is.null(confound_cols) && length(confound_cols) > 0L
   has_noproc <- !is.null(noproc_cols) && length(noproc_cols) > 0L
 
+  # verify that requested confound columns exist
+  if (has_confounds) {
+    confounds_to_filt <- subset(confounds, select = confound_cols)
+
+    if (ncol(confounds_to_filt) == 0L || nrow(confounds_to_filt) == 0L) {
+      to_log(lg, "warn", "Confound columns were requested but no usable data were found in {proc_files$confounds}; skipping confound filtering.")
+      has_confounds <- FALSE
+      confound_cols <- character()
+    }
+  }
+
   if (!has_confounds && !has_noproc) {
     if (isTRUE(cfg$confound_calculate$enable) || isTRUE(cfg$confound_regression$enable)) {
       to_log(lg, "info", "Confound postprocessing skipped; no confound columns matched the request and no noproc columns were supplied.")
@@ -118,8 +130,6 @@ postprocess_confounds <- function(proc_files, cfg, processing_sequence,
   }
 
   if (has_confounds) {
-    confounds_to_filt <- subset(confounds, select = confound_cols)
-
     # generate NIfTI with confound timeseries
     confounds_bids <- extract_bids_info(proc_files$confounds)
     tmp_out <- construct_bids_filename(modifyList(confounds_bids, list(description = cfg$bids_desc, directory=tempdir(), ext=NA)), full.names=TRUE)
@@ -202,10 +212,19 @@ postprocess_confounds <- function(proc_files, cfg, processing_sequence,
     )
 
     calc_cols <- cfg$confound_calculate$columns
+    df <- filtered_confounds[, integer(0), drop = FALSE]
+
     if (!is.null(calc_cols) && length(calc_cols) > 0L) {
-      df <- subset(filtered_confounds, select = calc_cols)
-    } else {
-      df <- filtered_confounds[, integer(0), drop = FALSE]
+      present_cols <- intersect(calc_cols, names(filtered_confounds))
+      missing_cols <- setdiff(calc_cols, names(filtered_confounds))
+
+      if (length(missing_cols) > 0L) {
+        to_log(lg, "warn", "Requested confound_calculate columns were not available after filtering and will be skipped: {paste(missing_cols, collapse = ', ')}")
+      }
+
+      if (length(present_cols) > 0L) {
+        df <- cbind(df, filtered_confounds[, present_cols, drop = FALSE])
+      }
     }
 
     calc_noproc <- cfg$confound_calculate$noproc_columns
@@ -254,13 +273,19 @@ postprocess_confounds <- function(proc_files, cfg, processing_sequence,
 
   if (isTRUE(cfg$confound_regression$enable)) {
     reg_cols <- cfg$confound_regression$columns
+    df <- filtered_confounds[, integer(0), drop = FALSE]
     if (!is.null(reg_cols) && length(reg_cols) > 0L) {
-      df <- subset(filtered_confounds, select = reg_cols)
-      if (ncol(df) > 0L) {
+      present_cols <- intersect(reg_cols, names(filtered_confounds))
+      missing_cols <- setdiff(reg_cols, names(filtered_confounds))
+
+      if (length(missing_cols) > 0L) {
+        to_log(lg, "warn", "Requested confound_regression columns were not available after filtering and will be skipped: {paste(missing_cols, collapse = ', ')}")
+      }
+
+      if (length(present_cols) > 0L) {
+        df <- filtered_confounds[, present_cols, drop = FALSE]
         df <- as.data.frame(lapply(df, function(cc) cc - mean(cc, na.rm = TRUE)))
       }
-    } else {
-      df <- filtered_confounds[, integer(0), drop = FALSE]
     }
 
     reg_noproc <- cfg$confound_regression$noproc_columns

tests/testthat/test-postprocess_confounds.R

@@ -247,3 +247,128 @@ test_that("postprocess_confounds recomputes framewise displacement when only nop
     replace(conf_df$csf, is.na(conf_df$csf), 0)
   )
 })
+
+test_that("postprocess_confounds skips processing when confound data are empty", {
+  skip_if_not_installed("RNifti")
+
+  tmpdir <- tempfile("postproc_confounds_empty_")
+  dir.create(tmpdir)
+  on.exit(unlink(tmpdir, recursive = TRUE), add = TRUE)
+
+  conf_df <- data.frame(rot_x = numeric(0))
+  conf_path <- file.path(tmpdir, "sub-01_task-rest_desc-confounds_timeseries.tsv")
+  data.table::fwrite(conf_df, conf_path, sep = "\t")
+
+  cfg <- list(
+    motion_filter = list(enable = FALSE),
+    scrubbing = list(enable = FALSE, apply = FALSE, add_to_confounds = FALSE),
+    confound_regression = list(enable = TRUE, columns = "rot_x", noproc_columns = NULL, prefix = "r"),
+    confound_calculate = list(enable = FALSE, columns = NULL, noproc_columns = NULL, demean = TRUE),
+    apply_aroma = list(enable = FALSE, nonaggressive = TRUE),
+    temporal_filter = list(low_pass_hz = NULL, high_pass_hz = NULL, method = "butterworth"),
+    bids_desc = "pp",
+    tr = 1,
+    overwrite = TRUE
+  )
+
+  output_bids_info <- list(
+    subject = "01",
+    task = "rest",
+    description = "denoise",
+    suffix = "bold",
+    ext = ".nii.gz",
+    directory = tmpdir
+  )
+
+  proc_files <- list(
+    confounds = conf_path,
+    melodic_mix = NULL,
+    noise_ics = integer(0)
+  )
+
+  expect_warning(
+    regress_path <- postprocess_confounds(
+      proc_files = proc_files,
+      cfg = cfg,
+      processing_sequence = character(0),
+      output_bids_info = output_bids_info,
+      fsl_img = NULL,
+      lg = NULL
+    ),
+    "Confound columns were requested but no usable data were found",
+    fixed = TRUE
+  )
+
+  expect_null(regress_path)
+
+  reg_file <- construct_bids_filename(
+    modifyList(output_bids_info, list(suffix = "regressors", ext = ".tsv")),
+    full.names = TRUE
+  )
+  expect_false(file.exists(reg_file))
+})
+
+test_that("postprocess_confounds handles empty confound data with calc/reg enabled", {
+  skip_if_not_installed("RNifti")
+
+  tmpdir <- tempfile("postproc_confounds_empty_calc_")
+  dir.create(tmpdir)
+  on.exit(unlink(tmpdir, recursive = TRUE), add = TRUE)
+
+  conf_df <- data.frame(rot_x = numeric(0), framewise_displacement = numeric(0))
+  conf_path <- file.path(tmpdir, "sub-01_task-rest_desc-confounds_timeseries.tsv")
+  data.table::fwrite(conf_df, conf_path, sep = "\t")
+
+  cfg <- list(
+    motion_filter = list(enable = FALSE),
+    scrubbing = list(enable = FALSE, apply = FALSE, add_to_confounds = FALSE),
+    confound_regression = list(enable = TRUE, columns = "rot_x", noproc_columns = NULL, prefix = "r"),
+    confound_calculate = list(enable = TRUE, columns = "framewise_displacement", noproc_columns = NULL, demean = TRUE),
+    apply_aroma = list(enable = FALSE, nonaggressive = TRUE),
+    temporal_filter = list(low_pass_hz = NULL, high_pass_hz = NULL, method = "butterworth"),
+    bids_desc = "pp",
+    tr = 1,
+    overwrite = TRUE
+  )
+
+  output_bids_info <- list(
+    subject = "01",
+    task = "rest",
+    description = "denoise",
+    suffix = "bold",
+    ext = ".nii.gz",
+    directory = tmpdir
+  )
+
+  proc_files <- list(
+    confounds = conf_path,
+    melodic_mix = NULL,
+    noise_ics = integer(0)
+  )
+
+  expect_warning(
+    regress_path <- postprocess_confounds(
+      proc_files = proc_files,
+      cfg = cfg,
+      processing_sequence = character(0),
+      output_bids_info = output_bids_info,
+      fsl_img = NULL,
+      lg = NULL
+    ),
+    "Confound columns were requested but no usable data were found",
+    fixed = TRUE
+  )
+
+  expect_null(regress_path)
+
+  reg_file <- construct_bids_filename(
+    modifyList(output_bids_info, list(suffix = "regressors", ext = ".tsv")),
+    full.names = TRUE
+  )
+  confound_file <- construct_bids_filename(
+    modifyList(output_bids_info, list(suffix = "confounds", ext = ".tsv")),
+    full.names = TRUE
+  )
+  expect_false(file.exists(reg_file))
+  expect_false(file.exists(confound_file))
+})