Add custom confounds for no_gsr

The added are global signals from CSF and WM.

Signed-off-by: Liang Zhang <psychelzh@outlook.com>

R/xcpd.R

@@ -50,10 +50,13 @@ commit_xcpd <- function(sublist, file_sublist = NULL, ...) {
   }
   num_jobs <- nrow(sublist)
   params_post <- clize_list(
-    config::get(
-      "params",
-      config = config_params,
-      file = file_config_xcpd
+    withr::with_envvar(
+      c(PROJECT_ROOT = project_root),
+      config::get(
+        "params",
+        config = config_params,
+        file = file_config_xcpd
+      )
     )
   )
   job_main <- fs::path(path_qsub, "xcpd.tmpl.qsub") |>

config/xcpd.yml

@@ -17,6 +17,7 @@ default:
 no_gsr:
   params:
     nuisance-regressors: 24P
+    custom-confounds: !expr fs::path(Sys.getenv("PROJECT_ROOT"), "xcp_d/custom_confounds")
 
 default_mni:
   params:

xcp_d/custom_confounds/.gitignore

@@ -0,0 +1,2 @@
+*
+!.gitignore

xcp_d/prepare_confounds.R

@@ -0,0 +1,20 @@
+# please use this in RStudio and set a proper conda environment
+library(tidyverse)
+reticulate::use_condaenv("bids")
+bids <- reticulate::import("bids")
+layout_confounds <- bids$BIDSLayout(
+  fs::path("derivatives/fmriprep"),
+  validate = FALSE,
+  database_path = fs::path("derivatives/layout_fmriprep")
+)$get(desc = "confounds", extension = "tsv")
+path_new <- "xcp_d/custom_confounds"
+for (layout in layout_confounds) {
+  cur_path <- layout$path
+  read_tsv(cur_path, show_col_types = FALSE, na = "n/a") |>
+    select(
+      # global signals for CSF and WM
+      (starts_with("csf") | starts_with("white_matter")) & !contains("wm")
+    ) |>
+    mutate(across(everything(), \(x) replace_na(x, 0))) |>
+    write_tsv(fs::path(path_new, fs::path_file(cur_path)), na = "")
+}