Working version of prefetch; correction for output spaces

Author: michaelhallquist

R/process_subject.R

@@ -324,10 +324,7 @@ submit_fmriprep <- function(scfg, sub_dir = NULL, sub_id = NULL, ses_id = NULL,
     return(NULL)
   }
 
-  if (isTRUE(scfg$aroma$enable) && (is.null(scfg$fmriprep$output_spaces) || !grepl("MNI152NLin6Asym:res-2", scfg$fmriprep$output_spaces, fixed = TRUE))) {
-    message("Adding MNI152NLin6Asym:res-2 to output spaces for fmriprep to allow AROMA to run.")
-    scfg$fmriprep$output_spaces <- paste(scfg$fmriprep$output_spaces, "MNI152NLin6Asym:res-2")
-  }
+  scfg <- ensure_aroma_output_space(scfg, require_aroma = isTRUE(scfg$aroma$enable), verbose = FALSE)
 
   # for the mem request, have fmriprep request a bit less than the job gets itself
   # https://neurostars.org/t/fmriprep-failing-on-hpc-via-singularity/26342/27
@@ -337,7 +334,7 @@ submit_fmriprep <- function(scfg, sub_dir = NULL, sub_id = NULL, ses_id = NULL,
     glue("--participant_label {sub_id}"),
     glue("-w {scfg$metadata$scratch_directory}"),
     glue("--fs-license-file {scfg$fmriprep$fs_license_file}"),
-    glue("--output-spaces {scfg$fmriprep$output_spaces}"),
+    glue("--output-spaces {shQuote(trimws(scfg$fmriprep$output_spaces))}"),
     glue("--mem {format(max(4, scfg$fmriprep$memgb - 4)*1000, scientific=FALSE)}") # convert to MB
   ), collapse = TRUE)
 
@@ -433,7 +430,8 @@ submit_aroma <- function(scfg, sub_dir = NULL, sub_id = NULL, ses_id = NULL, env
   ), collapse = TRUE)
 
   cleanup <- isTRUE(scfg$aroma$cleanup)
-  if (cleanup && !is.null(scfg$fmriprep$output_spaces) &&
+  auto_added_aroma <- isTRUE(scfg$fmriprep$auto_added_aroma_space)
+  if (cleanup && !auto_added_aroma && !is.null(scfg$fmriprep$output_spaces) &&
       grepl("MNI152NLin6Asym:res-2", scfg$fmriprep$output_spaces, fixed = TRUE)) {
     msg <- "AROMA cleanup requested but will not occur because MNI152NLin6Asym:res-2 is in fmriprep --output-spaces."
     if (!is.null(lg)) lg$warn(msg) else warning(msg)

R/run_project.R

@@ -191,6 +191,8 @@ run_project <- function(scfg, steps = NULL, subject_filter = NULL, postprocess_s
     stop("Cannot run postprocessing without a valid FSL container.")
   }
 
+  scfg <- ensure_aroma_output_space(scfg, require_aroma = isTRUE(steps["aroma"]))
+
   flywheel_id <- NULL
   if (isTRUE(steps["flywheel_sync"])) flywheel_id <- submit_flywheel_sync(scfg)
 
@@ -474,3 +476,29 @@ submit_prefetch_templates <- function(scfg, steps) {
 
   return(job_id)
 }
+
+ensure_aroma_output_space <- function(scfg, require_aroma = isTRUE(scfg$aroma$enable), verbose = TRUE) {
+  checkmate::assert_class(scfg, "bg_project_cfg")
+  if (!isTRUE(require_aroma)) return(scfg)
+
+  if (is.null(scfg$fmriprep$auto_added_aroma_space)) scfg$fmriprep$auto_added_aroma_space <- FALSE
+
+  spaces <- scfg$fmriprep$output_spaces
+  has_required_space <- !is.null(spaces) && grepl("MNI152NLin6Asym:res-2", spaces, fixed = TRUE)
+  if (has_required_space) return(scfg)
+
+  addition <- "MNI152NLin6Asym:res-2"
+  if (is.null(spaces) || !nzchar(trimws(spaces))) {
+    scfg$fmriprep$output_spaces <- addition
+  } else {
+    scfg$fmriprep$output_spaces <- trimws(paste(spaces, addition))
+  }
+
+  if (isTRUE(verbose)) {
+    message("Adding MNI152NLin6Asym:res-2 to output spaces for fmriprep to allow AROMA to run.")
+  }
+
+  scfg$fmriprep$auto_added_aroma_space <- TRUE
+
+  return(scfg)
+}

R/setup_extract.R

@@ -141,7 +141,7 @@ setup_extract_stream <- function(scfg, fields = NULL, stream_name = NULL) {
   }
 
   if (!is.null(stream_name)) {
-    cat(glue("\n--- Specifying extraction stream: {stream_name} ---\n"))
+    cat(glue("\n--- Specifying extraction stream: {stream_name} ---\n", .trim = FALSE))
   }
 
   defaults <- list(

R/setup_project.R

@@ -838,7 +838,7 @@ setup_compute_environment <- function(scfg = list(), fields = NULL) {
     if (nzchar(fw_path)) {
       use_fw <- prompt_input(
         instruct = glue("Found Flywheel CLI at {fw_path}"),
-        prompt = "Use this location?",
+        prompt = "Use this to run flywheel?",
         type = "flag",
         default = TRUE
       )