0.8.1: added cwp_thr

Author: slamballais

R/qdecr.R

@@ -36,6 +36,7 @@ qdecr <- function(id,
                               "w_g.pct", "white.H", "white.K"),
                   fwhm = ifelse(measure == "pial_lgi", 5, 10),
                   mcz_thr = 30, 
+                  cwp_thr = 0.025,
                   mgh = NULL,
                   mask = NULL,
                   mask_path = system.file("extdata", paste0(hemi, ".fsaverage.cortex.mask.mgh"), package = "QDECR"),
@@ -187,7 +188,7 @@ qdecr <- function(id,
   for ( i in seq_along(vw$stack$names)){
     message2("\n", verbose = verbose)
     runMriSurfCluster(vw$paths$final_path, vw$paths$dir_fshome, vw$input$hemi, vw$stack$p[[i]], vw$post$fwhm_est, 
-                      mask_path = vw$paths$final_mask_path, verbose = verbose, mczThr = mcz_thr, 
+                      mask_path = vw$paths$final_mask_path, verbose = verbose, mcz_thr = mcz_thr, cwp_thr = cwp_thr,
                       stack = i, stack_name = vw$stack$names[i])
   }
   vw$post$final_mask <- load.mgh(vw$paths$final_mask_path)$x

R/qdecr_fastlm.R

@@ -10,6 +10,7 @@
 #' @param target the target template (usually "fsaverage")
 #' @param fwhm full width half max (default = 10 mm, for pial_lgi it is 5 mm)
 #' @param mcz_thr the Monte Carlo simulation threshold times 10 (13 = 0.05, 20 = 0.01, 23 = 0.005 30 = 0.001, etc..)
+#' @param cwp_thr the cluster-wise p-value threshold on top of all correction (default = 0.025, as there are 2 hemispheres)
 #' @param mgh NOT IMPLEMENTED; path to existing merged mgh file, default is NULL
 #' @param mask mgh file to mask analysis; default is to use the cortex label from the target
 #' @param mask_path path to the mask; default is the cortex mask that is provided with the QDECR package
@@ -40,6 +41,7 @@ qdecr_fastlm <- function(formula,
                          target = "fsaverage",
                          fwhm = ifelse(measure == "pial_lgi", 5, 10),
                          mcz_thr = 30,
+                         cwp_thr = 0.025,
                          mgh = NULL,
                          mask = NULL,
                          mask_path = system.file("extdata", paste0(hemi, ".fsaverage.cortex.mask.mgh"), package = "QDECR"),
@@ -85,6 +87,7 @@ vw <- qdecr(id = id,
             target = target,
             fwhm = fwhm,
             mcz_thr = mcz_thr,
+            cwp_thr = cwp_thr,
             measure = qqt2,
             mgh = mgh,
             mask = mask,

R/qdecr_post.R

@@ -1,43 +1,38 @@
-
-
-
-calc_fwhm <- function(final_path, final_mask_path, est_fwhm_path, hemi, eres, mask = NULL, target = "fsaverage", verbose = FALSE) {
-  cmdStr <- paste("mris_fwhm", "--i", eres, "--hemi", hemi, "--subject", target, "--prune", "--cortex", "--dat", est_fwhm_path, "--out-mask", final_mask_path)
-  if (!is.null(mask)) paste(cmdStr, "--mask", mask)
-  message2(verbose = verbose, cmdStr)
-  system(cmdStr, ignore.stdout = !verbose)
-  fwhm <- read.table(est_fwhm_path)
-  fwhm <- round(fwhm)
-  return(fwhm)
-}
-
-runMriSurfCluster <- function(final_path, dir_fshome, hemi, pval, fwhm, mask_path = NULL, cwpThr = 0.025, mczThr = NULL, csdSign = "abs", verbose = FALSE, stack, stack_name) {
-
-  if (is.null(mczThr)){
-    mczThr = paste0("th", as.character(30))
-  }
-  else {
-    mczThr =  paste0("th", as.character(mczThr))
-  }
-
-  oBaseName <- paste0(final_path, ".stack", stack, ".cache.", mczThr, '.', csdSign, ".sig")
-  if (fwhm < 10) fwhm <- paste0('0', fwhm)
-  csd <- file.path(dir_fshome, "average/mult-comp-cor/fsaverage", hemi, paste0("cortex/fwhm", fwhm), csdSign, mczThr, "mc-z.csd")
-  cmdStr <- paste("mri_surfcluster",
-                  "--in", pval,
-                  "--csd", csd, 
-                  "--cwsig", paste0(oBaseName, ".cluster.mgh"),
-                  "--vwsig", paste0(oBaseName, ".voxel.mgh"),
-                  "--sum", paste0(oBaseName, ".cluster.summary"),
-                  "--ocn",  paste0(oBaseName, ".ocn.mgh"),
-                  "--oannot", paste0(oBaseName, ".ocn.annot"),
-                  "--annot", "aparc",
-                  "--csdpdf",  paste0(oBaseName, ".pdf.dat"),
-                  "--cwpvalthresh", cwpThr,
-                  "--o", paste0(oBaseName, ".masked.mgh"),
-                  "--no-fixmni",
-                  "--surf", "white")
-  cmdStr <- if (!is.null(mask_path)) paste(cmdStr, "--mask", mask_path) else paste(cmdStr, "--cortex")
-  system(cmdStr, ignore.stdout = !verbose)
-  NULL
+
+
+
+calc_fwhm <- function(final_path, final_mask_path, est_fwhm_path, hemi, eres, mask = NULL, target = "fsaverage", verbose = FALSE) {
+  cmdStr <- paste("mris_fwhm", "--i", eres, "--hemi", hemi, "--subject", target, "--prune", "--cortex", "--dat", est_fwhm_path, "--out-mask", final_mask_path)
+  if (!is.null(mask)) paste(cmdStr, "--mask", mask)
+  message2(verbose = verbose, cmdStr)
+  system(cmdStr, ignore.stdout = !verbose)
+  fwhm <- read.table(est_fwhm_path)
+  fwhm <- round(fwhm)
+  return(fwhm)
+}
+
+runMriSurfCluster <- function(final_path, dir_fshome, hemi, pval, fwhm, mask_path = NULL, cwp_thr = 0.025, mcz_thr = 30, csd_sign = "abs", verbose = FALSE, stack, stack_name) {
+
+  mcz_thr2 <- paste0("th", mcz_thr)
+
+  o_base_name <- paste0(final_path, ".stack", stack, ".cache.", mcz_thr2, '.', csd_sign, ".sig")
+  if (fwhm < 10) fwhm <- paste0("0", fwhm)
+  csd <- file.path(dir_fshome, "average/mult-comp-cor/fsaverage", hemi, paste0("cortex/fwhm", fwhm), csd_sign, mcz_thr2, "mc-z.csd")
+  cmd_str <- paste("mri_surfcluster",
+                   "--in", pval,
+                   "--csd", csd, 
+                   "--cwsig", paste0(o_base_name, ".cluster.mgh"),
+                   "--vwsig", paste0(o_base_name, ".voxel.mgh"),
+                   "--sum", paste0(o_base_name, ".cluster.summary"),
+                   "--ocn",  paste0(o_base_name, ".ocn.mgh"),
+                   "--oannot", paste0(o_base_name, ".ocn.annot"),
+                   "--annot", "aparc",
+                   "--csdpdf",  paste0(o_base_name, ".pdf.dat"),
+                   "--cwpvalthresh", cwp_thr,
+                   "--o", paste0(o_base_name, ".masked.mgh"),
+                   "--no-fixmni",
+                   "--surf", "white")
+  cmd_str <- if (!is.null(mask_path)) paste(cmd_str, "--mask", mask_path) else paste(cmd_str, "--cortex")
+  system(cmd_str, ignore.stdout = !verbose)
+  NULL
 }