R/ants_compcorr.R

In stnava/itkImageR: Examples using Rcpp to interface R and ITK

ants_compcorr <- function(moco_img = "", bm_img = "", avg_img = "", mocoparams_csv = "") {
  if (nchar(moco_img) == 0) {
    print(" please set a valid moco image ")
    print(" usage : ants_compcorr( <moco-image> , <brain-mask-image> , <average-image> , <mocoparams-csv> ) ")
    return
  }
  if (nchar(bm_img) == 0) {
    print(" please set a valid brain-mask image ")
    print(" usage : ants_compcorr( <moco-image> , <brain-mask-image> , <average-image> , <mocoparams-csv> ) ")
    return
  }
  if (nchar(avg_img) == 0) {
    print(" please set a valid average image ")
    print(" usage : ants_compcorr( <moco-image> , <brain-mask-image> , <average-image> , <mocoparams-csv> ) ")
    return
  }
  if (nchar(mocoparams_csv) == 0) {
    print(" please set a valid Moco-params csv file ")
    print(" usage : ants_compcorr_group( <moco-image> , <brain-mask-image> , <cortmask-image> , <mocoparams-csv> , <dosvd> ) ")
    return
  }
  
  # split the string into filename and extension
  split_img <- strsplit(moco_img, ".", fixed = TRUE)[[1]]
  filename <- split_img[1]
  if (length(split_img) == 2) {
    extension <- paste("", split_img[2], sep = ".")
  } else if (length(split_img) == 3) {
    extension <- paste("", split_img[2], split_img[3], sep = ".")
  }
  
  compcorr_img <- paste(filename, "_compcorr", extension, sep = "")
  ImageMath(4, compcorr_img, "CompCorrAuto", moco_img, bm_img, 6)
  
  N3BiasFieldCorrection(3, avg_img, avg_img, 2, bm_img)
  for (x in 1:3) {
    N3BiasFieldCorrection(3, avg_img, avg_img, 1, bm_img)
  }
  
  compcorr_variance_img <- paste(filename, "_compcorr_variance", extension, sep = "")
  seg_img <- paste(filename, "_seg", extension, sep = "")
  Atropos("-d", 3, "-a", avg_img, "-a", compcorr_variance_img, "-m", "[0.3,1x1x1]", "-o", seg_img, "-c", "[5,0]", 
    "-i", "kmeans[3]", "-x", bm_img)
  
  cortmask_img <- paste(filename, "_cortmask", extension, sep = "")
  ThresholdImage(3, seg_img, cortmask_img, 2, 2)
  csv <- paste(filename, ".csv", sep = "")
  sccan("--timeseriesimage-to-matrix", paste("[", paste(moco_img, cortmask_img, 0, 0, sep = ","), "]", sep = ""), 
    "-o", csv)
  
  compcorr_csv <- paste(filename, "_compcorr_compcorr", ".csv", sep = "")
  filt_csv <- paste(filename, "_filt", ".csv", sep = "")
  RSF_Networks_img <- paste(filename, "_RSF_Networks", extension, sep = "")
  antsr_frequency_filter(csv, filt_csv, 1.5, 0.03, 0.1, compcorr_csv)
  
  sccan("--svd", paste("sparse[", paste(filt_csv, cortmask_img, -0.15, sep = ","), "]", sep = ""), "-n", 40, 
    "-i", 40, "--PClusterThresh", 50, "-o", RSF_Networks_img)
  
  ea_rsf <- paste(filename, "_ea_rsf", sep = "")
  RSF_NetworksprojectionsView1vec_csv <- paste(filename, "_RSF_NetworksprojectionsView1vec", ".csv", sep = "")
  antsr_resting_state_corr_eigenanat(ea_rsf, RSF_NetworksprojectionsView1vec_csv, RSF_NetworksprojectionsView1vec_csv, 
    compcorr_csv, mocoparams_csv)
}