ct-tiqua_boutique_descriptor.json

{
  "author" : "Clement BROSSARD",
  "command-line" : "filename=$(basename '[INPUT_FILE]');filename=${filename%%.*} && ct-tiqua [INPUT_FILE] --output ct-tiqua_output_folder [ENSEMBLE] [KEEP_TMP_FILES] [VENTRICLES] && tar -cvzf ${filename}_CT-tiqua_output.tar.gz ct-tiqua_output_folder && rm -f ct-tiqua_output_folder",
  "container-image" : {
    "image" : "nifmgin/ct-tiqua:4.0",
    "index" : "index.docker.io",
    "type" : "docker"
  },
  "description" : "Computed Tomography based Traumatic Brain Injury Quantification (version 4.0). This software takes as input a CT-scan of a head injured patient and returns: 1/ the segmentation of 7 types of lesions typical from TBI, 2/ a structural and a vascular atlas dividing the input brain in 54 and 32 zones respectively, and 3/ two csv files containing the volume in mm3 of all type on lesion in all zone of the brain (one for each atlas). It was developed by Clement Brossard Theotime Fehr Delude and Benjamin Lemasson (benjamin.lemasson@univ-grenoble-alpes.fr).  If you use our software, please cite our work : Brossard, C., Grèze, J., de Busschère, JA. et al. Prediction of therapeutic intensity level from automatic multiclass segmentation of traumatic brain injury lesions on CT-scans. Sci Rep 13, 20155 (2023). https://doi.org/10.1038/s41598-023-46945-9",
  "inputs" : [
    {
      "command-line-flag" : "--input",
      "description" : "Input image (e.g. img.nii, img.nii.gz) to be processed. It must be a brain CT-scan.",
      "id" : "infile",
      "name" : "Input file",
      "optional" : false,
      "type" : "File",
      "value-key" : "[INPUT_FILE]"
    },
    {
      "command-line-flag" : "--keep_tmp_files",
      "description" : "Do not remove temporary files at the end of the pipeline, ie. include them in the output archive.",
      "id" : "keep_tmp_files",
      "name" : "Keep temporary files",
      "optional" : true,
      "type" : "Flag",
      "value-key" : "[KEEP_TMP_FILES]"
    },
    {
      "command-line-flag" : "--ventricles",
      "description" : "Compute ventricles volume using TotalSegmentator.",
      "id" : "ventricles",
      "name" : "ventricles volume computation",
      "optional" : true,
      "type" : "Flag",
      "value-key" : "[VENTRICLES]"
    }
  ],
 
  "name" : "ct-tiqua",
  "output-files" : [
    {
      "description" : "Tarball of all the outputs of CT-TIQUA. ",
      "id" : "outfile",
      "name" : "Output archive",
      "optional" : false,
      "path-template" : "CT-tiqua_output.tar.gz"
    }
  ],
  "schema-version" : "0.5",
  "tool-version" : "4.0"
}