Script to read multivolume images from Slicer DICOM database and save them as nrrd

mv_dicom_to_nrrd.py

directory = '.'
patientFolders = os.listdir(directory)
studyFolders = []
db = slicer.dicomDatabase

for index,patientFolder in enumerate(patientFolders):
  fullPath = os.path.join(directory,patientFolder)
  studyFolder = os.listdir(str(fullPath))[0]
  fullPathStudyFolder = os.path.join(fullPath,studyFolder)
  studyFolders.append(fullPathStudyFolder)

for i,studyFolder in enumerate(studyFolders):
  seriesFolders = os.listdir(studyFolder)
  for seriesFolder in seriesFolders:
    fileNames = os.listdir(os.path.join(studyFolder,seriesFolder))
    for index,fileName in enumerate(fileNames):
      fileNames[index] = os.path.join(directory, studyFolder , seriesFolder,fileName)
    plugin = slicer.modules.dicomPlugins['MultiVolumeImporterPlugin']()
    print '-------------------------------------------'
    if plugin:
      loadables = plugin.examine([fileNames])
    if len(loadables) == 0:
      print('plugin failed to interpret this series')
    else:
      patientID = db.fileValue(loadables[0].files[0],'0010,0020')
      seriesDescription = db.fileValue(loadables[0].files[0],'0008,103e')
      outputPath = "~/temp/"+ patientID + ' '+seriesDescription + ".nrrd" 
      print outputPath
      volume = plugin.load(loadables[0])
      slicer.util.saveNode(volume,outputPath)
      slicer.mrmlScene.RemoveNode(volume)
      slicer.app.processEvents()