set(basedir 'F:/Data/Atlas/Data/Normal/itkEMSResults/Subjects/')
set(basedirout 'F:/Data/Atlas/Data/Normal/Outputs/')

listdirindir(directories '$(basedir)')


foreach(subject ${directories})
  set(fullpath '${basedir}${subject}')
  set(t1 'T1/')

  listfileindir(t1_white '${fullpath}' subject0*_t12phantom_posterior0_itkEMS.mh*)
  listfileindir(t1_grey '${fullpath}' subject0*_t12phantom_posterior1_itkEMS.mh*)
  listfileindir(t1_csf '${fullpath}' subject0*_t12phantom_posterior2_itkEMS.mh*)
   
  set(t1_white '${fullpath}${t1_white}')
  set(t1_grey '${fullpath}${t1_grey}')
  set(t1_csf '${fullpath}${t1_csf}')

  SetApp(MaskCreator @MaskCreator)
  SetAppOption(MaskCreator.inWhite.filename ${t1_white})
  SetAppOption(MaskCreator.inGrey.filename ${t1_grey})
  SetAppOption(MaskCreator.inCsf.filename ${t1_csf})
  Set(fileName ${basedirout}${subject}${t1}subject00_t1_brain_white.mha)
  SetAppOption(MaskCreator.outWhite.filename ${fileName})
  Set(fileName ${basedirout}${subject}${t1}subject00_t1_brain_grey.mha)
  SetAppOption(MaskCreator.outGrey.filename ${fileName})
    
  echo(${MaskCreator})
  Run(output ${MaskCreator})

endforeach(subject)