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

listdirindir(directories '$(basedirout)')


set(listFile_white '')
set(listFile_grey '')

foreach(subject ${directories})
  set(fullpath '${basedirout}${subject}')
  listdirindir(dir_t1 '${fullpath}' T1)

  listfileindir(t1_mask_white '${fullpath}${dir_t1}' subject0*_t1_brain_white.mha)
  listfileindir(t1_mask_grey '${fullpath}${dir_t1}' subject0*_t1_brain_grey.mha)
 
  set(t1_mask_white '${fullpath}${dir_t1}${t1_mask_white}')
  set(t1_mask_grey '${fullpath}${dir_t1}${t1_mask_grey}')
 
  set(listFile_white '${listFile_white} ${t1_mask_white}')
  set(listFile_grey '${listFile_grey} ${t1_mask_grey}')
    
endforeach(subject)
#echo(${listFile_white})
Set(filename ${basedirout}STAPLE_white.odc)
Run(output '${ObjectDocumentBuilder} -in ${listFile_white} -out ${filename}')

#echo(${listFile_grey})
Set(filename ${basedirout}STAPLE_grey.odc)
Run(output '${ObjectDocumentBuilder} -in ${listFile_grey} -out ${filename}')


listFileInDir(ODC_white ${basedirout} STAPLE_white.odc)
listFileInDir(ODC_grey ${basedirout} STAPLE_grey.odc)

Set(ODC_white ${basedirout}${ODC_white})
Set(ODC_grey ${basedirout}${ODC_grey})

SetApp(STAPLEcor @STAPLECorrection)
SetAppOption(STAPLEcor.inODC.filename ${ODC_white})
Set(filename ${basedirout}STAPLE_white.mha)
SetAppOption(STAPLEcor.Output.filename ${filename})
SetAppOption(STAPLEcor.Foreground.value 1)

echo(${STAPLEcor})
Run(output ${STAPLEcor})

SetApp(STAPLEcor2 @STAPLECorrection)
SetAppOption(STAPLEcor2.inODC.filename ${ODC_grey})
Set(filename ${basedirout}STAPLE_grey.mha)
SetAppOption(STAPLEcor2.Output.filename ${filename})
SetAppOption(STAPLEcor2.Foreground.value 1)

echo(${STAPLEcor2})
Run(output ${STAPLEcor2})