old_contents: #!/usr/bin/env python
  
  ##
  ##  Copyright 2017 SRI International
  ##  See COPYING file distributed along with the package for the copyright and license terms
  ##
  
  import os
  import sys
  from sibispy import sibislogger as slog
  from sibispy import utils as sutils
  from sibispy import session as sess
  
  #if sys.argv.__len__() > 1 : 
  #    config_file = sys.argv[1]
  #else :
  #    config_file = os.path.join(os.path.dirname(sys.argv[0]), 'data', '.sibis-general-config.yml')
  
  slog.init_log(False, False,'test_sibis_utils', 'test_sibis_utils',None)
  
  (errcode, stdout, stderr) = sutils.dcm2image("--man")
  if errcode : 
      print "Error: dcm2image: ", stderr
  
  (errcode, stdout, stderr) = sutils.gzip("-h")
  if errcode : 
      print "Error: gzip: ", stderr
  
  (errcode, stdout, stderr) = sutils.zip(".","--help","")
  if errcode : 
      print "Error: zip: ", stderr
  
  (errcode, stdout, stderr) = sutils.tar("--help")
  if errcode : 
      print "Error: tar: ", stderr
  
  (errcode, stdout, stderr) = sutils.make_nifti("-h")
  if errcode : 
      print "Error: make_nifti: ", stderr
  else : 
      # required by make_nifti 
      (errcode, stdout, stderr) = sutils.sprlioadd("")
      if errcode : 
          print "Error: sprlioadd: ", stderr
  
  
  
  # Front end right now 
  print "=== Front End " 
  (errcode, stdout, stderr) = sutils.Rscript("--help")
  if errcode : 
      print "Error: Rscript: ", stderr
  
  (ecode,sout,eout) = sutils.htmldoc("--help")
  if ecode > 1 : 
      print "Error: htmldoc: ", eout
  
  (ecode,sout,eout) = sutils.dicom2bxh(None,None)
  if ecode != 255 : 
      print "Error: dicom2bxh: ", eout
  
  (ecode,sout,eout) = sutils.detect_adni_phantom("--man")
  if ecode : 
      print "Error: detect_adni_phantom: ", eout
  
  (ecode,sout,eout) = sutils.mdb_export("")
  if ecode : 
      print "Error: mdb_export: (" + str(ecode) +")", eout
  
  
  
new_contents: #!/usr/bin/env python
  
  ##
  ##  Copyright 2017 SRI International
  ##  See COPYING file distributed along with the package for the copyright and license terms
  ##
  
  import os
  import sys
  from sibispy import sibislogger as slog
  from sibispy import utils as sutils
  from sibispy import session as sess
  
  #if sys.argv.__len__() > 1 : 
  #    config_file = sys.argv[1]
  #else :
  #    config_file = os.path.join(os.path.dirname(sys.argv[0]), 'data', '.sibis-general-config.yml')
  
  slog.init_log(False, False,'test_sibis_utils', 'test_sibis_utils',None)
  
  (errcode, stdout, stderr) = sutils.dcm2image("--man")
  if errcode : 
      print "Error: dcm2image: ", stderr
  
  (errcode, stdout, stderr) = sutils.gzip("-h")
  if errcode : 
      print "Error: gzip: ", stderr
  
  (errcode, stdout, stderr) = sutils.zip(".","--help","")
  if errcode : 
      print "Error: zip: ", stderr
  
  (errcode, stdout, stderr) = sutils.tar("--help")
  if errcode : 
      print "Error: tar: ", stderr
  
  (errcode, stdout, stderr) = sutils.make_nifti("-h")
  if errcode : 
      print "Error: make_nifti: ", stderr
  else : 
      # required by make_nifti 
      (errcode, stdout, stderr) = sutils.sprlioadd("")
      if errcode : 
          print "Error: sprlioadd: ", stderr
  
  
  
  # Front end right now 
  print "=== Front End " 
  (errcode, stdout, stderr) = sutils.Rscript("--help")
  if errcode : 
      print "Error: Rscript: ", stderr
  
  (ecode,sout,eout) = sutils.htmldoc("--help")
  if ecode > 1 : 
      print "Error: htmldoc: ", eout
  
  (ecode,sout,eout) = sutils.dicom2bxh(None,None)
  if ecode != 255 : 
      print "Error: dicom2bxh: ", eout
  
  (ecode,sout,eout) = sutils.detect_adni_phantom("--man")
  if ecode : 
      print "Error: detect_adni_phantom: ", eout
  
  (ecode,sout,eout) = sutils.mdb_export("")
  if ecode > 1: 
      print "Error: mdb_export: (" + str(ecode) +")", eout
  
  
  
subject: set flag correctly