.. AUTO-GENERATED FILE -- DO NOT EDIT!

.. _example_smri_cbs_skullstripping:


========================================
sMRI: USing CBS Tools for skullstripping
========================================

This simple workflow uses SPECTRE2010 algorithm to skullstrip an MP2RAGE
anatomical scan.

::
  
  import nipype.pipeline.engine as pe
  from nipype.interfaces.mipav.developer import (JistIntensityMp2rageMasking,
                                                 MedicAlgorithmSPECTRE2010)
  
  wf = pe.Workflow("skullstripping")
  
  mask = pe.Node(JistIntensityMp2rageMasking(), name="masking")
  folder_path = '/Users/filo/7t_trt/niftis/sub001/session_1/'
  mask.inputs.inSecond = folder_path + "MP2RAGE_INV2.nii.gz"
  mask.inputs.inQuantitative = folder_path + "MP2RAGE_UNI.nii.gz"
  mask.inputs.inT1weighted = folder_path + "MP2RAGE_T1.nii.gz"
  mask.inputs.outMasked = True
  mask.inputs.outMasked2 = True
  mask.inputs.outSignal = True
  mask.inputs.outSignal2 = True
  
  skullstrip = pe.Node(MedicAlgorithmSPECTRE2010(), name="skullstrip")
  skullstrip.inputs.outStripped = True
  skullstrip.inputs.xDefaultMem = 6000
  
  wf.connect(mask, 'outMasked', skullstrip, 'inInput')
  wf.run()


.. include:: ../../links_names.txt



.. admonition:: Example source code

   You can download :download:`the full source code of this example <../../../examples/smri_cbs_skullstripping.py>`.
   This same script is also included in the Nipype source distribution under the
   :file:`examples` directory.

