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# 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")
    mask.inputs.inSecond = "/Users/filo/7t_trt/niftis/sub001/session_1/MP2RAGE_INV2.nii.gz"
    mask.inputs.inQuantitative = "/Users/filo/7t_trt/niftis/sub001/session_1/MP2RAGE_UNI.nii.gz"
    mask.inputs.inT1weighted = "/Users/filo/7t_trt/niftis/sub001/session_1/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()

Example source code

You can download `the full source code of this example`. This same script is also included in the Nipype source distribution under the `examples` directory.