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.