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,

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')

Example source code

You can download the full source code of this example. This same script is also included in Nipype1 Examples Niflow under the package/niflow/nipype1/examples directory.