add t1 skullstrip workflow

Author: josephmje

dmriprep/workflows/anatomical.py

@@ -0,0 +1,36 @@
+# -*- coding: utf-8 -*-
+
+"""
+Orchestrating the T1w preprocessing workflows
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autofunction:: init_anat_preproc_wf
+
+"""
+
+from nipype.pipeline import engine as pe
+from nipype.interfaces import utility as niu
+
+from niworkflows.anat.ants import init_brain_extraction_wf
+
+
+def init_anat_preproc_wf()
+    """
+    """
+
+    wf = pe.Workflow(name='init_anat_preproc_wf')
+
+    inputnode = pe.Node(niu.IdentityInterface(fields=['T1w_file']), name='inputnode')
+
+    outputnode = pe.Node(niu.IdentityInterface(fields=['out_file']), name='outputnode')
+
+    t1_skullstrip = init_brain_extraction_wf()
+
+    to_list = lambda x: [x]
+
+    wf.connect([
+        (inputnode, t1_skullstrip, [(('t1_file', to_list), 'inputnode.in_files')]),
+        (t1_skullstrip, outputnode, [('outputnode.out_file', 'out_file')])
+    ])
+
+    return wf

docs/dmriprep.workflows.rst

@@ -12,6 +12,14 @@ Subpackages
 Submodules
 ----------
 
+dmriprep.workflows.anatomical module
+------------------------------------
+
+.. automodule:: dmriprep.workflows.anatomical
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 dmriprep.workflows.base module
 ------------------------------