Apply suggestions from code review

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>

Author: oesteban

doc/examples.rst

@@ -5,6 +5,9 @@
 =======================
 User Guide and Examples
 =======================
+The following examples are `literate programming <https://en.wikipedia.org/wiki/Literate_programming>`__
+documents which solve specific problems using Nipype.
+In some cases, the same problem is solved with multiple underlying tools.
 
 .. admonition:: Michael Notter's User Guide
 

doc/interfaces.rst

@@ -12,6 +12,9 @@ Workflows
   The workflows that used to live as a module under
   ``nipype.workflows`` have been migrated to the
   new project `NiFlows <https://github.com/niflows>`__.
+  These may be installed with the
+  `niflow-nipype1-examples <https://pypi.org/project/niflow-nipype1-workflows/>`__
+  package, but their continued use is discouraged.
 
 Interfaces
 ----------

examples/fmri_spm_auditory.py

@@ -390,7 +390,7 @@ def getstripdir(subject_id):
 The code discussed above sets up all the necessary data structures
 with appropriate parameters and the connectivity between the
 processes, but does not generate any output. To actually run the
-analysis on the data the :func:`nipype.pipeline.engine.Workflow.run`
+analysis on the data the :func:`nipype.pipeline.engine.workflows.Workflow.run`
 function needs to be called.
 """
 

nipype/interfaces/cmtk/parcellation.py

@@ -669,7 +669,7 @@ def extract(Z, shape, position, fill):
         the original data
     shape : tuple
         tuple containing neighbourhood dimensions
-    position :
+    position : tuple
         tuple containing central point indexes
     fill : float
        value for the padding of Z