doc: ensure the new brain extraction workflow is plotted

Author: oesteban

docs/workflows.rst

@@ -93,8 +93,19 @@ single reference template (see `Longitudinal processing`_).
 Brain extraction, brain tissue segmentation and spatial normalization
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Then, the T1w image/average is skull-stripped using ANTs' ``antsBrainExtraction.sh``,
-which is an atlas-based brain extraction workflow.
+Then, the T1w reference is skull-stripped using a Nipype implementation of
+the ``antsBrainExtraction.sh`` tool (ANTs), which is an atlas-based 
+brain extraction workflow:
+
+.. workflow::
+    :graph2use: orig
+    :simple_form: yes
+
+    from niworkflows.anat.ants import init_brain_extraction_wf
+    wf = init_brain_extraction_wf()
+
+
+An example of brain extraction is shown below:
 
 .. figure:: _static/brainextraction_t1.svg
     :scale: 100%
@@ -254,31 +265,34 @@ BOLD preprocessing
     :graph2use: orig
     :simple_form: yes
 
+    from collections import namedtuple
+    BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
     from fmriprep.workflows.bold import init_func_preproc_wf
     wf = init_func_preproc_wf(
         '/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
-        omp_nthreads=1,
-        ignore=[],
-        freesurfer=True,
-        reportlets_dir='.',
-        output_dir='.',
-        template='MNI152NLin2009cAsym',
-        output_spaces=['T1w', 'fsnative', 'template', 'fsaverage5'],
-        medial_surface_nan=False,
+        aroma_melodic_dim=-200,
+        bold2t1w_dof=9,
         cifti_output=False,
         debug=False,
-        low_mem=False,
-        use_bbr=True,
-        t2s_coreg=False,
-        bold2t1w_dof=9,
+        err_on_aroma_warn=False,
         fmap_bspline=True,
         fmap_demean=True,
-        use_syn=True,
         force_syn=True,
+        freesurfer=True,
+        ignore=[],
+        layout=BIDSLayout(),
+        low_mem=False,
+        medial_surface_nan=False,
+        omp_nthreads=1,
+        output_dir='.',
+        output_spaces=['T1w', 'fsnative', 'template', 'fsaverage5'],
+        reportlets_dir='.',
+        t2s_coreg=False,
+        template='MNI152NLin2009cAsym',
         template_out_grid='native',
         use_aroma=False,
-        aroma_melodic_dim=-200,
-        err_on_aroma_warn=False,
+        use_bbr=True,
+        use_syn=True,
     )
 
 Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is

fmriprep/workflows/bold/base.py

@@ -61,6 +61,8 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         :simple_form: yes
 
         from fmriprep.workflows.bold import init_func_preproc_wf
+        from collections import namedtuple
+        BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
         wf = init_func_preproc_wf('/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
                                   omp_nthreads=1,
                                   ignore=[],
@@ -85,7 +87,8 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
                                   use_aroma=False,
                                   err_on_aroma_warn=False,
                                   aroma_melodic_dim=-200,
-                                  num_bold=1)
+                                  num_bold=1,
+                                  layout=BIDSLayout())
 
     **Parameters**