fix(docs): now documentation builds (depends on changes on sMRIPrep)

Author: oesteban

docs/usage.rst

@@ -37,6 +37,7 @@ Command-Line Arguments
    :nodefault:
    :nodefaultconst:
 
+
 Defining standard and nonstandard spaces where data will be resampled
 =====================================================================
 
@@ -46,7 +47,7 @@ That is achieved using the ``--output-spaces`` argument, where standard and
 nonstandard spaces can be inserted.
 
 Standard spaces
----------------
+"""""""""""""""
 
 When using fMRIPrep in a workflow that will investigate effects that span across
 analytical groupings, neuroimagers typically resample their data on to a standard,
@@ -88,7 +89,7 @@ FreeSurfer will be supported (e.g. ``fsaverage5``) although the use of the densi
 modifier would be preferred (i.e. ``fsaverage:den-10k`` for ``fsaverage5``).
 
 Custom standard spaces
-----------------------
+""""""""""""""""""""""
 
 Although the functionality is not available yet, the interface of the
 ``--output-spaces`` permits providing paths to custom templates that
@@ -107,7 +108,7 @@ must be found under under ``/path/to/custom/templates/tpl-MyCustom``: ::
 Although a more comprehensive coverage of standard files would be advised.
 
 Nonstandard spaces
-------------------
+""""""""""""""""""
 
 Additionally, ``--output-spaces`` accepts identifiers of spatial references
 that do not generate *standardized* coordinate spaces:
@@ -125,7 +126,7 @@ that do not generate *standardized* coordinate spaces:
 Modifiers are not allowed when providing nonstandard spaces.
 
 Preprocessing blocks depending on standard templates
-----------------------------------------------------
+""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 Some modules of the pipeline (e.g. the ICA-AROMA denoising, the generation of
 HCP compatible *grayordinates* files, or the *fieldmap-less* distortion correction)

docs/workflows.rst

@@ -19,44 +19,43 @@ is presented below:
     :simple_form: yes
 
     from fmriprep.workflows.base import init_single_subject_wf
-    from collections import namedtuple
+    from collections import namedtuple, OrderedDict
     BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
     wf = init_single_subject_wf(
-        layout=BIDSLayout(),
-        subject_id='test',
-        name='single_subject_wf',
-        task_id='',
+        anat_only=False,
+        aroma_melodic_dim=-200,
+        bold2t1w_dof=9,
+        cifti_output=False,
+        debug=False,
         echo_idx=None,
+        err_on_aroma_warn=False,
+        fmap_bspline=False,
+        fmap_demean=True,
+        force_syn=True,
+        freesurfer=True,
+        hires=True,
+        ignore=[],
+        layout=BIDSLayout(),
         longitudinal=False,
-        t2s_coreg=False,
+        low_mem=False,
+        medial_surface_nan=False,
+        name='single_subject_wf',
         omp_nthreads=1,
-        freesurfer=True,
-        reportlets_dir='.',
         output_dir='.',
-        skull_strip_template='OASIS30ANTs',
+        output_spaces=OrderedDict([
+            ('MNI152Lin', {}), ('fsaverage', {'density': '10k'}),
+            ('T1w', {}), ('fsnative', {})]),
+        reportlets_dir='.',
         skull_strip_fixed_seed=False,
-        template='MNI152NLin2009cAsym',
-        output_spaces=['T1w', 'fsnative', 'template', 'fsaverage5'],
-        medial_surface_nan=False,
-        cifti_output=False,
-        ignore=[],
-        debug=False,
-        low_mem=False,
-        anat_only=False,
-        hires=True,
+        skull_strip_template='OASIS30ANTs',
+        subject_id='test',
+        t2s_coreg=False,
+        task_id='',
+        use_aroma=False,
         use_bbr=True,
-        bold2t1w_dof=9,
-        fmap_bspline=False,
-        fmap_demean=True,
         use_syn=True,
-        force_syn=True,
-        template_out_grid='native',
-        use_aroma=False,
-        aroma_melodic_dim=-200,
-        err_on_aroma_warn=False,
     )
 
-
 T1w/T2w preprocessing
 ---------------------
 :mod:`fmriprep.workflows.anatomical.init_anat_preproc_wf`
@@ -65,22 +64,20 @@ T1w/T2w preprocessing
     :graph2use: orig
     :simple_form: yes
 
+    from collections import OrderedDict
     from fmriprep.workflows.anatomical import init_anat_preproc_wf
     wf = init_anat_preproc_wf(
         bids_root='.',
-        debug=False,
         freesurfer=True,
-        fs_spaces=['T1w', 'fsnative',
-                   'template', 'fsaverage5'],
         hires=True,
         longitudinal=False,
         num_t1w=1,
         omp_nthreads=1,
         output_dir='.',
+        output_spaces=OrderedDict([
+            ('MNI152NLin2009cAsym', {}), ('fsaverage5', {})]),
         reportlets_dir='.',
         skull_strip_template='MNI152NLin2009cAsym',
-        skull_strip_fixed_seed=False,
-        template='MNI152NLin2009cAsym',
     )
 
 The anatomical sub-workflow begins by constructing an average image by
@@ -274,13 +271,13 @@ BOLD preprocessing
     :graph2use: orig
     :simple_form: yes
 
-    from collections import namedtuple
+    from collections import namedtuple, OrderedDict
+    from fmriprep.workflows.bold.base import init_func_preproc_wf
     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',
         aroma_melodic_dim=-200,
         bold2t1w_dof=9,
+        bold_file='/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
         cifti_output=False,
         debug=False,
         err_on_aroma_warn=False,
@@ -289,19 +286,20 @@ BOLD preprocessing
         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'],
+        output_spaces=OrderedDict([
+            ('MNI152Lin', {}), ('fsaverage', {'density': '10k'}),
+            ('T1w', {}), ('fsnative', {})]),
         reportlets_dir='.',
         t2s_coreg=False,
-        template='MNI152NLin2009cAsym',
-        template_out_grid='native',
         use_aroma=False,
         use_bbr=True,
         use_syn=True,
+        layout=BIDSLayout(),
+        num_bold=1,
     )
 
 Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is
@@ -478,13 +476,14 @@ EPI to MNI transformation
     :graph2use: colored
     :simple_form: yes
 
+    from collections import OrderedDict
     from fmriprep.workflows.bold import init_bold_std_trans_wf
     wf = init_bold_std_trans_wf(
-        template='MNI152NLin2009cAsym',
-		freesurfer=True,
-        mem_gb=1,
+        standard_spaces=OrderedDict([('MNI152Lin', {}),
+                                     ('fsaverage', {'density': '10k'})]),
+        mem_gb=3,
         omp_nthreads=1,
-        template_out_grid='native')
+    )
 
 This sub-workflow concatenates the transforms calculated upstream (see
 `Head-motion estimation`_, `Susceptibility Distortion Correction (SDC)`_ --if

fmriprep/workflows/bold/confounds.py

@@ -439,8 +439,7 @@ def init_ica_aroma_wf(metadata, mem_gb, omp_nthreads,
         :simple_form: yes
 
         from fmriprep.workflows.bold.confounds import init_ica_aroma_wf
-        wf = init_ica_aroma_wf(template='MNI152NLin2009cAsym',
-                               metadata={'RepetitionTime': 1.0},
+        wf = init_ica_aroma_wf(metadata={'RepetitionTime': 1.0},
                                mem_gb=3,
                                omp_nthreads=1)
 

fmriprep/workflows/bold/resampling.py

@@ -191,7 +191,7 @@ def init_bold_std_trans_wf(
                                          ('fsaverage', {'density': '10k'})]),
             mem_gb=3,
             omp_nthreads=1,
-            template_out_grid='native')
+        )
 
     **Parameters**