enh: connect workflow

Author: oesteban

dmriprep/workflows/base.py

@@ -447,29 +447,27 @@ def init_single_subject_wf(
             use_syn=use_syn,
         )
 
-    #     workflow.connect([
-    #         (anat_preproc_wf, dwi_preproc_wf,
-    #          [(('outputnode.t1_preproc', _pop), 'inputnode.t1_preproc'),
-    #           ('outputnode.t1_brain', 'inputnode.t1_brain'),
-    #           ('outputnode.t1_mask', 'inputnode.t1_mask'),
-    #           ('outputnode.t1_seg', 'inputnode.t1_seg'),
-    #           ('outputnode.t1_aseg', 'inputnode.t1_aseg'),
-    #           ('outputnode.t1_aparc', 'inputnode.t1_aparc'),
-    #           ('outputnode.t1_tpms', 'inputnode.t1_tpms'),
-    #           ('outputnode.template', 'inputnode.template'),
-    #           ('outputnode.forward_transform', 'inputnode.anat2std_xfm'),
-    #           ('outputnode.reverse_transform', 'inputnode.std2anat_xfm'),
-    #           ('outputnode.joint_template', 'inputnode.joint_template'),
-    #           ('outputnode.joint_forward_transform', 'inputnode.joint_anat2std_xfm'),
-    #           ('outputnode.joint_reverse_transform', 'inputnode.joint_std2anat_xfm'),
-    #           # Undefined if --no-freesurfer, but this is safe
-    #           ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
-    #           ('outputnode.subject_id', 'inputnode.subject_id'),
-    #           ('outputnode.t1_2_fsnative_forward_transform',
-    #            'inputnode.t1_2_fsnative_forward_transform'),
-    #           ('outputnode.t1_2_fsnative_reverse_transform',
-    #            'inputnode.t1_2_fsnative_reverse_transform')]),
-    #     ])
+        workflow.connect([
+            (anat_preproc_wf, dwi_preproc_wf,
+             [(('outputnode.t1w_preproc', _pop), 'inputnode.t1w_preproc'),
+              ('outputnode.t1w_brain', 'inputnode.t1w_brain'),
+              ('outputnode.t1w_mask', 'inputnode.t1w_mask'),
+              ('outputnode.t1w_dseg', 'inputnode.t1w_dseg'),
+              ('outputnode.t1w_aseg', 'inputnode.t1w_aseg'),
+              ('outputnode.t1w_aparc', 'inputnode.t1w_aparc'),
+              ('outputnode.t1w_tpms', 'inputnode.t1w_tpms'),
+              ('outputnode.template', 'inputnode.template'),
+              ('outputnode.anat2std_xfm', 'inputnode.anat2std_xfm'),
+              ('outputnode.std2anat_xfm', 'inputnode.std2anat_xfm'),
+              ('outputnode.joint_template', 'inputnode.joint_template'),
+              ('outputnode.joint_anat2std_xfm', 'inputnode.joint_anat2std_xfm'),
+              ('outputnode.joint_std2anat_xfm', 'inputnode.joint_std2anat_xfm'),
+              # Undefined if --fs-no-reconall, but this is safe
+              ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
+              ('outputnode.subject_id', 'inputnode.subject_id'),
+              ('outputnode.t1w2fsnative_xfm', 'inputnode.t1w2fsnative_xfm'),
+              ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm')]),
+        ])
 
     return workflow
 

dmriprep/workflows/dwi/base.py

@@ -1,7 +1,4 @@
-"""
-Orchestrating the dMRI-preprocessing workflow.
-
-"""
+"""Orchestrating the dMRI-preprocessing workflow."""
 
 from nipype import logging
 
@@ -16,9 +13,6 @@
 from ...interfaces.reports import DiffusionSummary
 from ...interfaces.vectors import CheckGradientTable
 
-# dwi workflows
-from .util import init_dwi_reference_wf
-
 
 LOGGER = logging.getLogger('nipype.workflow')
 
@@ -109,6 +103,7 @@ def init_dwi_preproc_wf(
     * :py:func:`~dmriprep.workflows.dwi.util.init_dwi_reference_wf`
 
     """
+    from .util import init_dwi_reference_wf
 
     wf_name = _get_wf_name(dwi_file)
 
@@ -139,7 +134,12 @@ def init_dwi_preproc_wf(
         metadata = layout.get_metadata(dwi_file)
 
     inputnode = pe.Node(niu.IdentityInterface(
-        fields=['dwi_file', 'bvec_file', 'bval_file']),
+        fields=['dwi_file', 'bvec_file', 'bval_file',
+                'subjects_dir', 'subject_id',
+                't1w_preproc', 't1w_brain', 't1w_mask', 't1w_dseg', 't1w_tpms',
+                't1w_aseg', 't1w_aparc', 'anat2std_xfm', 'std2anat_xfm', 'template',
+                'joint_anat2std_xfm', 'joint_std2anat_xfm', 'joint_template',
+                't1w2fsnative_xfm', 'fsnative2t1w_xfm']),
         name='inputnode')
     inputnode.inputs.dwi_file = dwi_file
     inputnode.inputs.bvec_file = bvec_file
@@ -201,10 +201,12 @@ def init_dwi_preproc_wf(
 def _get_wf_name(dwi_fname):
     """
     Derive the workflow name for supplied dwi file.
+
     >>> _get_wf_name('/completely/made/up/path/sub-01_dwi.nii.gz')
     'dwi_preproc_wf'
     >>> _get_wf_name('/completely/made/up/path/sub-01_run-1_dwi.nii.gz')
     'dwi_preproc_run_1_wf'
+
     """
     from nipype.utils.filemanip import split_filename
     fname = split_filename(dwi_fname)[1]

dmriprep/workflows/dwi/util.py

@@ -14,8 +14,7 @@
 DEFAULT_MEMORY_MIN_GB = 0.01
 
 
-def init_dwi_reference_wf(omp_nthreads, dwi_file=None,
-                          name='dwi_reference_wf', gen_report=False):
+def init_dwi_reference_wf(omp_nthreads, name='dwi_reference_wf', gen_report=False):
     """
     Build a workflow that generates a reference b0 image from a DWI dataset.
 
@@ -37,8 +36,6 @@ def init_dwi_reference_wf(omp_nthreads, dwi_file=None,
 
     Parameters
     ----------
-    dwi_file : str
-        dwi NIfTI file
     omp_nthreads : int
         Maximum number of threads an individual process may use
     name : str
@@ -83,10 +80,6 @@ def init_dwi_reference_wf(omp_nthreads, dwi_file=None,
                                       'dwi_mask', 'validation_report']),
         name='outputnode')
 
-    # Simplify manually setting input image
-    if dwi_file is not None:
-        inputnode.inputs.dwi_file = dwi_file
-
     validate = pe.Node(ValidateImage(), name='validate', mem_gb=DEFAULT_MEMORY_MIN_GB)
 
     extract_b0 = pe.Node(ExtractB0(), name='extract_b0')