Address review comments

Author: emdupre

fmriprep/workflows/bold/base.py

@@ -465,18 +465,18 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
             ('subject_id', 'inputnode.subject_id'),
             ('t1_2_fsnative_reverse_transform', 'inputnode.t1_2_fsnative_reverse_transform')]),
         (inputnode, bold_t1_trans_wf, [
+            ('bold_file', 'inputnode.name_source'),
             ('t1_brain', 'inputnode.t1_brain'),
             ('t1_mask', 'inputnode.t1_mask'),
             ('t1_aseg', 'inputnode.t1_aseg'),
             ('t1_aparc', 'inputnode.t1_aparc')]),
-        (inputnode, bold_t1_trans_wf, [('bold_file', 'inputnode.name_source')]),
         (bold_split, bold_t1_trans_wf, [('out_files', 'inputnode.bold_split')]),
         (bold_hmc_wf, bold_t1_trans_wf, [('outputnode.xforms', 'inputnode.hmc_xforms')]),
-        (bold_t1_trans_wf, outputnode, [('outputnode.bold_aseg_t1', 'bold_aseg_t1'),
-                                        ('outputnode.bold_aparc_t1', 'bold_aparc_t1')]),
         (bold_reg_wf, bold_t1_trans_wf, [
             ('outputnode.itk_bold_to_t1', 'inputnode.itk_bold_to_t1')]),
-        (bold_t1_trans_wf, outputnode, [('outputnode.bold_t1', 'bold_t1')]),
+        (bold_t1_trans_wf, outputnode, [('outputnode.bold_t1', 'bold_t1'),
+                                        ('outputnode.bold_aseg_t1', 'bold_aseg_t1'),
+                                        ('outputnode.bold_aparc_t1', 'bold_aparc_t1')]),
         (bold_reg_wf, summary, [('outputnode.fallback', 'fallback')]),
         # SDC (or pass-through workflow)
         (inputnode, bold_sdc_wf, [

fmriprep/workflows/bold/registration.py

@@ -37,7 +37,7 @@
 def init_bold_reg_wf(freesurfer, use_bbr, bold2t1w_dof, mem_gb, omp_nthreads,
                      use_compression=True, write_report=True, name='bold_reg_wf'):
     """
-    The registration between a reference BOLD image and T1-space is calculated
+    Calculates the registration between a reference BOLD image and T1-space
     using a boundary-based registration (BBR) cost function.
 
     If FreeSurfer-based preprocessing is enabled, the ``bbregister`` utility
@@ -171,12 +171,6 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, use_fieldwarp=False,
     This workflow registers the reference BOLD image to T1-space, using a
     boundary-based registration (BBR) cost function.
 
-    If FreeSurfer-based preprocessing is enabled, the ``bbregister`` utility
-    is used to align the BOLD images to the reconstructed subject, and the
-    resulting transform is adjusted to target the T1 space.
-    If FreeSurfer-based preprocessing is disabled, FSL FLIRT is used with the
-    BBR cost function to directly target the T1 space.
-
     .. workflow::
         :graph2use: orig
         :simple_form: yes