Apply suggestions from code review

Co-authored-by: Chris Markiewicz <[email protected]>

Author: mgxd

fmriprep/cli/parser.py

@@ -349,9 +349,9 @@ def _slice_time_ref(value, parser):
         "--bold2anat-init",
         choices=["auto", "t1w", "header"],
         default="auto",
-        help="Method of BOLD to anatomical coregistration. If `auto`, a T2w image is used if "
+        help="Method of initial BOLD to anatomical coregistration. If `auto`, a T2w image is used if "
         "available, otherwise the T1w image. `t1w` forces use of the T1w, and `header` uses "
-        "the T1w header information.",
+        "the BOLD header information without an initial registration.",
     )
     g_conf.add_argument(
         "--bold2anat-dof",

fmriprep/workflows/base.py

@@ -624,7 +624,7 @@ def init_single_subject_wf(subject_id: str):
     )
 
     # Before initializing BOLD workflow, select/verify anatomical target for coregistration
-    if config.workflow.bold2anat_init in ('auto', 't2w'):
+    if config.workflow.bold2anat_init == 'auto':
         config.workflow.bold2anat_init = 't2w' if subject_data['t2w'] else 't1w'
 
     for bold_series in bold_runs:

fmriprep/workflows/bold/registration.py

@@ -289,7 +289,7 @@ def init_bbreg_wf(
     use_t2w = bold2anat_init == 't2w'
     if use_t2w:
         workflow.__desc__ += (
-            " A T2w reference was used as an intermediate volume to improve tissue contrast."
+            " The aligned T2w image was used for initial co-registration."
         )
 
     inputnode = pe.Node(
@@ -312,7 +312,7 @@ def init_bbreg_wf(
     )
 
     if bold2anat_init not in ty.get_args(RegistrationInit):
-        raise ValueError(f"Unknown BOLD-anat initialization option: {bold2anat_init}")
+        raise ValueError(f"Unknown BOLD-to-anatomical initialization option: {bold2anat_init}")
 
     # For now make BBR unconditional - in the future, we can fall back to identity,
     # but adding the flexibility without testing seems a bit dangerous
@@ -396,9 +396,6 @@ def init_bbreg_wf(
         (bbregister, transforms, [('out_lta_file', 'in1')]),
     ])  # fmt:skip
 
-    if use_t2w:
-        workflow.connect(fssource, 'T2', bbregister, 'intermediate_file')
-
     # Short-circuit workflow building, use boundary-based registration
     if use_bbr is True:
         outputnode.inputs.fallback = False