Apply suggestions from @oesteban

Co-authored-by: Oscar Esteban <[email protected]>

Author: slimnsour

dmriprep/cli/parser.py

@@ -227,15 +227,6 @@ def _bids_filter(value):
         help='Either "register" (the default) to initialize volumes at center or "header"'
         " to use the header information when coregistering BOLD to T1w images.",
     )
-    g_conf.add_argument(
-        "--bold2t1w-dof",
-        action="store",
-        default=6,
-        choices=[6, 9, 12],
-        type=int,
-        help="Degrees of freedom when registering BOLD to T1w images. "
-        "6 degrees (rotation and translation) are used by default.",
-    )
 
     #  ANTs options
     g_ants = parser.add_argument_group("Specific options for ANTs registrations")

dmriprep/config/__init__.py

@@ -436,11 +436,9 @@ class workflow(_Config):
     ignore = None
     """Ignore particular steps for *dMRIPrep*."""
     longitudinal = False
-    """Number of ICA components to be estimated by MELODIC
-    (positive = exact, negative = maximum)."""
-    bold2t1w_dof = None
-    """Degrees of freedom of the BOLD-to-T1w registration steps."""
     bold2t1w_init = "register"
+    """Whether to use standard coregistration ('register') or to initialize coregistration from the
+    BOLD image-header ('header')."""
     """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
     run_reconall = True
     """Run FreeSurfer's surface reconstruction."""

dmriprep/workflows/base.py

@@ -360,13 +360,16 @@ def init_single_subject_wf(subject_id):
         # Mask the T1
         t1w_brain = pe.Node(ApplyMask(), name='t1w_brain')
 
-        bbr_wf = init_bbreg_wf(use_bbr=True, bold2t1w_dof=config.workflow.bold2t1w_dof,
-                               bold2t1w_init=config.workflow.bold2t1w_init, omp_nthreads=config.nipype.omp_nthreads)
+        bbr_wf = init_bbreg_wf(
+            bold2t1w_init=config.workflow.bold2t1w_init,
+            omp_nthreads=config.nipype.omp_nthreads,
+            use_bbr=True,
+        )
 
         workflow.connect([
             # T1 Mask
             (anat_preproc_wf, t1w_brain, [('outputnode.t1w_preproc', 'in_file'),
-                                        ('outputnode.t1w_mask', 'in_mask')]),
+                                          ('outputnode.t1w_mask', 'in_mask')]),
             # BBregister
             (split_info, bbr_wf, [('dwi_file', 'inputnode.in_file')]),
             (t1w_brain, bbr_wf, [('out_file', 'inputnode.t1w_brain')]),