ENH: Add option to force t2w

Author: mgxd

fmriprep/cli/parser.py

@@ -347,11 +347,11 @@ def _slice_time_ref(value, parser):
     )
     g_conf.add_argument(
         "--bold2anat-init",
-        choices=["auto", "t1w", "header"],
+        choices=["auto", "t1w", "t2w", "header"],
         default="auto",
-        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 BOLD header information without an initial registration.",
+        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, `t2w` forces use of "
+        "the T2w, and `header` uses the BOLD header information without an initial registration.",
     )
     g_conf.add_argument(
         "--bold2anat-dof",

fmriprep/config.py

@@ -528,9 +528,9 @@ class workflow(_Config):
     bold2anat_dof = None
     """Degrees of freedom of the BOLD-to-anatomical registration steps."""
     bold2anat_init = "auto"
-    """Method of BOLD to anatomical coregistration. The target anatomical (``'t1w'``, ``'t2w'``)
-    can be specified, otherwise ``'auto'`` will prefer a T2w image but fall back to T1w if none
-    are available. Alternatively, ``'header'`` will use the T1w header information."""
+    """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, `t2w` forces use of
+    the T2w, and `header` uses the BOLD header information without an initial registration."""
     cifti_output = None
     """Generate HCP Grayordinates, accepts either ``'91k'`` (default) or ``'170k'``."""
     dummy_scans = None

fmriprep/workflows/base.py

@@ -624,8 +624,13 @@ def init_single_subject_wf(subject_id: str):
     )
 
     # Before initializing BOLD workflow, select/verify anatomical target for coregistration
-    if config.workflow.bold2anat_init == 'auto':
-        config.workflow.bold2anat_init = 't2w' if subject_data['t2w'] else 't1w'
+    if config.workflow.bold2anat_init in ('auto', 't2w'):
+        has_t2w = subject_data['t2w'] or 't2w_preproc' in anatomical_cache
+        if config.workflow.bold2anat_init == 't2w' and not has_t2w:
+            raise OSError(
+                "A T2w image is expected for BOLD-to-anatomical coregistration and was not found"
+            )
+        config.workflow.bold2anat_init = 't2w' if has_t2w else 't1w'
 
     for bold_series in bold_runs:
         bold_file = bold_series[0]
@@ -673,7 +678,6 @@ def init_single_subject_wf(subject_id: str):
                     f'outputnode.sphere_reg_{"msm" if msm_sulc else "fsLR"}',
                     'inputnode.sphere_reg_fsLR',
                 ),
-                ('outputnode.t2w_preproc', 'inputnode.t2w_preproc'),  # Optional
             ]),
         ])  # fmt:skip
         if fieldmap_id:

fmriprep/workflows/bold/registration.py

@@ -288,9 +288,7 @@ def init_bbreg_wf(
 
     use_t2w = bold2anat_init == 't2w'
     if use_t2w:
-        workflow.__desc__ += (
-            " The aligned T2w image was used for initial co-registration."
-        )
+        workflow.__desc__ += " The aligned T2w image was used for initial co-registration."
 
     inputnode = pe.Node(
         niu.IdentityInterface(
@@ -356,8 +354,6 @@ def init_bbreg_wf(
     concat_xfm = pe.Node(ConcatenateXFMs(inverse=True), name='concat_xfm')
 
     workflow.connect([
-        (inputnode, fssource, [('subjects_dir', 'subjects_dir'),
-                               ('subject_id', 'subject_id')]),
         (inputnode, merge_ltas, [('fsnative2t1w_xfm', 'in2')]),
         # Wire up the co-registration alternatives
         (transforms, select_transform, [('out', 'inlist')]),
@@ -377,7 +373,11 @@ def init_bbreg_wf(
         ])  # fmt:skip
 
         if use_t2w:
-            workflow.connect(fssource, 'T2', mri_coreg, 'reference_file')
+            workflow.connect([
+                (inputnode, fssource, [('subjects_dir', 'subjects_dir'),
+                                       ('subject_id', 'subject_id')]),
+                (fssource, mri_coreg, [('T2', 'reference_file')]),
+            ])  # fmt:skip
 
         # Short-circuit workflow building, use initial registration
         if use_bbr is False: