From b1b11eec203cff01e288b2cb10573a9199e70e99 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 12 Jan 2024 17:15:43 -0500
Subject: [PATCH 01/22] ENH: Make preprocessed T2w available to BOLD workflows

---
 fmriprep/workflows/base.py      | 1 +
 fmriprep/workflows/bold/base.py | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 55ff76266..2cfd40249 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -669,6 +669,7 @@ 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:
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index c7289c6d0..6c7c66cce 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -209,6 +209,7 @@ def init_bold_wf(
                 "t1w_mask",
                 "t1w_dseg",
                 "t1w_tpms",
+                "t2w_preproc",  # Optional
                 # FreeSurfer outputs
                 "subjects_dir",
                 "subject_id",
@@ -260,6 +261,7 @@ def init_bold_wf(
             ('t1w_preproc', 'inputnode.t1w_preproc'),
             ('t1w_mask', 'inputnode.t1w_mask'),
             ('t1w_dseg', 'inputnode.t1w_dseg'),
+            ('t2w_preproc', 'inputnode.t2w_preproc'),
             ('subjects_dir', 'inputnode.subjects_dir'),
             ('subject_id', 'inputnode.subject_id'),
             ('fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),

From 73e6c9f427f24d6b72bd78701c6f2c634ee650eb Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 12 Jan 2024 17:17:17 -0500
Subject: [PATCH 02/22] ENH: Add T2w as an intermediate during bbr if available

---
 fmriprep/interfaces/patches.py          | 25 ++++++++++++++++++
 fmriprep/workflows/bold/fit.py          |  9 +++++++
 fmriprep/workflows/bold/registration.py | 34 +++++++++++++++++++++----
 3 files changed, 63 insertions(+), 5 deletions(-)

diff --git a/fmriprep/interfaces/patches.py b/fmriprep/interfaces/patches.py
index f9773728b..9d660a019 100644
--- a/fmriprep/interfaces/patches.py
+++ b/fmriprep/interfaces/patches.py
@@ -29,7 +29,9 @@
 from random import randint
 from time import sleep
 
+import nipype.interfaces.freesurfer as fs
 from nipype.algorithms import confounds as nac
+from nipype.interfaces.base import File, traits
 from numpy.linalg.linalg import LinAlgError
 
 
@@ -77,3 +79,26 @@ def _run_interface(self, runtime):
                 sleep(randint(start + 4, start + 10))
 
         return runtime
+
+
+class MRICoregInputSpec(fs.registration.MRICoregInputSpec):
+    reference_file = File(
+        argstr="--ref %s",
+        desc="reference (target) file",
+        copyfile=False,
+    )
+    subject_id = traits.Str(
+        argstr="--s %s",
+        position=1,
+        requires=["subjects_dir"],
+        desc="freesurfer subject ID (implies ``reference_mask == "
+        "aparc+aseg.mgz`` unless otherwise specified)",
+    )
+
+
+class MRICoreg(fs.MRICoreg):
+    """
+    Patched that allows setting both a reference file and the subjects dir.
+    """
+
+    input_spec = MRICoregInputSpec
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index f81285e62..7ee12fb33 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -215,6 +215,11 @@ def init_bold_fit_wf(
         layout=layout,
     )
 
+    # T2w is not required, but if available, use to improve BOLD -> anat coreg
+    has_t2w = layout.get(
+        suffix='T2w', extension='.nii.gz', **config.execution.get().get('bids_filters', {})
+    )
+
     basename = os.path.basename(bold_file)
     sbref_msg = f"No single-band-reference found for {basename}."
     if sbref_files and "sbref" in config.workflow.ignore:
@@ -267,6 +272,8 @@ def init_bold_fit_wf(
                 "subjects_dir",
                 "subject_id",
                 "fsnative2t1w_xfm",
+                # Optional - improvements if available
+                "t2w_preproc",
             ],
         ),
         name="inputnode",
@@ -592,6 +599,7 @@ def init_bold_fit_wf(
             freesurfer=config.workflow.run_reconall,
             omp_nthreads=omp_nthreads,
             mem_gb=mem_gb["resampled"],
+            use_t2w=has_t2w,
             sloppy=config.execution.sloppy,
         )
 
@@ -609,6 +617,7 @@ def init_bold_fit_wf(
                 ("t1w_preproc", "inputnode.t1w_preproc"),
                 ("t1w_mask", "inputnode.t1w_mask"),
                 ("t1w_dseg", "inputnode.t1w_dseg"),
+                ("t2w_preproc", "inputnode.t2w_preproc"),
                 # Undefined if --fs-no-reconall, but this is safe
                 ("subjects_dir", "inputnode.subjects_dir"),
                 ("subject_id", "inputnode.subject_id"),
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index bde2423f2..6969c16da 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -48,12 +48,14 @@
 
 
 def init_bold_reg_wf(
+    *,
     freesurfer: bool,
     use_bbr: bool,
     bold2t1w_dof: AffineDOF,
     bold2t1w_init: RegistrationInit,
     mem_gb: float,
     omp_nthreads: int,
+    use_t2w: bool = False,
     name: str = 'bold_reg_wf',
     sloppy: bool = False,
 ):
@@ -97,6 +99,8 @@ def init_bold_reg_wf(
         Size of BOLD file in GB
     omp_nthreads : :obj:`int`
         Maximum number of threads an individual process may use
+    use_t2w: :obj:`bool` or None
+
     name : :obj:`str`
         Name of workflow (default: ``bold_reg_wf``)
 
@@ -196,13 +200,14 @@ def init_bbreg_wf(
     bold2t1w_dof: AffineDOF,
     bold2t1w_init: RegistrationInit,
     omp_nthreads: int,
+    use_t2w: bool = False,
     name: str = 'bbreg_wf',
 ):
     """
     Build a workflow to run FreeSurfer's ``bbregister``.
 
     This workflow uses FreeSurfer's ``bbregister`` to register a BOLD image to
-    a T1-weighted structural image.
+    a T2-weighted structural image (if available), and ultimately a T1-weighted structual image.
 
     It is a counterpart to :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`,
     which performs the same task using FSL's FLIRT with a BBR cost function.
@@ -266,11 +271,12 @@ def init_bbreg_wf(
         Boolean indicating whether BBR was rejected (mri_coreg registration returned)
 
     """
-    from nipype.interfaces.freesurfer import BBRegister, MRICoreg
+    from nipype.interfaces.freesurfer import BBRegister
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-    from niworkflows.interfaces.freesurfer import PatchedLTAConvert as LTAConvert
     from niworkflows.interfaces.nitransforms import ConcatenateXFMs
 
+    from fmriprep.interfaces.patches import MRICoreg
+
     workflow = Workflow(name=name)
     workflow.__desc__ = """\
 The BOLD reference was then co-registered to the T1w reference using
@@ -293,6 +299,7 @@ def init_bbreg_wf(
                 't1w_preproc',  # FLIRT BBR
                 't1w_mask',
                 't1w_dseg',
+                't2w_preproc',  # Conditional
             ]
         ),
         name='inputnode',
@@ -314,7 +321,6 @@ def init_bbreg_wf(
             LOGGER.warning("Initializing BBR with header; affine fallback disabled")
             use_bbr = True
 
-    # Define both nodes, but only connect conditionally
     mri_coreg = pe.Node(
         MRICoreg(dof=bold2t1w_dof, sep=[4], ftol=0.0001, linmintol=0.01),
         name='mri_coreg',
@@ -322,6 +328,10 @@ def init_bbreg_wf(
         mem_gb=5,
     )
 
+    # Create separate mri_coreg to initialize bbregister
+    mri_coreg_t2w = mri_coreg.clone('mri_coreg_t2w')
+    mri_coreg_t2w.inputs.reference_mask = False
+
     bbregister = pe.Node(
         BBRegister(
             dof=bold2t1w_dof,
@@ -362,6 +372,15 @@ def init_bbreg_wf(
             (mri_coreg, transforms, [('out_lta_file', 'in2')]),
         ])  # fmt:skip
 
+        if use_t2w:
+            workflow.connect([
+                (inputnode, mri_coreg_t2w, [
+                    ('subjects_dir', 'subjects_dir'),
+                    ('subject_id', 'subject_id'),
+                    ('in_file', 'source_file'),
+                    ('t2w_preproc', 'reference_file')]),
+            ])  # fmt:skip
+
         # Short-circuit workflow building, use initial registration
         if use_bbr is False:
             outputnode.inputs.fallback = True
@@ -369,7 +388,9 @@ def init_bbreg_wf(
             return workflow
 
         # Otherwise bbregister will also be used
-        workflow.connect(mri_coreg, 'out_lta_file', bbregister, 'init_reg_file')
+        workflow.connect(
+            mri_coreg_t2w if use_t2w else mri_coreg, 'out_lta_file', bbregister, 'init_reg_file'
+        )
 
     # Use bbregister
     workflow.connect([
@@ -379,6 +400,9 @@ def init_bbreg_wf(
         (bbregister, transforms, [('out_lta_file', 'in1')]),
     ])  # fmt:skip
 
+    if use_t2w:
+        workflow.connect(inputnode, 't2w_preproc', bbregister, 'intermediate_file')
+
     # Short-circuit workflow building, use boundary-based registration
     if use_bbr is True:
         outputnode.inputs.fallback = False

From 2fc94037cff85f102e264dda1296f2e7ea9cefa8 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Tue, 16 Jan 2024 15:56:57 -0500
Subject: [PATCH 03/22] FIX: Propagate T2w in bold_reg_wf

---
 fmriprep/workflows/bold/registration.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index 6969c16da..8af3539da 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -149,6 +149,7 @@ def init_bold_reg_wf(
                 'subjects_dir',
                 'subject_id',
                 'fsnative2t1w_xfm',
+                't2w_preproc',  # Optional
             ]
         ),
         name='inputnode',
@@ -162,6 +163,7 @@ def init_bold_reg_wf(
     if freesurfer:
         bbr_wf = init_bbreg_wf(
             use_bbr=use_bbr,
+            use_t2w=use_t2w,
             bold2t1w_dof=bold2t1w_dof,
             bold2t1w_init=bold2t1w_init,
             omp_nthreads=omp_nthreads,
@@ -184,6 +186,7 @@ def init_bold_reg_wf(
             ('t1w_preproc', 'inputnode.t1w_preproc'),
             ('t1w_mask', 'inputnode.t1w_mask'),
             ('t1w_dseg', 'inputnode.t1w_dseg'),
+            ('t2w_preproc', 'inputnode.t2w_preproc'),
         ]),
         (bbr_wf, outputnode, [
             ('outputnode.itk_bold_to_t1', 'itk_bold_to_t1'),
@@ -427,6 +430,7 @@ def init_fsl_bbr_wf(
     bold2t1w_init: RegistrationInit,
     omp_nthreads: int,
     sloppy: bool = False,
+    use_t2w: bool = False,
     name: str = 'fsl_bbr_wf',
 ):
     """
@@ -525,6 +529,7 @@ def init_fsl_bbr_wf(
                 't1w_preproc',  # FLIRT BBR
                 't1w_mask',
                 't1w_dseg',
+                't2w_preproc',
             ]
         ),
         name='inputnode',

From 0adca0d25a21cd2eb6e301351e2dccc0b76b8c6e Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 17 Jan 2024 21:10:24 -0500
Subject: [PATCH 04/22] DOC: Update docstring, workflow description

---
 fmriprep/workflows/bold/registration.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index 8af3539da..294af7165 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -210,7 +210,8 @@ def init_bbreg_wf(
     Build a workflow to run FreeSurfer's ``bbregister``.
 
     This workflow uses FreeSurfer's ``bbregister`` to register a BOLD image to
-    a T2-weighted structural image (if available), and ultimately a T1-weighted structual image.
+    a T1-weighted structual image, leveraging a T2-weighted image (if available)
+    in the intermediate for improved tissue contrast.
 
     It is a counterpart to :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`,
     which performs the same task using FSL's FLIRT with a BBR cost function.
@@ -244,6 +245,8 @@ def init_bbreg_wf(
     bold2t1w_init : str, 'header' or 'register'
         If ``'header'``, use header information for initialization of BOLD and T1 images.
         If ``'register'``, align volumes by their centers.
+    use_t2w : :obj:`bool`, optional
+        If a T2w reference image is available, use it as an intermediate for BBR.
     name : :obj:`str`, optional
         Workflow name (default: bbreg_wf)
 
@@ -263,6 +266,8 @@ def init_bbreg_wf(
         Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`)
     t1w_dseg
         Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`)
+    t2w_preproc
+        T2w reference in T1w space (Only used if ``use_t2w`` is ``True``)
 
     Outputs
     -------
@@ -292,6 +297,11 @@ def init_bbreg_wf(
         else 'to account for distortions remaining in the BOLD reference',
     )
 
+    if use_t2w:
+        workflow.__desc__ += (
+            " A T2w reference was used as an intermediate volume to improve tissue contrast." ""
+        )
+
     inputnode = pe.Node(
         niu.IdentityInterface(
             [
@@ -469,6 +479,8 @@ def init_fsl_bbr_wf(
     bold2t1w_init : str, 'header' or 'register'
         If ``'header'``, use header information for initialization of BOLD and T1 images.
         If ``'register'``, align volumes by their centers.
+    use_t2w : :obj:`bool`, optional
+        Unused
     name : :obj:`str`, optional
         Workflow name (default: fsl_bbr_wf)
 

From eacd39b3abc7008d4e603d965d938a93202652de Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 18 Jan 2024 09:51:34 -0500
Subject: [PATCH 05/22] RF: Ensure T2w check is bool

---
 fmriprep/workflows/bold/fit.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index 7ee12fb33..415106c26 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -216,8 +216,10 @@ def init_bold_fit_wf(
     )
 
     # T2w is not required, but if available, use to improve BOLD -> anat coreg
-    has_t2w = layout.get(
-        suffix='T2w', extension='.nii.gz', **config.execution.get().get('bids_filters', {})
+    has_t2w = bool(
+        layout.get(
+            suffix='T2w', extension='.nii.gz', **config.execution.get().get('bids_filters', {})
+        )
     )
 
     basename = os.path.basename(bold_file)

From 51d5ab58210e5e2f57d59e3e80577885f49c2dae Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 18 Jan 2024 11:50:52 -0500
Subject: [PATCH 06/22] RF: Extract bids filters, only use T2w filters

---
 fmriprep/workflows/bold/fit.py          | 7 +++----
 fmriprep/workflows/bold/registration.py | 2 +-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index 415106c26..d52a78408 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -203,6 +203,7 @@ def init_bold_fit_wf(
     from fmriprep.utils.misc import estimate_bold_mem_usage
 
     layout = config.execution.layout
+    bids_filters = config.execution.get().get('bids_filters', {})
 
     # Fitting operates on the shortest echo
     # This could become more complicated in the future
@@ -211,15 +212,13 @@ def init_bold_fit_wf(
     # Collect sbref files, sorted by EchoTime
     sbref_files = get_sbrefs(
         bold_series,
-        entity_overrides=config.execution.get().get('bids_filters', {}).get('sbref', {}),
+        entity_overrides=bids_filters.get('sbref', {}),
         layout=layout,
     )
 
     # T2w is not required, but if available, use to improve BOLD -> anat coreg
     has_t2w = bool(
-        layout.get(
-            suffix='T2w', extension='.nii.gz', **config.execution.get().get('bids_filters', {})
-        )
+        layout.get(suffix='T2w', extension=['.nii', '.nii.gz'], **bids_filters.get('t2w', {}))
     )
 
     basename = os.path.basename(bold_file)
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index 294af7165..b8401bf01 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -210,7 +210,7 @@ def init_bbreg_wf(
     Build a workflow to run FreeSurfer's ``bbregister``.
 
     This workflow uses FreeSurfer's ``bbregister`` to register a BOLD image to
-    a T1-weighted structual image, leveraging a T2-weighted image (if available)
+    a T1-weighted structural image, leveraging a T2-weighted image (if available)
     in the intermediate for improved tissue contrast.
 
     It is a counterpart to :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`,

From db948e8d4e404f095015975662c2f1c4e09c5596 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 18 Jan 2024 16:13:49 -0500
Subject: [PATCH 07/22] TST: Reflect new report generation exit code

The exit code for `--reports-only` should be an indicator of report generation status.
---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 648a4fed4..5956090df 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -667,7 +667,7 @@ jobs:
                 --reports-only --config-file /tmp/${DATASET}/work/${UUID}/config.toml -vv
             RET=$?
             set -e
-            [[ "$RET" -eq "1" ]]
+            [[ "$RET" -eq "0" ]]  # ensure report was generated successfully
       - run:
           name: Clean working directory
           when: on_success

From fd73828affe4d12c2b4071a21917ce296322676b Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 18 Jan 2024 16:17:37 -0500
Subject: [PATCH 08/22] RF: Deduplication

---
 fmriprep/cli/run.py | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index 551dc014c..69f8bf71b 100644
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -224,17 +224,14 @@ def main():
         write_bidsignore(config.execution.fmriprep_dir)
 
         if failed_reports:
-            config.loggers.cli.error(
-                "Report generation was not successful for the following participants : %s.",
-                ", ".join(failed_reports),
+            msg = (
+                'Report generation was not successful for the following participants '
+                f': {", ".join(failed_reports)}.'
             )
+            config.loggers.cli.error(msg)
+            if sentry_sdk is not None:
+                sentry_sdk.capture_message(msg, level="error")
 
-        if sentry_sdk is not None and failed_reports:
-            sentry_sdk.capture_message(
-                "Report generation was not successful for the following participants : %s.",
-                ", ".join(failed_reports),
-                level="error",
-            )
         sys.exit(int((errno + len(failed_reports)) > 0))
 
 

From 97edb514bd509d2e3335d91598349dbc80d77e6f Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 22 Jan 2024 12:28:24 -0500
Subject: [PATCH 09/22] MAINT: Modify arguments, add action for deprecations

---
 fmriprep/cli/parser.py | 55 +++++++++++++++++++++++++++++++++---------
 1 file changed, 43 insertions(+), 12 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 5da912240..dcf473d55 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -31,7 +31,7 @@ def _build_parser(**kwargs):
 
     ``kwargs`` are passed to ``argparse.ArgumentParser`` (mainly useful for debugging).
     """
-    from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
+    from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser
     from functools import partial
     from pathlib import Path
 
@@ -40,6 +40,27 @@ def _build_parser(**kwargs):
 
     from .version import check_latest, is_flagged
 
+    deprecations = {
+        # parser attribute name: (replacement flag, version slated to be removed in)
+        'use_aroma': (None, '24.0.0'),
+        'aroma_melodic_dim': (None, '24.0.0'),
+        'aroma_err_on_warn': (None, '24.0.0'),
+        'bold2t1w_init': ('--bold2anat-init', '24.2.0'),
+        'bold2t1w_dof': ('--bold2anat-dof', '24.2.0'),
+    }
+
+    class DeprecatedAction(Action):
+        def __call__(self, parser, namespace, values, option_string=None):
+            new_opt, rem_vers = deprecations.get(self.dest, (None, None))
+            msg = (
+                f"{self.option_strings} has been deprecated and will be removed in "
+                f"{rem_vers or 'a later version'}."
+            )
+            if new_opt:
+                msg += f" Please use `{new_opt}` instead."
+            print(msg, file=sys.stderr)
+            delattr(namespace, self.dest)
+
     def _path_exists(path, parser):
         """Ensure a given path exists."""
         if path is None or not Path(path).exists():
@@ -313,19 +334,32 @@ def _slice_time_ref(value, parser):
     )
     g_conf.add_argument(
         "--bold2t1w-init",
-        action="store",
-        default="register",
+        action=DeprecatedAction,
         choices=["register", "header"],
-        help='Either "register" (the default) to initialize volumes at center or "header"'
-        " to use the header information when coregistering BOLD to T1w images.",
+        help="Deprecated - use `--bold2anat-init` instead.",
     )
     g_conf.add_argument(
         "--bold2t1w-dof",
+        action=DeprecatedAction,
+        choices=[6, 9, 12],
+        type=int,
+        help="Deprecated - use `--bold2anat-dof` instead.",
+    )
+    g_conf.add_argument(
+        "--bold2anat-init",
+        choices=["auto", "t1w", "header"],
+        default="auto",
+        help="Method of 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.",
+    )
+    g_conf.add_argument(
+        "--bold2anat-dof",
         action="store",
         default=6,
         choices=[6, 9, 12],
         type=int,
-        help="Degrees of freedom when registering BOLD to T1w images. "
+        help="Degrees of freedom when registering BOLD to anatomical images. "
         "6 degrees (rotation and translation) are used by default.",
     )
     g_conf.add_argument(
@@ -445,23 +479,20 @@ def _slice_time_ref(value, parser):
     g_aroma = parser.add_argument_group("[DEPRECATED] Options for running ICA_AROMA")
     g_aroma.add_argument(
         "--use-aroma",
-        action="store_true",
-        default=False,
+        action=DeprecatedAction,
         help="Deprecated. Will raise an error in 24.0.",
     )
     g_aroma.add_argument(
         "--aroma-melodic-dimensionality",
         dest="aroma_melodic_dim",
-        action="store",
-        default=0,
+        action=DeprecatedAction,
         type=int,
         help="Deprecated. Will raise an error in 24.0.",
     )
     g_aroma.add_argument(
         "--error-on-aroma-warnings",
-        action="store_true",
+        action=DeprecatedAction,
         dest="aroma_err_on_warn",
-        default=False,
         help="Deprecated. Will raise an error in 24.0.",
     )
 

From 84d4bca187c1f9ddb0167c1001b3f1da7afdfd96 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 24 Jan 2024 14:30:04 -0500
Subject: [PATCH 10/22] RF: bold2t1w -> bold2anat

---
 fmriprep/config.py                      |  11 +-
 fmriprep/data/tests/config.toml         |   2 +-
 fmriprep/workflows/bold/fit.py          |   8 +-
 fmriprep/workflows/bold/registration.py | 128 +++++++++++-------------
 fmriprep/workflows/tests/test_base.py   |  22 ++--
 5 files changed, 82 insertions(+), 89 deletions(-)

diff --git a/fmriprep/config.py b/fmriprep/config.py
index f7ec4551b..aabea97c7 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -525,11 +525,12 @@ class workflow(_Config):
     aroma_melodic_dim = None
     """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')."""
+    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."""
     cifti_output = None
     """Generate HCP Grayordinates, accepts either ``'91k'`` (default) or ``'170k'``."""
     dummy_scans = None
diff --git a/fmriprep/data/tests/config.toml b/fmriprep/data/tests/config.toml
index 0519e4702..b1b7e31b6 100644
--- a/fmriprep/data/tests/config.toml
+++ b/fmriprep/data/tests/config.toml
@@ -32,7 +32,7 @@ write_graph = false
 anat_only = false
 aroma_err_on_warn = false
 aroma_melodic_dim = -200
-bold2t1w_dof = 6
+bold2anat_dof = 6
 fmap_bspline = false
 force_syn = false
 hires = true
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index d52a78408..e916dc9d3 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -320,8 +320,8 @@ def init_bold_fit_wf(
         FunctionalSummary(
             distortion_correction="None",  # Can override with connection
             registration=("FSL", "FreeSurfer")[config.workflow.run_reconall],
-            registration_dof=config.workflow.bold2t1w_dof,
-            registration_init=config.workflow.bold2t1w_init,
+            registration_dof=config.workflow.bold2anat_dof,
+            registration_init=config.workflow.bold2anat_init,
             pe_direction=metadata.get("PhaseEncodingDirection"),
             echo_idx=entities.get("echo", []),
             tr=metadata["RepetitionTime"],
@@ -594,8 +594,8 @@ def init_bold_fit_wf(
     if not boldref2anat_xform:
         # calculate BOLD registration to T1w
         bold_reg_wf = init_bold_reg_wf(
-            bold2t1w_dof=config.workflow.bold2t1w_dof,
-            bold2t1w_init=config.workflow.bold2t1w_init,
+            bold2anat_dof=config.workflow.bold2anat_dof,
+            bold2anat_init=config.workflow.bold2anat_init,
             use_bbr=config.workflow.use_bbr,
             freesurfer=config.workflow.run_reconall,
             omp_nthreads=omp_nthreads,
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index b8401bf01..aec6807aa 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -38,21 +38,20 @@
 from nipype.pipeline import engine as pe
 
 from ... import config, data
-from ...interfaces import DerivativesDataSink
 
 DEFAULT_MEMORY_MIN_GB = config.DEFAULT_MEMORY_MIN_GB
 LOGGER = config.loggers.workflow
 
 AffineDOF = ty.Literal[6, 9, 12]
-RegistrationInit = ty.Literal['register', 'header']
+RegistrationInit = ty.Literal['t1w', 't2w', 'header']
 
 
 def init_bold_reg_wf(
     *,
     freesurfer: bool,
     use_bbr: bool,
-    bold2t1w_dof: AffineDOF,
-    bold2t1w_init: RegistrationInit,
+    bold2anat_dof: AffineDOF,
+    bold2anat_init: RegistrationInit,
     mem_gb: float,
     omp_nthreads: int,
     use_t2w: bool = False,
@@ -80,8 +79,8 @@ def init_bold_reg_wf(
                                   mem_gb=3,
                                   omp_nthreads=1,
                                   use_bbr=True,
-                                  bold2t1w_dof=9,
-                                  bold2t1w_init='register')
+                                  bold2anat_dof=9,
+                                  bold2anat_init='auto')
 
     Parameters
     ----------
@@ -90,17 +89,16 @@ def init_bold_reg_wf(
     use_bbr : :obj:`bool` or None
         Enable/disable boundary-based registration refinement.
         If ``None``, test BBR result for distortion before accepting.
-    bold2t1w_dof : 6, 9 or 12
-        Degrees-of-freedom for BOLD-T1w registration
-    bold2t1w_init : str, 'header' or 'register'
+    bold2anat_dof : 6, 9 or 12
+        Degrees-of-freedom for BOLD-anatomical registration
+    bold2anat_init : str, 't1w', 't2w' or 'register'
         If ``'header'``, use header information for initialization of BOLD and T1 images.
-        If ``'register'``, align volumes by their centers.
+        If ``'t1w'``, align BOLD to T1w by their centers.
+        If ``'t2w'``, align BOLD to T1w using the T2w as an intermediate.
     mem_gb : :obj:`float`
         Size of BOLD file in GB
     omp_nthreads : :obj:`int`
         Maximum number of threads an individual process may use
-    use_t2w: :obj:`bool` or None
-
     name : :obj:`str`
         Name of workflow (default: ``bold_reg_wf``)
 
@@ -163,16 +161,15 @@ def init_bold_reg_wf(
     if freesurfer:
         bbr_wf = init_bbreg_wf(
             use_bbr=use_bbr,
-            use_t2w=use_t2w,
-            bold2t1w_dof=bold2t1w_dof,
-            bold2t1w_init=bold2t1w_init,
+            bold2anat_dof=bold2anat_dof,
+            bold2anat_init=bold2anat_init,
             omp_nthreads=omp_nthreads,
         )
     else:
         bbr_wf = init_fsl_bbr_wf(
             use_bbr=use_bbr,
-            bold2t1w_dof=bold2t1w_dof,
-            bold2t1w_init=bold2t1w_init,
+            bold2anat_dof=bold2anat_dof,
+            bold2anat_init=bold2anat_init,
             sloppy=sloppy,
             omp_nthreads=omp_nthreads,
         )
@@ -200,18 +197,16 @@ def init_bold_reg_wf(
 
 def init_bbreg_wf(
     use_bbr: bool,
-    bold2t1w_dof: AffineDOF,
-    bold2t1w_init: RegistrationInit,
+    bold2anat_dof: AffineDOF,
+    bold2anat_init: RegistrationInit,
     omp_nthreads: int,
-    use_t2w: bool = False,
     name: str = 'bbreg_wf',
 ):
     """
     Build a workflow to run FreeSurfer's ``bbregister``.
 
     This workflow uses FreeSurfer's ``bbregister`` to register a BOLD image to
-    a T1-weighted structural image, leveraging a T2-weighted image (if available)
-    in the intermediate for improved tissue contrast.
+    a T1-weighted structural image.
 
     It is a counterpart to :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`,
     which performs the same task using FSL's FLIRT with a BBR cost function.
@@ -231,8 +226,8 @@ def init_bbreg_wf(
             :simple_form: yes
 
             from fmriprep.workflows.bold.registration import init_bbreg_wf
-            wf = init_bbreg_wf(use_bbr=True, bold2t1w_dof=9,
-                               bold2t1w_init='register', omp_nthreads=1)
+            wf = init_bbreg_wf(use_bbr=True, bold2anat_dof=9,
+                               bold2anat_init='t1w', omp_nthreads=1)
 
 
     Parameters
@@ -240,11 +235,12 @@ def init_bbreg_wf(
     use_bbr : :obj:`bool` or None
         Enable/disable boundary-based registration refinement.
         If ``None``, test BBR result for distortion before accepting.
-    bold2t1w_dof : 6, 9 or 12
-        Degrees-of-freedom for BOLD-T1w registration
-    bold2t1w_init : str, 'header' or 'register'
+    bold2anat_dof : 6, 9 or 12
+        Degrees-of-freedom for BOLD-anatomical registration
+    bold2anat_init : str, 't1w', 't2w' or 'register'
         If ``'header'``, use header information for initialization of BOLD and T1 images.
-        If ``'register'``, align volumes by their centers.
+        If ``'t1w'``, align BOLD to T1w by their centers.
+        If ``'t2w'``, align BOLD to T1w using the T2w as an intermediate.
     use_t2w : :obj:`bool`, optional
         If a T2w reference image is available, use it as an intermediate for BBR.
     name : :obj:`str`, optional
@@ -267,7 +263,7 @@ def init_bbreg_wf(
     t1w_dseg
         Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`)
     t2w_preproc
-        T2w reference in T1w space (Only used if ``use_t2w`` is ``True``)
+        T2w reference in T1w space (Only used if ``bold2anat_init`` is ``t2w``)
 
     Outputs
     -------
@@ -291,15 +287,16 @@ def init_bbreg_wf(
 `bbregister` (FreeSurfer) which implements boundary-based registration [@bbr].
 Co-registration was configured with {dof} degrees of freedom{reason}.
 """.format(
-        dof={6: 'six', 9: 'nine', 12: 'twelve'}[bold2t1w_dof],
+        dof={6: 'six', 9: 'nine', 12: 'twelve'}[bold2anat_dof],
         reason=''
-        if bold2t1w_dof == 6
+        if bold2anat_dof == 6
         else 'to account for distortions remaining in the BOLD reference',
     )
 
+    use_t2w = bold2anat_init == 't2w'
     if use_t2w:
         workflow.__desc__ += (
-            " A T2w reference was used as an intermediate volume to improve tissue contrast." ""
+            " A T2w reference was used as an intermediate volume to improve tissue contrast."
         )
 
     inputnode = pe.Node(
@@ -322,12 +319,12 @@ def init_bbreg_wf(
         name='outputnode',
     )
 
-    if bold2t1w_init not in ("register", "header"):
-        raise ValueError(f"Unknown BOLD-T1w initialization option: {bold2t1w_init}")
+    if bold2anat_init not in ty.get_args(RegistrationInit):
+        raise ValueError(f"Unknown BOLD-anat 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
-    if bold2t1w_init == "header":
+    if bold2anat_init == "header":
         if use_bbr is False:
             raise ValueError("Cannot disable BBR and use header registration")
         if use_bbr is None:
@@ -335,26 +332,24 @@ def init_bbreg_wf(
             use_bbr = True
 
     mri_coreg = pe.Node(
-        MRICoreg(dof=bold2t1w_dof, sep=[4], ftol=0.0001, linmintol=0.01),
+        MRICoreg(dof=bold2anat_dof, sep=[4], ftol=0.0001, linmintol=0.01),
         name='mri_coreg',
         n_procs=omp_nthreads,
         mem_gb=5,
     )
-
-    # Create separate mri_coreg to initialize bbregister
-    mri_coreg_t2w = mri_coreg.clone('mri_coreg_t2w')
-    mri_coreg_t2w.inputs.reference_mask = False
+    if use_t2w:
+        mri_coreg.inputs.reference_mask = False
 
     bbregister = pe.Node(
         BBRegister(
-            dof=bold2t1w_dof,
+            dof=bold2anat_dof,
             contrast_type='t2',
             out_lta_file=True,
         ),
         name='bbregister',
         mem_gb=12,
     )
-    if bold2t1w_init == "header":
+    if bold2anat_init == "header":
         bbregister.inputs.init = "header"
 
     transforms = pe.Node(niu.Merge(2), run_without_submitting=True, name='transforms')
@@ -377,7 +372,7 @@ def init_bbreg_wf(
     ])  # fmt:skip
 
     # Do not initialize with header, use mri_coreg
-    if bold2t1w_init == "register":
+    if bold2anat_init == "register":
         workflow.connect([
             (inputnode, mri_coreg, [('subjects_dir', 'subjects_dir'),
                                     ('subject_id', 'subject_id'),
@@ -386,13 +381,7 @@ def init_bbreg_wf(
         ])  # fmt:skip
 
         if use_t2w:
-            workflow.connect([
-                (inputnode, mri_coreg_t2w, [
-                    ('subjects_dir', 'subjects_dir'),
-                    ('subject_id', 'subject_id'),
-                    ('in_file', 'source_file'),
-                    ('t2w_preproc', 'reference_file')]),
-            ])  # fmt:skip
+            workflow.connect(inputnode, 't2w_preproc', mri_coreg, 'reference_file')
 
         # Short-circuit workflow building, use initial registration
         if use_bbr is False:
@@ -401,9 +390,7 @@ def init_bbreg_wf(
             return workflow
 
         # Otherwise bbregister will also be used
-        workflow.connect(
-            mri_coreg_t2w if use_t2w else mri_coreg, 'out_lta_file', bbregister, 'init_reg_file'
-        )
+        workflow.connect(mri_coreg, 'out_lta_file', bbregister, 'init_reg_file')
 
     # Use bbregister
     workflow.connect([
@@ -422,7 +409,7 @@ def init_bbreg_wf(
 
         return workflow
 
-    # Only reach this point if bold2t1w_init is "register" and use_bbr is None
+    # Only reach this point if bold2anat_init is "register" and use_bbr is None
     compare_transforms = pe.Node(niu.Function(function=compare_xforms), name='compare_transforms')
 
     workflow.connect([
@@ -436,8 +423,8 @@ def init_bbreg_wf(
 
 def init_fsl_bbr_wf(
     use_bbr: bool,
-    bold2t1w_dof: AffineDOF,
-    bold2t1w_init: RegistrationInit,
+    bold2anat_dof: AffineDOF,
+    bold2anat_init: RegistrationInit,
     omp_nthreads: int,
     sloppy: bool = False,
     use_t2w: bool = False,
@@ -466,7 +453,7 @@ def init_fsl_bbr_wf(
             :simple_form: yes
 
             from fmriprep.workflows.bold.registration import init_fsl_bbr_wf
-            wf = init_fsl_bbr_wf(use_bbr=True, bold2t1w_dof=9, bold2t1w_init='register', omp_nthreads=1)
+            wf = init_fsl_bbr_wf(use_bbr=True, bold2anat_dof=9, bold2anat_init='t1w', omp_nthreads=1)
 
 
     Parameters
@@ -474,11 +461,12 @@ def init_fsl_bbr_wf(
     use_bbr : :obj:`bool` or None
         Enable/disable boundary-based registration refinement.
         If ``None``, test BBR result for distortion before accepting.
-    bold2t1w_dof : 6, 9 or 12
-        Degrees-of-freedom for BOLD-T1w registration
-    bold2t1w_init : str, 'header' or 'register'
+    bold2anat_dof : 6, 9 or 12
+        Degrees-of-freedom for BOLD-anatomical registration
+    bold2anat_init : str, 't1w', 't2w' or 'register'
         If ``'header'``, use header information for initialization of BOLD and T1 images.
-        If ``'register'``, align volumes by their centers.
+        If ``'t1w'``, align BOLD to T1w by their centers.
+        If ``'t2w'``, align BOLD to T1w using the T2w as an intermediate.
     use_t2w : :obj:`bool`, optional
         Unused
     name : :obj:`str`, optional
@@ -525,9 +513,9 @@ def init_fsl_bbr_wf(
 Co-registration was configured with {dof} degrees of freedom{reason}.
 """.format(
         fsl_ver=fsl.FLIRT().version or '<ver>',
-        dof={6: 'six', 9: 'nine', 12: 'twelve'}[bold2t1w_dof],
+        dof={6: 'six', 9: 'nine', 12: 'twelve'}[bold2anat_dof],
         reason=''
-        if bold2t1w_dof == 6
+        if bold2anat_dof == 6
         else 'to account for distortions remaining in the BOLD reference',
     )
 
@@ -554,17 +542,21 @@ def init_fsl_bbr_wf(
     wm_mask = pe.Node(niu.Function(function=_dseg_label), name='wm_mask')
     wm_mask.inputs.label = 2  # BIDS default is WM=2
 
-    if bold2t1w_init not in ("register", "header"):
-        raise ValueError(f"Unknown BOLD-T1w initialization option: {bold2t1w_init}")
+    if bold2anat_init not in ty.get_args(RegistrationInit):
+        raise ValueError(f"Unknown BOLD-T1w initialization option: {bold2anat_init}")
 
-    if bold2t1w_init == "header":
+    if bold2anat_init == "header":
         raise NotImplementedError("Header-based registration initialization not supported for FSL")
+    if bold2anat_init == "t2w":
+        LOGGER.warning(
+            "T2w intermediate for FSL is not implemented, registering with T1w instead."
+        )
 
     # Mask T1w_preproc with T1w_mask to make T1w_brain
     mask_t1w_brain = pe.Node(ApplyMask(), name='mask_t1w_brain')
 
     mri_coreg = pe.Node(
-        MRICoreg(dof=bold2t1w_dof, sep=[4], ftol=0.0001, linmintol=0.01),
+        MRICoreg(dof=bold2anat_dof, sep=[4], ftol=0.0001, linmintol=0.01),
         name='mri_coreg',
         n_procs=omp_nthreads,
         mem_gb=5,
@@ -618,7 +610,7 @@ def init_fsl_bbr_wf(
         return workflow
 
     flt_bbr = pe.Node(
-        fsl.FLIRT(cost_func='bbr', dof=bold2t1w_dof, args="-basescale 1"),
+        fsl.FLIRT(cost_func='bbr', dof=bold2anat_dof, args="-basescale 1"),
         name='flt_bbr',
     )
 
diff --git a/fmriprep/workflows/tests/test_base.py b/fmriprep/workflows/tests/test_base.py
index 027609459..0bea4c510 100644
--- a/fmriprep/workflows/tests/test_base.py
+++ b/fmriprep/workflows/tests/test_base.py
@@ -105,7 +105,7 @@ def bids_root(tmp_path_factory):
 
 
 def _make_params(
-    bold2t1w_init: str = "register",
+    bold2anat_init: str = "auto",
     use_bbr: bool | None = None,
     dummy_scans: int | None = None,
     me_output_echos: bool = False,
@@ -125,7 +125,7 @@ def _make_params(
     if bids_filters is None:
         bids_filters = {}
     return (
-        bold2t1w_init,
+        bold2anat_init,
         use_bbr,
         dummy_scans,
         me_output_echos,
@@ -146,7 +146,7 @@ def _make_params(
 @pytest.mark.parametrize("anat_only", [False, True])
 @pytest.mark.parametrize(
     (
-        "bold2t1w_init",
+        "bold2anat_init",
         "use_bbr",
         "dummy_scans",
         "me_output_echos",
@@ -163,12 +163,12 @@ def _make_params(
     ),
     [
         _make_params(),
-        _make_params(bold2t1w_init="header"),
+        _make_params(bold2anat_init="header"),
         _make_params(use_bbr=True),
         _make_params(use_bbr=False),
-        _make_params(bold2t1w_init="header", use_bbr=True),
+        _make_params(bold2anat_init="header", use_bbr=True),
         # Currently disabled
-        # _make_params(bold2t1w_init="header", use_bbr=False),
+        # _make_params(bold2anat_init="header", use_bbr=False),
         _make_params(dummy_scans=2),
         _make_params(me_output_echos=True),
         _make_params(medial_surface_nan=True),
@@ -183,9 +183,9 @@ def _make_params(
         _make_params(freesurfer=False, use_bbr=True),
         _make_params(freesurfer=False, use_bbr=False),
         # Currently unsupported:
-        # _make_params(freesurfer=False, bold2t1w_init="header"),
-        # _make_params(freesurfer=False, bold2t1w_init="header", use_bbr=True),
-        # _make_params(freesurfer=False, bold2t1w_init="header", use_bbr=False),
+        # _make_params(freesurfer=False, bold2anat_init="header"),
+        # _make_params(freesurfer=False, bold2anat_init="header", use_bbr=True),
+        # _make_params(freesurfer=False, bold2anat_init="header", use_bbr=False),
         # Regression test for gh-3154:
         _make_params(bids_filters={'sbref': {'suffix': 'sbref'}}),
     ],
@@ -195,7 +195,7 @@ def test_init_fmriprep_wf(
     tmp_path: Path,
     level: str,
     anat_only: bool,
-    bold2t1w_init: str,
+    bold2anat_init: str,
     use_bbr: bool | None,
     dummy_scans: int | None,
     me_output_echos: bool,
@@ -213,7 +213,7 @@ def test_init_fmriprep_wf(
     with mock_config(bids_dir=bids_root):
         config.workflow.level = level
         config.workflow.anat_only = anat_only
-        config.workflow.bold2t1w_init = bold2t1w_init
+        config.workflow.bold2anat_init = bold2anat_init
         config.workflow.use_bbr = use_bbr
         config.workflow.dummy_scans = dummy_scans
         config.execution.me_output_echos = me_output_echos

From 3b335fcd57ac621df1844b8003494c24f573d6d7 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 24 Jan 2024 15:37:29 -0500
Subject: [PATCH 11/22] ENH: Patch FSSource output T2, simplify in-workflow T2
 use logic

---
 fmriprep/interfaces/patches.py          | 17 +++++++++++++++--
 fmriprep/workflows/base.py              |  4 ++++
 fmriprep/workflows/bold/fit.py          |  1 -
 fmriprep/workflows/bold/registration.py | 22 +++++++---------------
 4 files changed, 26 insertions(+), 18 deletions(-)

diff --git a/fmriprep/interfaces/patches.py b/fmriprep/interfaces/patches.py
index 9d660a019..49351a23d 100644
--- a/fmriprep/interfaces/patches.py
+++ b/fmriprep/interfaces/patches.py
@@ -30,6 +30,7 @@
 from time import sleep
 
 import nipype.interfaces.freesurfer as fs
+import nipype.interfaces.io as nio
 from nipype.algorithms import confounds as nac
 from nipype.interfaces.base import File, traits
 from numpy.linalg.linalg import LinAlgError
@@ -81,7 +82,7 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class MRICoregInputSpec(fs.registration.MRICoregInputSpec):
+class _MRICoregInputSpec(fs.registration.MRICoregInputSpec):
     reference_file = File(
         argstr="--ref %s",
         desc="reference (target) file",
@@ -101,4 +102,16 @@ class MRICoreg(fs.MRICoreg):
     Patched that allows setting both a reference file and the subjects dir.
     """
 
-    input_spec = MRICoregInputSpec
+    input_spec = _MRICoregInputSpec
+
+
+class _FSSourceOutputSpec(nio.FSSourceOutputSpec):
+    T2 = File(desc="Intensity normalized whole-head volume", loc="mri")
+
+
+class FreeSurferSource(nio.FreeSurferSource):
+    """
+    Patch to allow grabbing the T2 volume, if available
+    """
+
+    output_spec = _FSSourceOutputSpec
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 2cfd40249..acc2951b9 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -623,6 +623,10 @@ def init_single_subject_wf(subject_id: str):
         num_bold=len(bold_runs)
     )
 
+    # Before initializing BOLD workflow, select/verify anatomical target for coregistration
+    if config.workflow.bold2anat_init in ('auto', 't2w'):
+        config.workflow.bold2anat_init = 't2w' if subject_data['t2w'] else 't1w'
+
     for bold_series in bold_runs:
         bold_file = bold_series[0]
         fieldmap_id = estimator_map.get(bold_file)
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index e916dc9d3..a550293e6 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -600,7 +600,6 @@ def init_bold_fit_wf(
             freesurfer=config.workflow.run_reconall,
             omp_nthreads=omp_nthreads,
             mem_gb=mem_gb["resampled"],
-            use_t2w=has_t2w,
             sloppy=config.execution.sloppy,
         )
 
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index aec6807aa..85ffbacf9 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -54,7 +54,6 @@ def init_bold_reg_wf(
     bold2anat_init: RegistrationInit,
     mem_gb: float,
     omp_nthreads: int,
-    use_t2w: bool = False,
     name: str = 'bold_reg_wf',
     sloppy: bool = False,
 ):
@@ -147,7 +146,6 @@ def init_bold_reg_wf(
                 'subjects_dir',
                 'subject_id',
                 'fsnative2t1w_xfm',
-                't2w_preproc',  # Optional
             ]
         ),
         name='inputnode',
@@ -183,7 +181,6 @@ def init_bold_reg_wf(
             ('t1w_preproc', 'inputnode.t1w_preproc'),
             ('t1w_mask', 'inputnode.t1w_mask'),
             ('t1w_dseg', 'inputnode.t1w_dseg'),
-            ('t2w_preproc', 'inputnode.t2w_preproc'),
         ]),
         (bbr_wf, outputnode, [
             ('outputnode.itk_bold_to_t1', 'itk_bold_to_t1'),
@@ -241,8 +238,6 @@ def init_bbreg_wf(
         If ``'header'``, use header information for initialization of BOLD and T1 images.
         If ``'t1w'``, align BOLD to T1w by their centers.
         If ``'t2w'``, align BOLD to T1w using the T2w as an intermediate.
-    use_t2w : :obj:`bool`, optional
-        If a T2w reference image is available, use it as an intermediate for BBR.
     name : :obj:`str`, optional
         Workflow name (default: bbreg_wf)
 
@@ -262,8 +257,6 @@ def init_bbreg_wf(
         Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`)
     t1w_dseg
         Unused (see :py:func:`~fmriprep.workflows.bold.registration.init_fsl_bbr_wf`)
-    t2w_preproc
-        T2w reference in T1w space (Only used if ``bold2anat_init`` is ``t2w``)
 
     Outputs
     -------
@@ -279,7 +272,7 @@ def init_bbreg_wf(
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
     from niworkflows.interfaces.nitransforms import ConcatenateXFMs
 
-    from fmriprep.interfaces.patches import MRICoreg
+    from fmriprep.interfaces.patches import FreeSurferSource, MRICoreg
 
     workflow = Workflow(name=name)
     workflow.__desc__ = """\
@@ -309,7 +302,6 @@ def init_bbreg_wf(
                 't1w_preproc',  # FLIRT BBR
                 't1w_mask',
                 't1w_dseg',
-                't2w_preproc',  # Conditional
             ]
         ),
         name='inputnode',
@@ -331,6 +323,8 @@ def init_bbreg_wf(
             LOGGER.warning("Initializing BBR with header; affine fallback disabled")
             use_bbr = True
 
+    fssource = pe.Node(FreeSurferSource(), name='fssource')
+
     mri_coreg = pe.Node(
         MRICoreg(dof=bold2anat_dof, sep=[4], ftol=0.0001, linmintol=0.01),
         name='mri_coreg',
@@ -362,6 +356,8 @@ 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')]),
@@ -381,7 +377,7 @@ def init_bbreg_wf(
         ])  # fmt:skip
 
         if use_t2w:
-            workflow.connect(inputnode, 't2w_preproc', mri_coreg, 'reference_file')
+            workflow.connect(fssource, 'T2', mri_coreg, 'reference_file')
 
         # Short-circuit workflow building, use initial registration
         if use_bbr is False:
@@ -401,7 +397,7 @@ def init_bbreg_wf(
     ])  # fmt:skip
 
     if use_t2w:
-        workflow.connect(inputnode, 't2w_preproc', bbregister, 'intermediate_file')
+        workflow.connect(fssource, 'T2', bbregister, 'intermediate_file')
 
     # Short-circuit workflow building, use boundary-based registration
     if use_bbr is True:
@@ -427,7 +423,6 @@ def init_fsl_bbr_wf(
     bold2anat_init: RegistrationInit,
     omp_nthreads: int,
     sloppy: bool = False,
-    use_t2w: bool = False,
     name: str = 'fsl_bbr_wf',
 ):
     """
@@ -467,8 +462,6 @@ def init_fsl_bbr_wf(
         If ``'header'``, use header information for initialization of BOLD and T1 images.
         If ``'t1w'``, align BOLD to T1w by their centers.
         If ``'t2w'``, align BOLD to T1w using the T2w as an intermediate.
-    use_t2w : :obj:`bool`, optional
-        Unused
     name : :obj:`str`, optional
         Workflow name (default: fsl_bbr_wf)
 
@@ -529,7 +522,6 @@ def init_fsl_bbr_wf(
                 't1w_preproc',  # FLIRT BBR
                 't1w_mask',
                 't1w_dseg',
-                't2w_preproc',
             ]
         ),
         name='inputnode',

From b92a4c9c07389aefc8d8fa464f88391e3b9d69e2 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 24 Jan 2024 15:40:38 -0500
Subject: [PATCH 12/22] FIX: Update FunctionalSummary expected values

---
 fmriprep/interfaces/reports.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/fmriprep/interfaces/reports.py b/fmriprep/interfaces/reports.py
index 5108e6236..0ba92fb14 100644
--- a/fmriprep/interfaces/reports.py
+++ b/fmriprep/interfaces/reports.py
@@ -213,11 +213,12 @@ class FunctionalSummaryInputSpec(TraitedSpec):
         6, 9, 12, desc='Registration degrees of freedom', mandatory=True
     )
     registration_init = traits.Enum(
-        'register',
+        't1w',
+        't2w',
         'header',
         mandatory=True,
         desc='Whether to initialize registration with the "header"'
-        ' or by centering the volumes ("register")',
+        ' or by centering the volumes ("t1w" or "t2w")',
     )
     tr = traits.Float(desc='Repetition time', mandatory=True)
     dummy_scans = traits.Either(traits.Int(), None, desc='number of dummy scans specified by user')

From 8ef01535dddc156c5fcdcfe4436d2b618447cc99 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 24 Jan 2024 15:43:17 -0500
Subject: [PATCH 13/22] FIX: Drop unused connection

---
 fmriprep/workflows/bold/fit.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index a550293e6..740fa84ec 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -617,7 +617,6 @@ def init_bold_fit_wf(
                 ("t1w_preproc", "inputnode.t1w_preproc"),
                 ("t1w_mask", "inputnode.t1w_mask"),
                 ("t1w_dseg", "inputnode.t1w_dseg"),
-                ("t2w_preproc", "inputnode.t2w_preproc"),
                 # Undefined if --fs-no-reconall, but this is safe
                 ("subjects_dir", "inputnode.subjects_dir"),
                 ("subject_id", "inputnode.subject_id"),

From ddcee99f02a606f0ea4a4410440d98b9c4a723cc Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 24 Jan 2024 17:21:31 -0500
Subject: [PATCH 14/22] FIX: Remove brittle query

---
 fmriprep/workflows/bold/fit.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index 740fa84ec..8bca33670 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -216,11 +216,6 @@ def init_bold_fit_wf(
         layout=layout,
     )
 
-    # T2w is not required, but if available, use to improve BOLD -> anat coreg
-    has_t2w = bool(
-        layout.get(suffix='T2w', extension=['.nii', '.nii.gz'], **bids_filters.get('t2w', {}))
-    )
-
     basename = os.path.basename(bold_file)
     sbref_msg = f"No single-band-reference found for {basename}."
     if sbref_files and "sbref" in config.workflow.ignore:

From 00772918d08bf1031014970ccb26c59bb9833182 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 24 Jan 2024 17:22:02 -0500
Subject: [PATCH 15/22] FIX: Purge traces of "register" value

---
 fmriprep/workflows/bold/registration.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index 85ffbacf9..c73f24dff 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -90,7 +90,7 @@ def init_bold_reg_wf(
         If ``None``, test BBR result for distortion before accepting.
     bold2anat_dof : 6, 9 or 12
         Degrees-of-freedom for BOLD-anatomical registration
-    bold2anat_init : str, 't1w', 't2w' or 'register'
+    bold2anat_init : str, 't1w', 't2w' or 'header'
         If ``'header'``, use header information for initialization of BOLD and T1 images.
         If ``'t1w'``, align BOLD to T1w by their centers.
         If ``'t2w'``, align BOLD to T1w using the T2w as an intermediate.
@@ -234,7 +234,7 @@ def init_bbreg_wf(
         If ``None``, test BBR result for distortion before accepting.
     bold2anat_dof : 6, 9 or 12
         Degrees-of-freedom for BOLD-anatomical registration
-    bold2anat_init : str, 't1w', 't2w' or 'register'
+    bold2anat_init : str, 't1w', 't2w' or 'header'
         If ``'header'``, use header information for initialization of BOLD and T1 images.
         If ``'t1w'``, align BOLD to T1w by their centers.
         If ``'t2w'``, align BOLD to T1w using the T2w as an intermediate.
@@ -368,7 +368,7 @@ def init_bbreg_wf(
     ])  # fmt:skip
 
     # Do not initialize with header, use mri_coreg
-    if bold2anat_init == "register":
+    if bold2anat_init != "header":
         workflow.connect([
             (inputnode, mri_coreg, [('subjects_dir', 'subjects_dir'),
                                     ('subject_id', 'subject_id'),
@@ -405,7 +405,7 @@ def init_bbreg_wf(
 
         return workflow
 
-    # Only reach this point if bold2anat_init is "register" and use_bbr is None
+    # Only reach this point if bold2anat_init is "t1w" or "t2w" and use_bbr is None
     compare_transforms = pe.Node(niu.Function(function=compare_xforms), name='compare_transforms')
 
     workflow.connect([
@@ -458,7 +458,7 @@ def init_fsl_bbr_wf(
         If ``None``, test BBR result for distortion before accepting.
     bold2anat_dof : 6, 9 or 12
         Degrees-of-freedom for BOLD-anatomical registration
-    bold2anat_init : str, 't1w', 't2w' or 'register'
+    bold2anat_init : str, 't1w', 't2w' or 'header'
         If ``'header'``, use header information for initialization of BOLD and T1 images.
         If ``'t1w'``, align BOLD to T1w by their centers.
         If ``'t2w'``, align BOLD to T1w using the T2w as an intermediate.

From 4524d165b18746d5dfb3eb2570d1382d966954d8 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 24 Jan 2024 17:50:43 -0500
Subject: [PATCH 16/22] TST: Set proper default

---
 fmriprep/workflows/tests/test_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep/workflows/tests/test_base.py b/fmriprep/workflows/tests/test_base.py
index 0bea4c510..74ae6633f 100644
--- a/fmriprep/workflows/tests/test_base.py
+++ b/fmriprep/workflows/tests/test_base.py
@@ -105,7 +105,7 @@ def bids_root(tmp_path_factory):
 
 
 def _make_params(
-    bold2anat_init: str = "auto",
+    bold2anat_init: str = "t1w",
     use_bbr: bool | None = None,
     dummy_scans: int | None = None,
     me_output_echos: bool = False,

From 6c448a257bdf728ee4e7261d0b2f7766c3240dab Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 24 Jan 2024 21:02:05 -0500
Subject: [PATCH 17/22] TST: Parametrize bold2anat in test

---
 fmriprep/workflows/bold/tests/test_base.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/fmriprep/workflows/bold/tests/test_base.py b/fmriprep/workflows/bold/tests/test_base.py
index 93035c640..e4597100c 100644
--- a/fmriprep/workflows/bold/tests/test_base.py
+++ b/fmriprep/workflows/bold/tests/test_base.py
@@ -35,6 +35,7 @@ def bids_root(tmp_path_factory):
 @pytest.mark.parametrize("fieldmap_id", ["phasediff", None])
 @pytest.mark.parametrize("freesurfer", [False, True])
 @pytest.mark.parametrize("level", ["minimal", "resampling", "full"])
+@pytest.mark.parametrize("bold2anat_init", ["t1w", "t2w"])
 def test_bold_wf(
     bids_root: Path,
     tmp_path: Path,
@@ -42,6 +43,7 @@ def test_bold_wf(
     fieldmap_id: str | None,
     freesurfer: bool,
     level: str,
+    bold2anat_init: str,
 ):
     """Test as many combinations of precomputed files and input
     configurations as possible."""
@@ -65,6 +67,7 @@ def test_bold_wf(
         img.to_filename(path)
 
     with mock_config(bids_dir=bids_root):
+        config.workflow.bold2anat_init = bold2anat_init
         config.workflow.level = level
         config.workflow.run_reconall = freesurfer
         wf = init_bold_wf(

From 91265b0aa83511c875bcf80fe90a4bc71565cc03 Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <goncalves.mathias@gmail.com>
Date: Thu, 25 Jan 2024 08:03:48 -0500
Subject: [PATCH 18/22] Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 fmriprep/cli/parser.py                  | 4 ++--
 fmriprep/workflows/base.py              | 2 +-
 fmriprep/workflows/bold/registration.py | 7 ++-----
 3 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index dcf473d55..1ee8dbd04 100644
--- a/fmriprep/cli/parser.py
+++ b/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",
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index acc2951b9..1367edeeb 100644
--- a/fmriprep/workflows/base.py
+++ b/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:
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index c73f24dff..a8a64fdeb 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/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

From d5a282e31730c582de91e103a112f255f3c58719 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 25 Jan 2024 11:29:04 -0500
Subject: [PATCH 19/22] ENH: Add option to force t2w

---
 fmriprep/cli/parser.py                  |  8 ++++----
 fmriprep/config.py                      |  6 +++---
 fmriprep/workflows/base.py              | 10 +++++++---
 fmriprep/workflows/bold/registration.py | 12 ++++++------
 4 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 1ee8dbd04..519fde2f6 100644
--- a/fmriprep/cli/parser.py
+++ b/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",
diff --git a/fmriprep/config.py b/fmriprep/config.py
index aabea97c7..ad0761f35 100644
--- a/fmriprep/config.py
+++ b/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
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 1367edeeb..a152ce357 100644
--- a/fmriprep/workflows/base.py
+++ b/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:
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index a8a64fdeb..716ac7a0e 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/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:

From 08dfd68984d30d5d6c77350a313bbe764d6ccd87 Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <goncalves.mathias@gmail.com>
Date: Thu, 25 Jan 2024 13:13:56 -0500
Subject: [PATCH 20/22] Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 fmriprep/workflows/bold/base.py       | 2 --
 fmriprep/workflows/bold/fit.py        | 2 --
 fmriprep/workflows/tests/test_base.py | 4 +++-
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 6c7c66cce..c7289c6d0 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -209,7 +209,6 @@ def init_bold_wf(
                 "t1w_mask",
                 "t1w_dseg",
                 "t1w_tpms",
-                "t2w_preproc",  # Optional
                 # FreeSurfer outputs
                 "subjects_dir",
                 "subject_id",
@@ -261,7 +260,6 @@ def init_bold_wf(
             ('t1w_preproc', 'inputnode.t1w_preproc'),
             ('t1w_mask', 'inputnode.t1w_mask'),
             ('t1w_dseg', 'inputnode.t1w_dseg'),
-            ('t2w_preproc', 'inputnode.t2w_preproc'),
             ('subjects_dir', 'inputnode.subjects_dir'),
             ('subject_id', 'inputnode.subject_id'),
             ('fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index 8bca33670..a652c2ef1 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -268,8 +268,6 @@ def init_bold_fit_wf(
                 "subjects_dir",
                 "subject_id",
                 "fsnative2t1w_xfm",
-                # Optional - improvements if available
-                "t2w_preproc",
             ],
         ),
         name="inputnode",
diff --git a/fmriprep/workflows/tests/test_base.py b/fmriprep/workflows/tests/test_base.py
index 74ae6633f..05463549c 100644
--- a/fmriprep/workflows/tests/test_base.py
+++ b/fmriprep/workflows/tests/test_base.py
@@ -105,7 +105,7 @@ def bids_root(tmp_path_factory):
 
 
 def _make_params(
-    bold2anat_init: str = "t1w",
+    bold2anat_init: str = "auto",
     use_bbr: bool | None = None,
     dummy_scans: int | None = None,
     me_output_echos: bool = False,
@@ -163,6 +163,8 @@ def _make_params(
     ),
     [
         _make_params(),
+        _make_params(bold2anat_init="t1w"),
+        _make_params(bold2anat_init="t2w"),
         _make_params(bold2anat_init="header"),
         _make_params(use_bbr=True),
         _make_params(use_bbr=False),

From 6fb9f1767bef16a6a05f2ac6996f49dd7a10a622 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 25 Jan 2024 16:23:14 -0500
Subject: [PATCH 21/22] TST: Remove test now that functionality has changed

---
 .circleci/config.yml | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 5956090df..600db1caf 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -647,27 +647,6 @@ jobs:
                 --output-spaces MNI152NLin2009cAsym:res-2 anat func \
                 --mem-mb 14336 --nthreads 4 -vv --debug compcor
       - run: *check_outputs
-      - run:
-          name: Generate report with one artificial error
-          command: |
-            set -x
-            sudo mv /tmp/${DATASET}/fmriprep/sub-100185.html \
-                    /tmp/${DATASET}/fmriprep/sub-100185_noerror.html
-            UUID=$(grep uuid /tmp/${DATASET}/work/*/config.toml | cut -d\" -f 2 | tail -n 1)
-            mkdir -p /tmp/${DATASET}/fmriprep/sub-100185/log/$UUID/
-            cp /tmp/src/fmriprep/fmriprep/data/tests/crash_files/*.txt \
-                /tmp/${DATASET}/fmriprep/sub-100185/log/$UUID/
-            set +e
-            fmriprep-docker -i nipreps/fmriprep:latest \
-                -e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
-                --config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
-                /tmp/data/${DATASET} /tmp/${DATASET}/fmriprep participant \
-                --fs-no-reconall --sloppy --write-graph \
-                --output-spaces MNI152NLin2009cAsym:res-2 anat func \
-                --reports-only --config-file /tmp/${DATASET}/work/${UUID}/config.toml -vv
-            RET=$?
-            set -e
-            [[ "$RET" -eq "0" ]]  # ensure report was generated successfully
       - run:
           name: Clean working directory
           when: on_success

From e4235189eb0d8f3d62a8f1e7ac29ff8d7ac26247 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 25 Jan 2024 16:31:18 -0500
Subject: [PATCH 22/22] Support lists in bids_filter containing null or *

---
 fmriprep/cli/parser.py | 21 ++++++++++++++++-----
 fmriprep/config.py     | 17 +++++++++++++----
 2 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index a62ab7f7f..9e426b771 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -90,13 +90,24 @@ def _to_gb(value):
     def _drop_sub(value):
         return value[4:] if value.startswith("sub-") else value
 
-    def _filter_pybids_none_any(dct):
+    def _process_value(value):
         import bids
 
-        return {
-            k: bids.layout.Query.NONE if v is None else (bids.layout.Query.ANY if v == "*" else v)
-            for k, v in dct.items()
-        }
+        if value is None:
+            return bids.layout.Query.NONE
+        elif value == "*":
+            return bids.layout.Query.ANY
+        else:
+            return value
+
+    def _filter_pybids_none_any(dct):
+        d = {}
+        for k, v in dct.items():
+            if isinstance(v, list):
+                d[k] = [_process_value(val) for val in v]
+            else:
+                d[k] = _process_value(v)
+        return d
 
     def _bids_filter(value, parser):
         from json import JSONDecodeError, loads
diff --git a/fmriprep/config.py b/fmriprep/config.py
index ad0761f35..1dfc7783f 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -493,12 +493,21 @@ def init(cls):
         if cls.bids_filters:
             from bids.layout import Query
 
+            def _process_value(value):
+                """Convert string with "Query" in it to Query object."""
+                if isinstance(value, list):
+                    return [_process_value(val) for val in value]
+                else:
+                    return (
+                        getattr(Query, value[7:-4])
+                        if not isinstance(value, Query) and "Query" in value
+                        else value
+                    )
+
             # unserialize pybids Query enum values
             for acq, filters in cls.bids_filters.items():
-                cls.bids_filters[acq] = {
-                    k: getattr(Query, v[7:-4]) if not isinstance(v, Query) and "Query" in v else v
-                    for k, v in filters.items()
-                }
+                for k, v in filters.items():
+                    cls.bids_filters[acq][k] = _process_value(v)
 
         if "all" in cls.debug:
             cls.debug = list(DEBUG_MODES)