started updating the main part 'base'

dmriprep/cli/parser.py

@@ -23,20 +23,20 @@
 """Parser."""
 import os
 import sys
+
 from .. import config
 
 
 def _build_parser():
     """Build parser object."""
+    from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
     from functools import partial
     from pathlib import Path
-    from argparse import (
-        ArgumentParser,
-        ArgumentDefaultsHelpFormatter,
-    )
+
+    from niworkflows.utils.spaces import OutputReferencesAction, Reference
     from packaging.version import Version
+
     from .version import check_latest, is_flagged
-    from niworkflows.utils.spaces import Reference, OutputReferencesAction
 
     def _path_exists(path, parser):
         """Ensure a given path exists."""
@@ -52,7 +52,7 @@ def _min_one(value, parser):
         return value
 
     def _to_gb(value):
-        scale = {"G": 1, "T": 10 ** 3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
+        scale = {"G": 1, "T": 10**3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
         digits = "".join([c for c in value if c.isdigit()])
         units = value[len(digits) :] or "M"
         return int(digits) * scale[units[0]]
@@ -70,7 +70,11 @@ def _bids_filter(value):
     verstr = f"dMRIPrep v{config.environment.version}"
     currentv = Version(config.environment.version)
     is_release = not any(
-        (currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease)
+        (
+            currentv.is_devrelease,
+            currentv.is_prerelease,
+            currentv.is_postrelease,
+        )
     )
 
     parser = ArgumentParser(
@@ -96,7 +100,8 @@ def _bids_filter(value):
         "output_dir",
         action="store",
         type=Path,
-        help="the output path for the outcomes of preprocessing and visual " "reports",
+        help="the output path for the outcomes of preprocessing and visual "
+        "reports",
     )
     parser.add_argument(
         "analysis_level",
@@ -181,7 +186,9 @@ def _bids_filter(value):
         help="nipype plugin configuration file",
     )
     g_perfm.add_argument(
-        "--anat-only", action="store_true", help="run anatomical workflows only"
+        "--anat-only",
+        action="store_true",
+        help="run anatomical workflows only",
     )
     g_perfm.add_argument(
         "--boilerplate_only",
@@ -249,7 +256,9 @@ def _bids_filter(value):
     )
 
     #  ANTs options
-    g_ants = parser.add_argument_group("Specific options for ANTs registrations")
+    g_ants = parser.add_argument_group(
+        "Specific options for ANTs registrations"
+    )
     g_ants.add_argument(
         "--skull-strip-template",
         default="OASIS30ANTs",
@@ -264,7 +273,9 @@ def _bids_filter(value):
     )
 
     # SyN-unwarp options
-    g_syn = parser.add_argument_group("Specific options for SyN distortion correction")
+    g_syn = parser.add_argument_group(
+        "Specific options for SyN distortion correction"
+    )
     g_syn.add_argument(
         "--use-syn-sdc",
         action="store_true",
@@ -287,7 +298,9 @@ def _bids_filter(value):
     )
 
     # FreeSurfer options
-    g_fs = parser.add_argument_group("Specific options for FreeSurfer preprocessing")
+    g_fs = parser.add_argument_group(
+        "Specific options for FreeSurfer preprocessing"
+    )
     g_fs.add_argument(
         "--fs-license-file",
         metavar="PATH",
@@ -415,11 +428,14 @@ def _bids_filter(value):
 def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
     import logging
+
     from niworkflows.utils.spaces import Reference, SpatialReferences
 
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
-    config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
+    config.execution.log_level = int(
+        max(25 - 5 * opts.verbose_count, logging.DEBUG)
+    )
     config.from_dict(vars(opts))
     config.loggers.init()
 
@@ -469,18 +485,33 @@ def parse_args(args=None, namespace=None):
     output_dir = config.execution.output_dir
     work_dir = config.execution.work_dir
     version = config.environment.version
+    output_layout = config.execution.output_layout
 
     if config.execution.fs_subjects_dir is None:
         config.execution.fs_subjects_dir = output_dir / "freesurfer"
-
+    if config.execution.fs_subjects_dir is None:
+        if output_layout == "bids":
+            config.execution.fs_subjects_dir = (
+                output_dir / "sourcedata" / "freesurfer"
+            )
+        elif output_layout == "legacy":
+            config.execution.fs_subjects_dir = output_dir / "freesurfer"
+    if config.execution.fmriprep_dir is None:
+        if output_layout == "bids":
+            config.execution.fmriprep_dir = output_dir
+        elif output_layout == "legacy":
+            config.execution.fmriprep_dir = output_dir / "dmriprep"
     # Wipe out existing work_dir
     if opts.clean_workdir and work_dir.exists():
         from niworkflows.utils.misc import clean_directory
 
-        build_log.log("Clearing previous dMRIPrep working directory: %s", work_dir)
+        build_log.log(
+            "Clearing previous dMRIPrep working directory: %s", work_dir
+        )
         if not clean_directory(work_dir):
             build_log.warning(
-                "Could not clear all contents of working directory: %s", work_dir
+                "Could not clear all contents of working directory: %s",
+                work_dir,
             )
 
     # Ensure input and output folders are not the same
@@ -533,4 +564,6 @@ def parse_args(args=None, namespace=None):
         )
 
     config.execution.participant_label = sorted(participant_label)
-    config.workflow.skull_strip_template = config.workflow.skull_strip_template[0]
+    config.workflow.skull_strip_template = (
+        config.workflow.skull_strip_template[0]
+    )

dmriprep/config/__init__.py

@@ -67,16 +67,20 @@
     :py:class:`~bids.layout.BIDSLayout`, etc.)
 
 """
-from multiprocessing import set_start_method
 import warnings
+from multiprocessing import set_start_method
 
 # cmp is not used by dmriprep, so ignore nipype-generated warnings
 warnings.filterwarnings("ignore", "cmp not installed")
 warnings.filterwarnings(
     "ignore", "This has not been fully tested. Please report any failures."
 )
-warnings.filterwarnings("ignore", "sklearn.externals.joblib is deprecated in 0.21")
-warnings.filterwarnings("ignore", "can't resolve package from __spec__ or __package__")
+warnings.filterwarnings(
+    "ignore", "sklearn.externals.joblib is deprecated in 0.21"
+)
+warnings.filterwarnings(
+    "ignore", "can't resolve package from __spec__ or __package__"
+)
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 warnings.filterwarnings("ignore", category=FutureWarning)
 warnings.filterwarnings("ignore", category=ResourceWarning)
@@ -89,28 +93,35 @@
 finally:
     # Defer all custom import for after initializing the forkserver and
     # ignoring the most annoying warnings
+    import logging
     import os
     import sys
-    import logging
-
-    from uuid import uuid4
     from pathlib import Path
     from time import strftime
-    from niworkflows.utils.spaces import SpatialReferences as _SRs, Reference as _Ref
-    from nipype import logging as nlogging, __version__ as _nipype_ver
+    from uuid import uuid4
+
+    from nipype import __version__ as _nipype_ver
+    from nipype import logging as nlogging
+    from niworkflows.utils.spaces import Reference as _Ref
+    from niworkflows.utils.spaces import SpatialReferences as _SRs
     from templateflow import __version__ as _tf_ver
+
     from .. import __version__
 
 
-def redirect_warnings(message, category, filename, lineno, file=None, line=None):
+def redirect_warnings(
+    message, category, filename, lineno, file=None, line=None
+):
     """Redirect other warnings."""
     logger = logging.getLogger()
     logger.debug("Captured warning (%s): %s", category, message)
 
 
 warnings.showwarning = redirect_warnings
 
-logging.addLevelName(25, "IMPORTANT")  # Add a new level between INFO and WARNING
+logging.addLevelName(
+    25, "IMPORTANT"
+)  # Add a new level between INFO and WARNING
 logging.addLevelName(15, "VERBOSE")  # Add a new level between INFO and DEBUG
 
 DEFAULT_MEMORY_MIN_GB = 0.01
@@ -133,14 +144,15 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
 
 _templateflow_home = Path(
     os.getenv(
-        "TEMPLATEFLOW_HOME", os.path.join(os.getenv("HOME"), ".cache", "templateflow")
+        "TEMPLATEFLOW_HOME",
+        os.path.join(os.getenv("HOME"), ".cache", "templateflow"),
     )
 )
 
 try:
     from psutil import virtual_memory
 
-    _free_mem_at_start = round(virtual_memory().free / 1024 ** 3, 1)
+    _free_mem_at_start = round(virtual_memory().free / 1024**3, 1)
 except Exception:
     _free_mem_at_start = None
 
@@ -341,6 +353,8 @@ class execution(_Config):
     """Only generate a boilerplate."""
     debug = False
     """Run in sloppy mode (meaning, suboptimal parameters that minimize run-time)."""
+    dmriprep_dir = None
+    """Root of dMRIPrep BIDS Derivatives dataset. Depends on output_layout."""
     fs_license_file = _fs_license
     """An existing file containing a FreeSurfer license."""
     fs_subjects_dir = None
@@ -359,6 +373,8 @@ class execution(_Config):
     """Do not monitor *dMRIPrep* using Google Analytics."""
     output_dir = None
     """Folder where derivatives will be stored."""
+    output_layout = "bids"
+    """Layout of derivatives within output_dir."""
     output_spaces = None
     """List of (non)standard spaces designated (with the ``--output-spaces`` flag of
     the command line) as spatial references for outputs."""
@@ -392,8 +408,11 @@ class execution(_Config):
     @classmethod
     def init(cls):
         """Create a new BIDS Layout accessible with :attr:`~execution.layout`."""
+        if cls.fs_license_file and Path(cls.fs_license_file).is_file():
+            os.environ["FS_LICENSE"] = str(cls.fs_license_file)
         if cls._layout is None:
             import re
+
             from bids.layout import BIDSLayout
 
             work_dir = cls.work_dir / "bids.db"
@@ -412,6 +431,20 @@ def init(cls):
                 ),
             )
         cls.layout = cls._layout
+        if cls.bids_filters:
+            from bids.layout import Query
+
+            # 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()
+                }
+
+        if "all" in cls.debug:
+            cls.debug = list(DEBUG_MODES)
 
 
 # These variables are not necessary anymore
@@ -462,7 +495,9 @@ class workflow(_Config):
 class loggers:
     """Keep loggers easily accessible (see :py:func:`init`)."""
 
-    _fmt = "%(asctime)s,%(msecs)d %(name)-2s " "%(levelname)-2s:\n\t %(message)s"
+    _fmt = (
+        "%(asctime)s,%(msecs)d %(name)-2s " "%(levelname)-2s:\n\t %(message)s"
+    )
     _datefmt = "%y%m%d-%H:%M:%S"
 
     default = logging.getLogger()
@@ -489,15 +524,22 @@ def init(cls):
         from nipype import config as ncfg
 
         _handler = logging.StreamHandler(stream=sys.stdout)
-        _handler.setFormatter(logging.Formatter(fmt=cls._fmt, datefmt=cls._datefmt))
+        _handler.setFormatter(
+            logging.Formatter(fmt=cls._fmt, datefmt=cls._datefmt)
+        )
         cls.cli.addHandler(_handler)
         cls.default.setLevel(execution.log_level)
         cls.cli.setLevel(execution.log_level)
         cls.interface.setLevel(execution.log_level)
         cls.workflow.setLevel(execution.log_level)
         cls.utils.setLevel(execution.log_level)
         ncfg.update_config(
-            {"logging": {"log_directory": str(execution.log_dir), "log_to_file": True}}
+            {
+                "logging": {
+                    "log_directory": str(execution.log_dir),
+                    "log_to_file": True,
+                }
+            }
         )
 
 
@@ -560,7 +602,11 @@ def init_spaces(checkpoint=True):
     spaces = execution.output_spaces or SpatialReferences()
     if not isinstance(spaces, SpatialReferences):
         spaces = SpatialReferences(
-            [ref for s in spaces.split(" ") for ref in Reference.from_string(s)]
+            [
+                ref
+                for s in spaces.split(" ")
+                for ref in Reference.from_string(s)
+            ]
         )
 
     if checkpoint and not spaces.is_cached():

dmriprep/data/tests/config.toml

@@ -6,7 +6,7 @@ overcommit_policy = "heuristic"
 overcommit_limit = "50%"
 nipype_version = "1.4.2"
 templateflow_version = "0.4.2"
-version = "0.2.2"
+version = "0.4.0"
 
 [execution]
 bids_dir = "THP002/"

dmriprep/workflows/base.py

@@ -31,24 +31,24 @@
 import os
 import sys
 from copy import deepcopy
+from pathlib import Path
 
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.utils.misc import fix_multi_T1w_source_name
 from niworkflows.utils.spaces import Reference
 from packaging.version import Version
-from smriprep.workflows.anatomical import init_anat_preproc_wf
 
 from .. import config
-from ..interfaces import BIDSDataGrabber, DerivativesDataSink
+from ..interfaces import DerivativesDataSink
 from ..interfaces.reports import AboutSummary, SubjectSummary
 from ..utils.bids import collect_data
 from .dwi import init_dwi_preproc_wf
 
 
 def init_dmriprep_wf():
     """
-    Create the base workflow.
+    Build *dMRIPrep*'s pipeline.
 
     This workflow organizes the execution of *dMRIPrep*, with a sub-workflow for
     each subject. If FreeSurfer's recon-all is to be run, a FreeSurfer derivatives folder is
@@ -66,9 +66,11 @@ def init_dmriprep_wf():
 
     """
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-    from niworkflows.interfaces.bids import BIDSFreeSurferDir, BIDSInfo
+    from niworkflows.interfaces.bids import BIDSFreeSurferDir
 
-    dmriprep_wf = Workflow(name="dmriprep_wf")
+    ver = Version(config.environment.version)
+
+    dmriprep_wf = Workflow(name=f"dmriprep_{ver.major}_{ver.minor}_wf")
     dmriprep_wf.base_dir = config.execution.work_dir
 
     freesurfer = config.workflow.run_reconall
@@ -91,8 +93,7 @@ def init_dmriprep_wf():
         single_subject_wf = init_single_subject_wf(subject_id)
 
         single_subject_wf.config["execution"]["crashdump_dir"] = str(
-            config.execution.output_dir
-            / "dmriprep"
+            Path(config.execution.dmriprep_dir)
             / f"sub-{subject_id}"
             / "log"
             / config.execution.run_uuid
@@ -112,8 +113,7 @@ def init_dmriprep_wf():
 
         # Dump a copy of the config file into the log directory
         log_dir = (
-            config.execution.output_dir
-            / "dmriprep"
+            Path(config.execution.dmriprep_dir)
             / f"sub-{subject_id}"
             / "log"
             / config.execution.run_uuid
@@ -159,29 +159,55 @@ def init_single_subject_wf(subject_id):
         FreeSurfer's ``$SUBJECTS_DIR``
 
     """
+    from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+    from niworkflows.interfaces.bids import BIDSDataGrabber, BIDSInfo
+    from smriprep.workflows.anatomical import init_anat_preproc_wf
+
     from ..utils.misc import sub_prefix as _prefix
 
     name = f"single_subject_{subject_id}_wf"
-    subject_data = collect_data(config.execution.layout, subject_id)[0]
+    subject_data = collect_data(
+        config.execution.layout,
+        subject_id,
+        bids_filters=config.execution.bids_filters,
+    )[0]
 
     if "flair" in config.workflow.ignore:
         subject_data["flair"] = []
     if "t2w" in config.workflow.ignore:
         subject_data["t2w"] = []
 
     anat_only = config.workflow.anat_only
-
+    anat_derivatives = config.execution.anat_derivatives
+    spaces = config.workflow.spaces
     # Make sure we always go through these two checks
     if not anat_only and not subject_data["dwi"]:
         raise Exception(
             f"No DWI data found for participant {subject_id}. "
             "All workflows require DWI images."
         )
+    if anat_derivatives:
+        from smriprep.utils.bids import collect_derivatives
 
-    if not subject_data["t1w"]:
+        std_spaces = spaces.get_spaces(nonstandard=False, dim=(3,))
+        anat_derivatives = collect_derivatives(
+            anat_derivatives.absolute(),
+            subject_id,
+            std_spaces,
+            config.workflow.run_reconall,
+        )
+        if anat_derivatives is None:
+            config.loggers.workflow.warning(
+                f"""\
+Attempted to access pre-existing anatomical derivatives at \
+<{config.execution.anat_derivatives}>, however not all expectations of fMRIPrep \
+were met (for participant <{subject_id}>, spaces <{', '.join(std_spaces)}>, \
+reconall <{config.workflow.run_reconall}>)."""
+            )
+    if not anat_derivatives and not subject_data["t1w"]:
         raise Exception(
-            f"No T1w images found for participant {subject_id}. "
-            "All workflows require T1w images."
+            "No T1w images found for participant {}. "
+            "All workflows require T1w images.".format(subject_id)
         )
 
     workflow = Workflow(name=name)
@@ -212,15 +238,19 @@ def init_single_subject_wf(subject_id):
 ### References
 
 """
-    spaces = config.workflow.spaces
-    output_dir = config.execution.output_dir
+    dmriprep_dir = str(config.execution.dmriprep_dir)
 
     fsinputnode = pe.Node(
         niu.IdentityInterface(fields=["subjects_dir"]), name="fsinputnode"
     )
 
     bidssrc = pe.Node(
-        BIDSDataGrabber(subject_data=subject_data, anat_only=anat_only),
+        BIDSDataGrabber(
+            subject_data=subject_data,
+            anat_only=anat_only,
+            anat_derivatives=anat_derivatives,
+            subject_id=subject_id,
+        ),
         name="bidssrc",
     )
 
@@ -248,32 +278,22 @@ def init_single_subject_wf(subject_id):
 
     ds_report_summary = pe.Node(
         DerivativesDataSink(
-            base_directory=str(output_dir), desc="summary", datatype="figures"
+            base_directory=dmriprep_dir,
+            desc="summary",
+            datatype="figures",
         ),
         name="ds_report_summary",
         run_without_submitting=True,
     )
 
     ds_report_about = pe.Node(
         DerivativesDataSink(
-            base_directory=str(output_dir), desc="about", datatype="figures"
+            base_directory=dmriprep_dir, desc="about", datatype="figures"
         ),
         name="ds_report_about",
         run_without_submitting=True,
     )
 
-    anat_derivatives = config.execution.anat_derivatives
-    if anat_derivatives:
-        from smriprep.utils.bids import collect_derivatives
-
-        std_spaces = spaces.get_spaces(nonstandard=False, dim=(3,))
-        anat_derivatives = collect_derivatives(
-            anat_derivatives.absolute(),
-            subject_id,
-            std_spaces,
-            config.workflow.run_reconall,
-        )
-
     # Preprocessing of T1w (includes registration to MNI)
     anat_preproc_wf = init_anat_preproc_wf(
         bids_root=str(config.execution.bids_dir),
@@ -283,7 +303,7 @@ def init_single_subject_wf(subject_id):
         hires=config.workflow.hires,
         longitudinal=config.workflow.longitudinal,
         omp_nthreads=config.nipype.omp_nthreads,
-        output_dir=str(output_dir),
+        output_dir=dmriprep_dir,
         skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
         skull_strip_mode="force",
         skull_strip_template=Reference.from_string(
@@ -292,39 +312,116 @@ def init_single_subject_wf(subject_id):
         spaces=spaces,
         t1w=subject_data["t1w"],
     )
-    anat_preproc_wf.__desc__ = f"\n\n{anat_preproc_wf.__desc__}"
+    workflow.connect(
+        [
+            (
+                fsinputnode,
+                anat_preproc_wf,
+                [("subjects_dir", "inputnode.subjects_dir")],
+            ),
+            (fsinputnode, summary, [("subjects_dir", "subjects_dir")]),
+            (bids_info, summary, [("subject", "subject_id")]),
+            (
+                bids_info,
+                anat_preproc_wf,
+                [(("subject", _prefix), "inputnode.subject_id")],
+            ),
+            (
+                bidssrc,
+                anat_preproc_wf,
+                [
+                    ("t1w", "inputnode.t1w"),
+                    ("t2w", "inputnode.t2w"),
+                    ("roi", "inputnode.roi"),
+                    ("flair", "inputnode.flair"),
+                ],
+            ),
+            (summary, ds_report_summary, [("out_report", "in_file")]),
+            (about, ds_report_about, [("out_report", "in_file")]),
+        ]
+    )
+
+    if not anat_derivatives:
+        workflow.connect(
+            [
+                (
+                    bidssrc,
+                    bids_info,
+                    [(("t1w", fix_multi_T1w_source_name), "in_file")],
+                ),
+                (bidssrc, summary, [("t1w", "t1w"), ("t2w", "t2w")]),
+                (
+                    bidssrc,
+                    ds_report_summary,
+                    [(("t1w", fix_multi_T1w_source_name), "source_file")],
+                ),
+                (
+                    bidssrc,
+                    ds_report_about,
+                    [(("t1w", fix_multi_T1w_source_name), "source_file")],
+                ),
+            ]
+        )
+    else:
+        workflow.connect(
+            [
+                (
+                    anat_preproc_wf,
+                    summary,
+                    [("outputnode.t1w_preproc", "t1w")],
+                ),
+                (
+                    anat_preproc_wf,
+                    ds_report_summary,
+                    [("outputnode.t1w_preproc", "source_file")],
+                ),
+                (
+                    anat_preproc_wf,
+                    ds_report_about,
+                    [("outputnode.t1w_preproc", "source_file")],
+                ),
+            ]
+        )
 
-    # fmt:off
-    workflow.connect([
-        (fsinputnode, anat_preproc_wf, [("subjects_dir", "inputnode.subjects_dir")]),
-        (bidssrc, bids_info, [(("t1w", fix_multi_T1w_source_name), "in_file")]),
-        (fsinputnode, summary, [("subjects_dir", "subjects_dir")]),
-        (bidssrc, summary, [("t1w", "t1w"), ("t2w", "t2w"), ("dwi", "dwi")]),
-        (bids_info, summary, [("subject", "subject_id")]),
-        (bids_info, anat_preproc_wf, [(("subject", _prefix), "inputnode.subject_id")]),
-        (bidssrc, anat_preproc_wf, [
-            ("t1w", "inputnode.t1w"),
-            ("t2w", "inputnode.t2w"),
-            ("roi", "inputnode.roi"),
-            ("flair", "inputnode.flair"),
-        ]),
-        (bidssrc, ds_report_summary, [
-            (("t1w", fix_multi_T1w_source_name), "source_file"),
-        ]),
-        (summary, ds_report_summary, [("out_report", "in_file")]),
-        (bidssrc, ds_report_about, [
-            (("t1w", fix_multi_T1w_source_name), "source_file")
-        ]),
-        (about, ds_report_about, [("out_report", "in_file")]),
-    ])
-    # fmt:off
     # Overwrite ``out_path_base`` of smriprep's DataSinks
     for node in workflow.list_node_names():
         if node.split(".")[-1].startswith("ds_"):
-            workflow.get_node(node).interface.out_path_base = "dmriprep"
+            workflow.get_node(node).interface.out_path_base = ""
 
     if anat_only:
         return workflow
+    # fmt:off
+    # workflow.connect([
+    #     (fsinputnode, anat_preproc_wf, [("subjects_dir", "inputnode.subjects_dir")]),
+    #     (bidssrc, bids_info, [(("t1w", fix_multi_T1w_source_name), "in_file")]),
+    #     (fsinputnode, summary, [("subjects_dir", "subjects_dir")]),
+    #     (bidssrc, summary, [("t1w", "t1w"), ("t2w", "t2w"), ("dwi", "dwi")]),
+    #     (bids_info, summary, [("subject", "subject_id")]),
+    #     (bids_info, anat_preproc_wf, [(("subject", _prefix), "inputnode.subject_id")]),
+    #     (bidssrc, anat_preproc_wf, [
+    #         ("t1w", "inputnode.t1w"),
+    #         ("t2w", "inputnode.t2w"),
+    #         ("roi", "inputnode.roi"),
+    #         ("flair", "inputnode.flair"),
+    #     ]),
+    #     (bidssrc, ds_report_summary, [
+    #         (("t1w", fix_multi_T1w_source_name), "source_file"),
+    #     ]),
+    #     (summary, ds_report_summary, [("out_report", "in_file")]),
+    #     (bidssrc, ds_report_about, [
+    #         (("t1w", fix_multi_T1w_source_name), "source_file")
+    #     ]),
+    #     (about, ds_report_about, [("out_report", "in_file")]),
+    # ])
+    # # fmt:off
+    # # Overwrite ``out_path_base`` of smriprep's DataSinks
+    # for node in workflow.list_node_names():
+    #     if node.split(".")[-1].startswith("ds_"):
+    #         workflow.get_node(node).interface.out_path_base = "dmriprep"
+
+    # if anat_only:
+    #     return workflow
+    return workflow
 
     from .dwi.base import init_dwi_preproc_wf