ENH: Restore resampling to FreeSurfer surfaces

effigies · effigies · commit d378af375249 · 2023-11-07T11:11:12.000-05:00
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
@@ -442,6 +442,26 @@ def init_bold_wf(
             (bold_std_wf, ds_bold_std_wf, [('outputnode.bold_file', 'inputnode.bold')]),
         ])  # fmt:skip
 
+    if config.workflow.run_reconall and freesurfer_spaces:
+        config.loggers.workflow.debug("Creating BOLD surface-sampling workflow.")
+        bold_surf_wf = init_bold_surf_wf(
+            mem_gb=mem_gb["resampled"],
+            surface_spaces=freesurfer_spaces,
+            medial_surface_nan=config.workflow.medial_surface_nan,
+            metadata=all_metadata[0],
+            output_dir=fmriprep_dir,
+            name="bold_surf_wf",
+        )
+        bold_surf_wf.inputs.inputnode.source_file = bold_file
+        workflow.connect([
+            (inputnode, bold_surf_wf, [
+                ("subjects_dir", "inputnode.subjects_dir"),
+                ("subject_id", "inputnode.subject_id"),
+                ("fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm"),
+            ]),
+            (bold_anat_wf, bold_surf_wf, [("outputnode.bold_file", "inputnode.bold_t1w")]),
+        ])  # fmt:skip
+
     bold_confounds_wf = init_bold_confs_wf(
         mem_gb=mem_gb["largemem"],
         metadata=all_metadata[0],
@@ -723,27 +743,6 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
     )
 
     # SURFACES ##################################################################################
-    # Freesurfer
-    if freesurfer and freesurfer_spaces:
-        config.loggers.workflow.debug("Creating BOLD surface-sampling workflow.")
-        bold_surf_wf = init_bold_surf_wf(
-            mem_gb=mem_gb["resampled"],
-            surface_spaces=freesurfer_spaces,
-            medial_surface_nan=config.workflow.medial_surface_nan,
-            name="bold_surf_wf",
-        )
-        # fmt:off
-        workflow.connect([
-            (inputnode, bold_surf_wf, [
-                ("subjects_dir", "inputnode.subjects_dir"),
-                ("subject_id", "inputnode.subject_id"),
-                ("fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm"),
-            ]),
-            (bold_t1_trans_wf, bold_surf_wf, [("outputnode.bold_t1", "inputnode.source_file")]),
-            (bold_surf_wf, outputnode, [("outputnode.surfaces", "surfaces")]),
-            (bold_surf_wf, func_derivatives_wf, [("outputnode.target", "inputnode.surf_refs")]),
-        ])
-        # fmt:on
 
     # CIFTI output
     if config.workflow.cifti_output:
diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
@@ -907,15 +907,6 @@ def init_func_derivatives_wf(
     nonstd_spaces = set(spaces.get_nonstandard())
     workflow = Workflow(name=name)
 
-    # BOLD series will generally be unmasked unless multiecho,
-    # as the optimal combination is undefined outside a bounded mask
-    masked = multiecho
-    t2star_meta = {
-        'Units': 's',
-        'EstimationReference': 'doi:10.1002/mrm.20900',
-        'EstimationAlgorithm': 'monoexponential decay model',
-    }
-
     inputnode = pe.Node(
         niu.IdentityInterface(
             fields=[
@@ -967,51 +958,6 @@ def init_func_derivatives_wf(
     ])
     # fmt:on
 
-    fs_outputs = spaces.cached.get_fs_spaces()
-    if freesurfer and fs_outputs:
-        from niworkflows.interfaces.surf import Path2BIDS
-
-        select_fs_surf = pe.Node(
-            KeySelect(fields=['surfaces', 'surf_kwargs']),
-            name='select_fs_surf',
-            run_without_submitting=True,
-            mem_gb=DEFAULT_MEMORY_MIN_GB,
-        )
-        select_fs_surf.iterables = [('key', fs_outputs)]
-        select_fs_surf.inputs.surf_kwargs = [{'space': s} for s in fs_outputs]
-
-        name_surfs = pe.MapNode(
-            Path2BIDS(pattern=r'(?P<hemi>[lr])h.\w+'),
-            iterfield='in_file',
-            name='name_surfs',
-            run_without_submitting=True,
-        )
-
-        ds_bold_surfs = pe.MapNode(
-            DerivativesDataSink(
-                base_directory=output_dir,
-                extension=".func.gii",
-                TaskName=metadata.get('TaskName'),
-                **timing_parameters,
-            ),
-            iterfield=['in_file', 'hemi'],
-            name='ds_bold_surfs',
-            run_without_submitting=True,
-            mem_gb=DEFAULT_MEMORY_MIN_GB,
-        )
-        # fmt:off
-        workflow.connect([
-            (inputnode, select_fs_surf, [
-                ('surf_files', 'surfaces'),
-                ('surf_refs', 'keys')]),
-            (select_fs_surf, name_surfs, [('surfaces', 'in_file')]),
-            (inputnode, ds_bold_surfs, [('source_file', 'source_file')]),
-            (select_fs_surf, ds_bold_surfs, [('surfaces', 'in_file'),
-                                             ('key', 'space')]),
-            (name_surfs, ds_bold_surfs, [('hemi', 'hemi')]),
-        ])
-        # fmt:on
-
     if freesurfer and project_goodvoxels:
         ds_goodvoxels_mask = pe.Node(
             DerivativesDataSink(
diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py
@@ -46,6 +46,7 @@
 
 from ...config import DEFAULT_MEMORY_MIN_GB
 from ...interfaces.workbench import MetricDilate, MetricMask, MetricResample
+from .outputs import prepare_timing_parameters
 
 if ty.TYPE_CHECKING:
     from niworkflows.utils.spaces import SpatialReferences
@@ -56,6 +57,8 @@ def init_bold_surf_wf(
     mem_gb: float,
     surface_spaces: ty.List[str],
     medial_surface_nan: bool,
+    metadata: dict,
+    output_dir: str,
     name: str = "bold_surf_wf",
 ):
     """
@@ -90,6 +93,8 @@ def init_bold_surf_wf(
     Inputs
     ------
     source_file
+        Original BOLD series
+    bold_t1w
         Motion-corrected BOLD series in T1 space
     subjects_dir
         FreeSurfer SUBJECTS_DIR
@@ -109,6 +114,10 @@ def init_bold_surf_wf(
     from niworkflows.interfaces.nitransforms import ConcatenateXFMs
     from niworkflows.interfaces.surf import GiftiSetAnatomicalStructure
 
+    from fmriprep.interfaces import DerivativesDataSink
+
+    timing_parameters = prepare_timing_parameters(metadata)
+
     workflow = Workflow(name=name)
     workflow.__desc__ = """\
 The BOLD time-series were resampled onto the following surfaces
@@ -120,7 +129,13 @@ def init_bold_surf_wf(
 
     inputnode = pe.Node(
         niu.IdentityInterface(
-            fields=["source_file", "subject_id", "subjects_dir", "fsnative2t1w_xfm"]
+            fields=[
+                "source_file",
+                "bold_t1w",
+                "subject_id",
+                "subjects_dir",
+                "fsnative2t1w_xfm",
+            ]
         ),
         name="inputnode",
     )
@@ -140,13 +155,6 @@ def select_target(subject_id, space):
         mem_gb=DEFAULT_MEMORY_MIN_GB,
     )
 
-    # Rename the source file to the output space to simplify naming later
-    rename_src = pe.Node(
-        niu.Rename(format_string="%(subject)s", keep_ext=True),
-        name="rename_src",
-        run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB,
-    )
     itk2lta = pe.Node(
         ConcatenateXFMs(out_fmt="fs", inverse=True), name="itk2lta", run_without_submitting=True
     )
@@ -172,47 +180,43 @@ def select_target(subject_id, space):
         mem_gb=DEFAULT_MEMORY_MIN_GB,
     )
 
-    joinnode = pe.JoinNode(
-        niu.IdentityInterface(fields=["surfaces", "target"]),
-        joinsource="itersource",
-        name="joinnode",
-    )
-
-    outputnode = pe.Node(
-        niu.IdentityInterface(fields=["surfaces", "target"]),
-        name="outputnode",
+    ds_bold_surfs = pe.MapNode(
+        DerivativesDataSink(
+            base_directory=output_dir,
+            extension=".func.gii",
+            TaskName=metadata.get('TaskName'),
+            **timing_parameters,
+        ),
+        iterfield=['in_file', 'hemi'],
+        name='ds_bold_surfs',
+        run_without_submitting=True,
+        mem_gb=DEFAULT_MEMORY_MIN_GB,
     )
+    ds_bold_surfs.inputs.hemi = ["L", "R"]
 
-    # fmt: off
     workflow.connect([
         (inputnode, get_fsnative, [
             ("subject_id", "subject_id"),
             ("subjects_dir", "subjects_dir")
         ]),
         (inputnode, targets, [("subject_id", "subject_id")]),
         (inputnode, itk2lta, [
-            ("source_file", "reference"),
+            ("bold_t1w", "reference"),
             ("fsnative2t1w_xfm", "in_xfms"),
         ]),
         (get_fsnative, itk2lta, [("T1", "moving")]),
         (inputnode, sampler, [
             ("subjects_dir", "subjects_dir"),
             ("subject_id", "subject_id"),
+            ("bold_t1w", "source_file"),
         ]),
         (itersource, targets, [("target", "space")]),
-        (inputnode, rename_src, [("source_file", "in_file")]),
-        (itersource, rename_src, [("target", "subject")]),
-        (rename_src, sampler, [("out_file", "source_file")]),
         (itk2lta, sampler, [("out_inv", "reg_file")]),
         (targets, sampler, [("out", "target_subject")]),
-        (update_metadata, joinnode, [("out_file", "surfaces")]),
-        (itersource, joinnode, [("target", "target")]),
-        (joinnode, outputnode, [
-            ("surfaces", "surfaces"),
-            ("target", "target"),
-        ]),
-    ])
-    # fmt: on
+        (inputnode, ds_bold_surfs, [("source_file", "source_file")]),
+        (itersource, ds_bold_surfs, [("target", "space")]),
+        (update_metadata, ds_bold_surfs, [("out_file", "in_file")]),
+    ])  # fmt:skip
 
     # Refine if medial vertices should be NaNs
     medial_nans = pe.MapNode(
