ENH: Restore resampling to surface GIFTIs (#3126)

## Changes proposed in this pull request

This PR moves the datasinks for GIFTI files into the surface resampling
workflow, and adds the resampling workflow to the main BOLD workflow.

Previously we used these GIFTI files as intermediates for CIFTI, which
required collation across multiple sub-workflows. With that now being
done by other means, we have the opportunity to remove several
metadata-collation nodes. We are also able to get rid of a `JoinNode`
altogether, as iteration is all we need.

This workflow might now belong in `workflows.bold.outputs`, but that
would make the overall changes harder to assess.

This builds on #3120. It also has a cleanup commit that removes portions
of the derivatives workflow that have been reimplemented elsewhere.

Author: effigies

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: