RF: Switch to more targeted morphometry datasinks

nipreps · Oct 2, 2023 · 3b5b230 · 3b5b230
1 parent b49ac4c
commit 3b5b230
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Showing 3 changed files with 11 additions and 36 deletions.
diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
@@ -312,6 +312,9 @@ def init_anat_preproc_wf(
         ds_surfaces_wf = init_ds_surfaces_wf(
             bids_root=bids_root, output_dir=output_dir, surfaces=["inflated"]
         )
+        ds_curv_wf = init_ds_surface_metrics_wf(
+            bids_root=bids_root, output_dir=output_dir, metrics=["curv"], name="ds_curv_wf"
+        )
 
         # fmt:off
         workflow.connect([
@@ -320,18 +323,20 @@ def init_anat_preproc_wf(
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                 ('outputnode.subject_id', 'inputnode.subject_id'),
                 ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
-                # Just for collation. These can probably go away at some point.
-                ('outputnode.thickness', 'inputnode.thickness'),
-                ('outputnode.sulc', 'inputnode.sulc'),
             ]),
             (anat_fit_wf, ds_surfaces_wf, [
                 ('outputnode.t1w_valid_list', 'inputnode.source_files'),
             ]),
             (surface_derivatives_wf, ds_surfaces_wf, [
                 ('outputnode.inflated', 'inputnode.inflated'),
             ]),
+            (anat_fit_wf, ds_curv_wf, [
+                ('outputnode.t1w_valid_list', 'inputnode.source_files'),
+            ]),
+            (surface_derivatives_wf, ds_curv_wf, [
+                ('outputnode.curv', 'inputnode.curv'),
+            ]),
             (surface_derivatives_wf, anat_second_derivatives_wf, [
-                ('outputnode.morphometrics', 'inputnode.morphometrics'),
                 ('outputnode.out_aseg', 'inputnode.t1w_fs_aseg'),
                 ('outputnode.out_aparc', 'inputnode.t1w_fs_aparc'),
                 ('outputnode.cifti_morph', 'inputnode.cifti_morph'),

diff --git a/smriprep/workflows/outputs.py b/smriprep/workflows/outputs.py
@@ -876,7 +876,6 @@ def init_anat_second_derivatives_wf(
                 "anat2std_xfm",
                 "sphere_reg",
                 "sphere_reg_fsLR",
-                "morphometrics",
                 "t1w_fs_aseg",
                 "t1w_fs_aparc",
                 "cifti_morph",
@@ -1011,22 +1010,6 @@ def init_anat_second_derivatives_wf(
     if not freesurfer:
         return workflow
 
-    from niworkflows.interfaces.surf import Path2BIDS
-
-    # Morphometrics
-    name_morphs = pe.MapNode(
-        Path2BIDS(),
-        iterfield="in_file",
-        name="name_morphs",
-        run_without_submitting=True,
-    )
-    ds_morphs = pe.MapNode(
-        DerivativesDataSink(base_directory=output_dir, extension=".shape.gii"),
-        iterfield=["in_file", "hemi", "suffix"],
-        name="ds_morphs",
-        run_without_submitting=True,
-    )
-
     # Parcellations
     ds_t1w_fsaseg = pe.Node(
         DerivativesDataSink(base_directory=output_dir, desc="aseg", suffix="dseg", compress=True),
@@ -1043,11 +1026,6 @@ def init_anat_second_derivatives_wf(
 
     # fmt:off
     workflow.connect([
-        (inputnode, name_morphs, [('morphometrics', 'in_file')]),
-        (inputnode, ds_morphs, [('morphometrics', 'in_file'),
-                                ('source_files', 'source_file')]),
-        (name_morphs, ds_morphs, [('hemi', 'hemi'),
-                                  ('suffix', 'suffix')]),
         (inputnode, ds_t1w_fsaseg, [('t1w_fs_aseg', 'in_file'),
                                     ('source_files', 'source_file')]),
         (inputnode, ds_t1w_fsparc, [('t1w_fs_aparc', 'in_file'),

diff --git a/smriprep/workflows/surfaces.py b/smriprep/workflows/surfaces.py
@@ -630,8 +630,6 @@ def init_surface_derivatives_wf(
                 "subject_id",
                 "fsnative2t1w_xfm",
                 "reference",
-                "thickness",
-                "sulc",
             ]
         ),
         name="inputnode",
@@ -640,7 +638,7 @@ def init_surface_derivatives_wf(
         niu.IdentityInterface(
             fields=[
                 "inflated",
-                "morphometrics",
+                "curv",
                 "out_aseg",
                 "out_aparc",
                 "cifti_morph",
@@ -655,8 +653,6 @@ def init_surface_derivatives_wf(
     aseg_to_native_wf = init_segs_to_native_wf()
     aparc_to_native_wf = init_segs_to_native_wf(segmentation="aparc_aseg")
 
-    all_morph = pe.Node(niu.Merge(3), name="all_morph")
-
     # fmt:off
     workflow.connect([
         # Configuration
@@ -682,15 +678,11 @@ def init_surface_derivatives_wf(
             ('fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
         ]),
 
-        # Collate morphometry from inputnode and workflows
-        (inputnode, all_morph, [('thickness', 'in1'), ('sulc', 'in2')]),
-        (gifti_morph_wf, all_morph, [('outputnode.curv', 'in3')]),
-
         # Output
         (gifti_surfaces_wf, outputnode, [('outputnode.inflated', 'inflated')]),
         (aseg_to_native_wf, outputnode, [('outputnode.out_file', 'out_aseg')]),
         (aparc_to_native_wf, outputnode, [('outputnode.out_file', 'out_aparc')]),
-        (all_morph, outputnode, [('out', 'morphometrics')]),
+        (gifti_morph_wf, outputnode, [('outputnode.curv', 'curv')]),
     ])
     # fmt:on