Merge pull request #363 from effigies/enh/simplify-ribbon

RF: Replace most of anat_ribbon_wf with a Python function

Author: effigies

.circleci/config.yml

@@ -282,6 +282,8 @@ jobs:
 
   test:
     <<: *machine_defaults
+    environment:
+      - FS_LICENSE: /tmp/fslicense/license.txt
     steps:
       - attach_workspace:
           at: /tmp
@@ -811,6 +813,7 @@ workflows:
           context:
             - nipreps-common
           requires:
+            - get_data
             - build
           filters:
             branches:

smriprep/interfaces/surf.py

@@ -157,6 +157,32 @@ def _run_interface(self, runtime):
         return runtime
 
 
+class MakeRibbonInputSpec(TraitedSpec):
+    white_distvols = traits.List(
+        File(exists=True), minlen=2, maxlen=2, desc="White matter distance volumes"
+    )
+    pial_distvols = traits.List(
+        File(exists=True), minlen=2, maxlen=2, desc="Pial matter distance volumes"
+    )
+
+
+class MakeRibbonOutputSpec(TraitedSpec):
+    ribbon = File(desc="Binary ribbon mask")
+
+
+class MakeRibbon(SimpleInterface):
+    """Create a binary ribbon mask from white and pial distance volumes."""
+
+    input_spec = MakeRibbonInputSpec
+    output_spec = MakeRibbonOutputSpec
+
+    def _run_interface(self, runtime):
+        self._results["ribbon"] = make_ribbon(
+            self.inputs.white_distvols, self.inputs.pial_distvols, newpath=runtime.cwd
+        )
+        return runtime
+
+
 def normalize_surfs(
     in_file: str, transform_file: str | None, newpath: Optional[str] = None
 ) -> str:
@@ -209,7 +235,7 @@ def normalize_surfs(
             for RAS in "RAS":
                 pointset.meta.pop(f"VolGeom{XYZC}_{RAS}", None)
 
-    if newpath is not None:
+    if newpath is None:
         newpath = os.getcwd()
     out_file = os.path.join(newpath, fname)
     img.to_filename(out_file)
@@ -233,8 +259,32 @@ def fix_gifti_metadata(in_file: str, newpath: Optional[str] = None) -> str:
     if pointset.meta.get("GeometricType") == "Sphere":
         pointset.meta["GeometricType"] = "Spherical"
 
-    if newpath is not None:
+    if newpath is None:
         newpath = os.getcwd()
     out_file = os.path.join(newpath, os.path.basename(in_file))
     img.to_filename(out_file)
     return out_file
+
+
+def make_ribbon(
+    white_distvols: list[str],
+    pial_distvols: list[str],
+    newpath: Optional[str] = None,
+) -> str:
+    base_img = nb.load(white_distvols[0])
+    header = base_img.header
+    header.set_data_dtype("uint8")
+
+    ribbons = [
+        (np.array(nb.load(white).dataobj) > 0) & (np.array(nb.load(pial).dataobj) < 0)
+        for white, pial in zip(white_distvols, pial_distvols)
+    ]
+
+    if newpath is None:
+        newpath = os.getcwd()
+    out_file = os.path.join(newpath, "ribbon.nii.gz")
+
+    ribbon_data = ribbons[0] | ribbons[1]
+    ribbon = base_img.__class__(ribbon_data, base_img.affine, header)
+    ribbon.to_filename(out_file)
+    return out_file

smriprep/interfaces/tests/__init__.py

@@ -0,0 +1,36 @@
+import nibabel as nb
+from nipype.pipeline import engine as pe
+import numpy as np
+
+from ...data import load_resource
+from ..surf import MakeRibbon
+
+
+def test_MakeRibbon(tmp_path):
+    res_template = "{path}/sub-fsaverage_res-4_hemi-{hemi}_desc-cropped_{surf}dist.nii.gz"
+    white, pial = [
+        [
+            load_resource(
+                res_template.format(path="../interfaces/tests/data", hemi=hemi, surf=surf)
+            )
+            for hemi in "LR"
+        ]
+        for surf in ("wm", "pial")
+    ]
+
+    make_ribbon = pe.Node(
+        MakeRibbon(white_distvols=white, pial_distvols=pial),
+        name="make_ribbon",
+        base_dir=tmp_path,
+    )
+
+    result = make_ribbon.run()
+
+    ribbon = nb.load(result.outputs.ribbon)
+    expected = nb.load(
+        load_resource("../interfaces/tests/data/sub-fsaverage_res-4_desc-cropped_ribbon.nii.gz")
+    )
+
+    assert ribbon.shape == expected.shape
+    assert np.allclose(ribbon.affine, expected.affine)
+    assert np.array_equal(ribbon.dataobj, expected.dataobj)

smriprep/interfaces/tests/data/sub-fsaverage_res-4_desc-cropped_ribbon.nii.gz

@@ -310,7 +310,7 @@ def init_anat_preproc_wf(
                 ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
             ]),
             (anat_fit_wf, anat_ribbon_wf, [
-                ('outputnode.t1w_mask', 'inputnode.t1w_mask'),
+                ('outputnode.t1w_mask', 'inputnode.ref_file'),
             ]),
             (surface_derivatives_wf, anat_ribbon_wf, [
                 ('outputnode.white', 'inputnode.white'),