Merge pull request #301 from nipreps/fix/goodvoxels

FIX: Goodvoxel projection

Author: mgxd

.circleci/bcp_anat_outputs.txt

@@ -23,16 +23,20 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNIInfant+1_to-T1w_mode-image_xf
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-fsnative_mode-image_xfm.txt
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-MNIInfant+1_mode-image_xfm.h5
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii

.circleci/bcp_full_outputs.txt

@@ -23,16 +23,20 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNIInfant+1_to-T1w_mode-image_xf
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-fsnative_mode-image_xfm.txt
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-MNIInfant+1_mode-image_xfm.h5
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii

nibabies/data/__init__.py

@@ -0,0 +1,25 @@
+import atexit
+from contextlib import ExitStack
+from pathlib import Path
+
+try:
+    from functools import cache
+except ImportError:  # PY38
+    from functools import lru_cache as cache
+
+try:  # Prefer backport to leave consistency to dependency spec
+    from importlib_resources import as_file, files
+except ImportError:
+    from importlib.resources import as_file, files
+
+__all__ = ["load_resource"]
+
+exit_stack = ExitStack()
+atexit.register(exit_stack.close)
+
+path = files(__package__)
+
+
+@cache
+def load_resource(fname: str) -> Path:
+    return exit_stack.enter_context(as_file(path.joinpath(fname)))

nibabies/data/atlases/dHCP/dHCP.week42.L.sphere.surf.gii

@@ -0,0 +1,64 @@
+import os
+import re
+
+from nipype.interfaces.base import (
+    BaseInterfaceInputSpec,
+    File,
+    InputMultiObject,
+    OutputMultiObject,
+    SimpleInterface,
+    TraitedSpec,
+    traits,
+)
+
+
+class CiftiSelectInputSpec(BaseInterfaceInputSpec):
+    hemi = traits.Enum("L", "R", desc="Hemisphere")
+    surfaces = InputMultiObject(File(exists=True), desc="Surfaces")
+    morphometrics = InputMultiObject(File(exists=True), desc="Surface morphometrics")
+    spherical_registrations = InputMultiObject(
+        File(exists=True), desc="Spherical registration to fsLR"
+    )
+    template_spheres = InputMultiObject(File(exists=True), desc="fsLR sphere")
+    template_surfaces = InputMultiObject(File(exists=True), desc="fsLR midthickness")
+    template_rois = InputMultiObject(File(exists=True), desc="fsLR ROIs")
+
+
+class CiftiSelectOutputSpec(TraitedSpec):
+    white = OutputMultiObject(File, desc="white surface")
+    pial = OutputMultiObject(File, desc="pial surface")
+    midthickness = OutputMultiObject(File, desc="midthickness surface")
+    thickness = OutputMultiObject(File, desc="thickness surface")
+    sphere_reg = OutputMultiObject(File, desc="fsLR spherical regisration")
+    template_sphere = OutputMultiObject(File, desc="fsLR sphere")
+    template_surface = OutputMultiObject(File, desc="fsLR surface (midthickness)")
+    template_roi = OutputMultiObject(File, desc="fsLR ROIs")
+
+
+class CiftiSelect(SimpleInterface):
+    input_spec = CiftiSelectInputSpec
+    output_spec = CiftiSelectOutputSpec
+
+    def _run_interface(self, runtime):
+        idx = 0 if self.inputs.hemi == "L" else 1
+        all_surfaces = (self.inputs.surfaces or []) + (self.inputs.morphometrics or [])
+        container = {
+            'white': [],
+            'pial': [],
+            'midthickness': [],
+            'thickness': [],
+            'sphere_reg': self.inputs.spherical_registrations or [],
+            'template_sphere': self.inputs.template_spheres or [],
+            'template_surface': self.inputs.template_surfaces or [],
+            'template_roi': self.inputs.template_rois or [],
+        }
+        find_name = re.compile(r'(?:^|[^d])(?P<name>white|pial|midthickness|thickness)')
+        for surface in all_surfaces:
+            match = find_name.search(os.path.basename(surface))
+            if match:
+                container[match.group('name')].append(surface)
+
+        for name, vals in container.items():
+            if vals:
+                self._results[name] = sorted(vals, key=os.path.basename)[idx]
+        return runtime