ENH: Project fsLR mesh onto native sphere to enable single-shot resampling into fsLR

.circleci/ds005_outputs.txt

@@ -21,19 +21,23 @@ smriprep/sub-01/anat/sub-01_dseg.nii.gz
 smriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
 smriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 smriprep/sub-01/anat/sub-01_hemi-L_curv.shape.gii
+smriprep/sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-L_inflated.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
-smriprep/sub-01/anat/sub-01_hemi-L_smoothwm.surf.gii
+smriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 smriprep/sub-01/anat/sub-01_hemi-L_thickness.shape.gii
+smriprep/sub-01/anat/sub-01_hemi-L_white.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_curv.shape.gii
+smriprep/sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_inflated.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
-smriprep/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
+smriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_sulc.shape.gii
 smriprep/sub-01/anat/sub-01_hemi-R_thickness.shape.gii
+smriprep/sub-01/anat/sub-01_hemi-R_white.surf.gii
 smriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
 smriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
 smriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz

docs/conf.py

@@ -229,7 +229,7 @@
 
 apidoc_module_dir = "../smriprep"
 apidoc_output_dir = "api"
-apidoc_excluded_paths = ["conftest.py", "*/tests/*", "tests/*", "data/*", "conf/*"]
+apidoc_excluded_paths = ["conftest.py", "*/conftest.py", "*/tests/*", "tests/*", "data/*", "conf/*"]
 apidoc_separate_modules = True
 apidoc_extra_args = ["--module-first", "-d 1", "-T"]
 

setup.cfg

@@ -19,6 +19,7 @@ classifiers =
 [options]
 python_requires = >=3.8
 install_requires =
+    importlib_resources >= 1.3; python_version < '3.9'
     indexed_gzip >= 0.8.8
     lockfile
     looseversion
@@ -71,9 +72,11 @@ all =
 [options.package_data]
 smriprep =
     VERSION
-    data/boilerplate.bib
-    data/io_spec.json
-    data/itkIdentityTransform.txt
+    data/*
+    data/atlases/*
+    data/atlases/fs_L/*
+    data/atlases/fs_R/*
+    interfaces/tests/data/*
 
 [options.entry_points]
 console_scripts =

smriprep/conftest.py

@@ -1,22 +1,3 @@
 import os
-from pathlib import Path
-from tempfile import TemporaryDirectory
-import pytest
 
 os.environ['NO_ET'] = '1'
-
-
-@pytest.fixture(autouse=True, scope="session")
-def default_cwd():
-    cwd = os.getcwd()
-    with TemporaryDirectory(prefix="smriprepTest") as tmpdir:
-        try:
-            os.chdir(tmpdir)
-            yield Path(tmpdir)
-        finally:
-            os.chdir(cwd)
-
-
-@pytest.fixture(autouse=True, scope="session")
-def populate_default_cwd(default_cwd):
-    Path.write_bytes(default_cwd / 'lh.white', b'')

smriprep/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 files, as_file
+except ImportError:
+    from importlib.resources import files, as_file
+
+__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)))

smriprep/data/atlases/L.atlasroi.32k_fs_LR.shape.gii

@@ -0,0 +1,77 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<GIFTI xmlns:xsi="true"
+       xsi:noNamespaceSchemaLocation="true"
+       Version="1"
+       NumberOfDataArrays="1">
+   <MetaData>
+      <MD>
+         <Name><![CDATA[AnatomicalStructurePrimary]]></Name>
+         <Value><![CDATA[CortexLeft]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[Caret-Version]]></Name>
+         <Value><![CDATA[5.65]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[Date]]></Name>
+         <Value><![CDATA[2012-11-13T05:25:24]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[UniqueID]]></Name>
+         <Value><![CDATA[{1fbd4629-1f40-4e61-a530-3f24c4dd18b4}]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[comment]]></Name>
+         <Value><![CDATA[Deformed from: CCNMD_MyelinMapping.L.Atlas_Cortex_ROI.164k_fs_LR.func.gii
+Deformed with: 164k_fs_LR232k_fs_LR.L.deform_map
+
+Appended File: /media/2TBB/MyelinMapping_Project/CommonFiles/FS_LR/fsaverage.L+R.MedialWall.164k_fs_LR.metric
+Deformed from: fsaverage.L.ProbabilisticArchitectonic.164k_fs_L.metric
+Deformed with: fsaverage.L.registered-to-fs_LR.164k_fs_LR.deform_map
+Appended File: /Users/vanessen/BRAIN_MAP_DATA/PALS_B12_HUMAN/FREESURFER-to-PALS/FREESURFER_AVG-to-PALS/FS_AVERAGE/FS_LR/fsaverage.R.ProbabilisticArchitectonic.164k_fs_LR.metric
+Deformed from: fsaverage.R.ProbabilisticArchitectonic.164k_fs_R.metric
+Deformed with: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[encoding]]></Name>
+         <Value><![CDATA[XML_BASE64_GZIP]]></Value>
+      </MD>
+   </MetaData>
+   <LabelTable>
+      <Label Key="0" Red="1" Green="1" Blue="1" Alpha="0"><![CDATA[???]]></Label>
+   </LabelTable>
+<DataArray Intent="NIFTI_INTENT_NONE"
+           DataType="NIFTI_TYPE_FLOAT32"
+           ArrayIndexingOrder="RowMajorOrder"
+           Dimensionality="1"
+           Dim0="32492"
+           Encoding="GZipBase64Binary"
+           Endian="LittleEndian"
+           ExternalFileName=""
+           ExternalFileOffset="0">
+   <MetaData>
+      <MD>
+         <Name><![CDATA[Description]]></Name>
+         <Value><![CDATA[Multiplied -1.0 by Atlas_Cortex_ROI
+Deformed with: 164k_fs_LR232k_fs_LR.L.deform_map]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[Name]]></Name>
+         <Value><![CDATA[deformed_Atlas_Cortex_ROI]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[UniqueID]]></Name>
+         <Value><![CDATA[{75dd580c-28b9-4aff-b96a-2b3e5ebf0b26}]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[column-color-mapping]]></Name>
+         <Value><![CDATA[-1.0 1.0]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[column-threshold]]></Name>
+         <Value><![CDATA[0.0 0.0]]></Value>
+      </MD>
+   </MetaData>
+   <Data>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</Data>
+</DataArray>
+</GIFTI>

smriprep/data/atlases/R.atlasroi.32k_fs_LR.shape.gii

@@ -0,0 +1,77 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<GIFTI xmlns:xsi="true"
+       xsi:noNamespaceSchemaLocation="true"
+       Version="1"
+       NumberOfDataArrays="1">
+   <MetaData>
+      <MD>
+         <Name><![CDATA[AnatomicalStructurePrimary]]></Name>
+         <Value><![CDATA[CortexRight]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[Caret-Version]]></Name>
+         <Value><![CDATA[5.65]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[Date]]></Name>
+         <Value><![CDATA[2012-11-13T05:40:22]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[UniqueID]]></Name>
+         <Value><![CDATA[{e3d82af6-38dd-4115-9a0b-ff874545cc6e}]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[comment]]></Name>
+         <Value><![CDATA[Deformed from: CCNMD_MyelinMapping.R.Atlas_Cortex_ROI.164k_fs_LR.func.gii
+Deformed with: 164k_fs_LR232k_fs_LR.R.deform_map
+
+Appended File: /media/2TBB/MyelinMapping_Project/CommonFiles/FS_LR/fsaverage.L+R.MedialWall.164k_fs_LR.metric
+Deformed from: fsaverage.L.ProbabilisticArchitectonic.164k_fs_L.metric
+Deformed with: fsaverage.L.registered-to-fs_LR.164k_fs_LR.deform_map
+Appended File: /Users/vanessen/BRAIN_MAP_DATA/PALS_B12_HUMAN/FREESURFER-to-PALS/FREESURFER_AVG-to-PALS/FS_AVERAGE/FS_LR/fsaverage.R.ProbabilisticArchitectonic.164k_fs_LR.metric
+Deformed from: fsaverage.R.ProbabilisticArchitectonic.164k_fs_R.metric
+Deformed with: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[encoding]]></Name>
+         <Value><![CDATA[XML_BASE64_GZIP]]></Value>
+      </MD>
+   </MetaData>
+   <LabelTable>
+      <Label Key="0" Red="1" Green="1" Blue="1" Alpha="0"><![CDATA[???]]></Label>
+   </LabelTable>
+<DataArray Intent="NIFTI_INTENT_NONE"
+           DataType="NIFTI_TYPE_FLOAT32"
+           ArrayIndexingOrder="RowMajorOrder"
+           Dimensionality="1"
+           Dim0="32492"
+           Encoding="GZipBase64Binary"
+           Endian="LittleEndian"
+           ExternalFileName=""
+           ExternalFileOffset="0">
+   <MetaData>
+      <MD>
+         <Name><![CDATA[Description]]></Name>
+         <Value><![CDATA[Multiplied -1.0 by Atlas_Cortex_ROI
+Deformed with: 164k_fs_LR232k_fs_LR.R.deform_map]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[Name]]></Name>
+         <Value><![CDATA[deformed_Atlas_Cortex_ROI]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[UniqueID]]></Name>
+         <Value><![CDATA[{ee75ce91-2bc7-4415-8c13-69d60a3f4da4}]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[column-color-mapping]]></Name>
+         <Value><![CDATA[-1.0 1.0]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[column-threshold]]></Name>
+         <Value><![CDATA[0.0 0.0]]></Value>
+      </MD>
+   </MetaData>
+   <Data>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</Data>
+</DataArray>
+</GIFTI>

smriprep/data/io_spec.json

@@ -70,7 +70,7 @@
         "datatype": "anat",
         "hemi": ["L", "R"],
         "extension": "surf.gii",
-        "suffix": [ "inflated", "midthickness", "pial", "smoothwm"]
+        "suffix": [ "inflated", "midthickness", "pial", "white"]
       },
       "morphometrics": {
         "datatype": "anat",
@@ -89,7 +89,7 @@
   "patterns": [
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio>}.{extension<nii|nii.gz|json>|nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_hemi-{hemi<L|R>}_{suffix<wm|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|thickness|sulc|curv>}.{extension<surf.gii|shape.gii>}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_hemi-{hemi<L|R>}_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|thickness|sulc|curv>}.{extension<surf.gii|shape.gii>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}]_desc-{desc}_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}.{extension<nii|nii.gz|json>|nii.gz}"
   ]

smriprep/interfaces/cifti.py

@@ -73,8 +73,8 @@ def _prepare_cifti(grayordinates: str) -> ty.Tuple[list, dict]:
     Examples
     --------
     >>> surface_labels, metadata = _prepare_cifti('91k')
-    >>> surface_labels  # doctest: +ELLIPSIS
-    ['.../tpl-fsLR_hemi-L_den-32k_desc-nomedialwall_dparc.label.gii', \
+    >>> surface_labels  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    ['.../tpl-fsLR_hemi-L_den-32k_desc-nomedialwall_dparc.label.gii',
      '.../tpl-fsLR_hemi-R_den-32k_desc-nomedialwall_dparc.label.gii']
     >>> metadata # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
     {'Density': '91,282 grayordinates corresponding to all of the grey matter sampled at a \

smriprep/interfaces/conftest.py

@@ -0,0 +1,35 @@
+from pathlib import Path
+from shutil import copytree
+
+import pytest
+
+try:
+    from contextlib import chdir as _chdir
+except ImportError:  # PY310
+    import os
+    from contextlib import contextmanager
+
+    @contextmanager  # type: ignore
+    def _chdir(path):
+        cwd = os.getcwd()
+        os.chdir(path)
+        try:
+            yield
+        finally:
+            os.chdir(cwd)
+
+
+@pytest.fixture(autouse=True)
+def _docdir(request, tmp_path):
+    # Trigger ONLY for the doctests.
+    doctest_plugin = request.config.pluginmanager.getplugin("doctest")
+    if isinstance(request.node, doctest_plugin.DoctestItem):
+        copytree(Path(__file__).parent / "tests" / "data", tmp_path, dirs_exist_ok=True)
+
+        # Chdir only for the duration of the test.
+        with _chdir(tmp_path):
+            yield
+
+    else:
+        # For normal tests, we have to yield, since this is a yield-fixture.
+        yield