ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate

.circleci/ds005_bids_outputs.txt

@@ -23,19 +23,23 @@ sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
 sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
 sub-01/anat/sub-01_hemi-L_curv.shape.gii
+sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_inflated.surf.gii
 sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 sub-01/anat/sub-01_hemi-L_pial.surf.gii
-sub-01/anat/sub-01_hemi-L_smoothwm.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 sub-01/anat/sub-01_hemi-L_thickness.shape.gii
+sub-01/anat/sub-01_hemi-L_white.surf.gii
 sub-01/anat/sub-01_hemi-R_curv.shape.gii
+sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_inflated.surf.gii
 sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
 sub-01/anat/sub-01_hemi-R_pial.surf.gii
-sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_sulc.shape.gii
 sub-01/anat/sub-01_hemi-R_thickness.shape.gii
+sub-01/anat/sub-01_hemi-R_white.surf.gii
 sub-01/anat/sub-01_label-CSF_probseg.nii.gz
 sub-01/anat/sub-01_label-GM_probseg.nii.gz
 sub-01/anat/sub-01_label-WM_probseg.nii.gz

.circleci/ds005_legacy_outputs.txt

@@ -24,19 +24,23 @@ fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
 fmriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
 fmriprep/sub-01/anat/sub-01_hemi-L_curv.shape.gii
+fmriprep/sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_inflated.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
-fmriprep/sub-01/anat/sub-01_hemi-L_smoothwm.surf.gii
+fmriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_thickness.shape.gii
+fmriprep/sub-01/anat/sub-01_hemi-L_white.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_curv.shape.gii
+fmriprep/sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_inflated.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
-fmriprep/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
+fmriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_sulc.shape.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_thickness.shape.gii
+fmriprep/sub-01/anat/sub-01_hemi-R_white.surf.gii
 fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz

.circleci/ds005_legacy_partial_outputs.txt

@@ -26,19 +26,23 @@ fmriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
 fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
 fmriprep/sub-01/anat/sub-01_hemi-L_curv.shape.gii
+fmriprep/sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_inflated.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
-fmriprep/sub-01/anat/sub-01_hemi-L_smoothwm.surf.gii
+fmriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_thickness.shape.gii
+fmriprep/sub-01/anat/sub-01_hemi-L_white.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_curv.shape.gii
+fmriprep/sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_inflated.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
-fmriprep/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
+fmriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_sulc.shape.gii
 fmriprep/sub-01/anat/sub-01_hemi-R_thickness.shape.gii
+fmriprep/sub-01/anat/sub-01_hemi-R_white.surf.gii
 fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz

Dockerfile

@@ -128,6 +128,7 @@ RUN apt-get update && \
                     bc \
                     ca-certificates \
                     curl \
+                    git \
                     gnupg \
                     lsb-release \
                     netbase \

fmriprep/config.py

@@ -765,7 +765,6 @@ def init_spaces(checkpoint=True):
     if cifti_output:
         # CIFTI grayordinates to corresponding FSL-MNI resolutions.
         vol_res = "2" if cifti_output == "91k" else "1"
-        spaces.add(Reference("fsaverage", {"den": "164k"}))
         spaces.add(Reference("MNI152NLin6Asym", {"res": vol_res}))
 
     # Make the SpatialReferences object available

fmriprep/conftest.py

@@ -15,14 +15,6 @@
 os.environ['NO_ET'] = '1'
 
 
-def chdir_or_skip():
-    data_dir = ir_files('fmriprep') / 'data'
-    try:
-        os.chdir(data_dir)
-    except OSError:
-        pytest.skip(f"Cannot chdir into {data_dir!r}. Probably in a zipped distribution.")
-
-
 def copytree_or_skip(source, target):
     data_dir = ir_files('fmriprep') / source
     if not data_dir.exists():
@@ -36,7 +28,6 @@ def copytree_or_skip(source, target):
 
 @pytest.fixture(autouse=True)
 def populate_namespace(doctest_namespace, tmp_path):
-    doctest_namespace['chdir_or_skip'] = chdir_or_skip
     doctest_namespace['copytree_or_skip'] = copytree_or_skip
     doctest_namespace['testdir'] = tmp_path
 

fmriprep/interfaces/confounds.py

@@ -207,14 +207,6 @@ class GatherConfounds(SimpleInterface):
     r"""
     Combine various sources of confounds in one TSV file
 
-    .. testsetup::
-
-    >>> from tempfile import TemporaryDirectory
-    >>> tmpdir = TemporaryDirectory()
-    >>> os.chdir(tmpdir.name)
-
-    .. doctest::
-
     >>> pd.DataFrame({'a': [0.1]}).to_csv('signals.tsv', index=False, na_rep='n/a')
     >>> pd.DataFrame({'b': [0.2]}).to_csv('dvars.tsv', index=False, na_rep='n/a')
 
@@ -230,10 +222,6 @@ class GatherConfounds(SimpleInterface):
          a    b
     0  0.1  0.2
 
-    .. testcleanup::
-
-    >>> tmpdir.cleanup()
-
     """
     input_spec = GatherConfoundsInputSpec
     output_spec = GatherConfoundsOutputSpec
@@ -274,9 +262,6 @@ def _gather_confounds(
     Load confounds from the filenames, concatenate together horizontally
     and save new file.
 
-    >>> from tempfile import TemporaryDirectory
-    >>> tmpdir = TemporaryDirectory()
-    >>> os.chdir(tmpdir.name)
     >>> pd.DataFrame({'Global Signal': [0.1]}).to_csv('signals.tsv', index=False, na_rep='n/a')
     >>> pd.DataFrame({'stdDVARS': [0.2]}).to_csv('dvars.tsv', index=False, na_rep='n/a')
     >>> out_file, confound_list = _gather_confounds('signals.tsv', 'dvars.tsv')
@@ -287,7 +272,6 @@ def _gather_confounds(
     ...             engine='python')  # doctest: +NORMALIZE_WHITESPACE
        global_signal  std_dvars
     0            0.1        0.2
-    >>> tmpdir.cleanup()
 
 
     """

fmriprep/interfaces/conftest.py

@@ -0,0 +1,40 @@
+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(scope="module")
+def data_dir():
+    return Path(__file__).parent / "tests" / "data"
+
+
+@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

fmriprep/interfaces/gifti.py

@@ -0,0 +1,65 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Interfaces for manipulating GIFTI files."""
+import os
+
+import nibabel as nb
+import numpy as np
+from nipype.interfaces.base import File, SimpleInterface, TraitedSpec, isdefined, traits
+from nipype.utils.filemanip import fname_presuffix
+
+
+class CreateROIInputSpec(TraitedSpec):
+    subject_id = traits.Str(desc='subject ID')
+    hemisphere = traits.Enum(
+        "L",
+        "R",
+        mandatory=True,
+        desc='hemisphere',
+    )
+    thickness_file = File(exists=True, mandatory=True, desc='input GIFTI file')
+
+
+class CreateROIOutputSpec(TraitedSpec):
+    roi_file = File(desc='output GIFTI file')
+
+
+class CreateROI(SimpleInterface):
+    """Prepare GIFTI shape file for use in"""
+
+    input_spec = CreateROIInputSpec
+    output_spec = CreateROIOutputSpec
+
+    def _run_interface(self, runtime):
+        subject, hemi = self.inputs.subject_id, self.inputs.hemisphere
+        if not isdefined(subject):
+            subject = 'sub-XYZ'
+        img = nb.GiftiImage.from_filename(self.inputs.thickness_file)
+        # wb_command -set-structure
+        img.meta["AnatomicalStructurePrimary"] = {'L': 'CortexLeft', 'R': 'CortexRight'}[hemi]
+        darray = img.darrays[0]
+        # wb_command -set-map-names
+        meta = darray.meta
+        meta['Name'] = f"{subject}_{hemi}_ROI"
+        # wb_command -metric-palette calls have no effect on ROI files
+
+        # Compiling an odd sequence of math operations that works out to:
+        # wb_command -metric-math "abs(var * -1) > 0"
+        roi = np.abs(darray.data) > 0
+
+        darray = nb.gifti.GiftiDataArray(
+            roi,
+            intent=darray.intent,
+            datatype=darray.datatype,
+            encoding=darray.encoding,
+            endian=darray.endian,
+            coordsys=darray.coordsys,
+            ordering=darray.ind_ord,
+            meta=meta,
+        )
+
+        out_filename = os.path.join(runtime.cwd, f"{subject}.{hemi}.roi.native.shape.gii")
+        img.to_filename(out_filename)
+        self._results["roi_file"] = out_filename
+        return runtime