From d03d28262b0c62d1c7099da6682cbcbe690d6529 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Mon, 29 Jan 2024 09:59:28 -0500
Subject: [PATCH] Support MCRIBS derivatives (#1029)

---
 xcp_d/__main__.py                            |   1 +
 xcp_d/cli/parser_utils.py                    |   1 +
 xcp_d/ingression/__init__.py                 |   1 +
 xcp_d/ingression/ukbiobank.py                |   1 +
 xcp_d/interfaces/ants.py                     |   1 +
 xcp_d/interfaces/bids.py                     | 157 +++++++++++++++++++
 xcp_d/interfaces/censoring.py                |   7 +-
 xcp_d/interfaces/concatenation.py            |   1 +
 xcp_d/interfaces/nilearn.py                  |   1 +
 xcp_d/interfaces/utils.py                    |   1 +
 xcp_d/interfaces/workbench.py                |   1 +
 xcp_d/tests/conftest.py                      |   1 +
 xcp_d/tests/test_TR.py                       |   1 +
 xcp_d/tests/test_cli.py                      |   1 +
 xcp_d/tests/test_cli_run.py                  |   1 +
 xcp_d/tests/test_cli_utils.py                |   1 +
 xcp_d/tests/test_confounds.py                |   1 +
 xcp_d/tests/test_despike.py                  |   1 +
 xcp_d/tests/test_filtering.py                |   1 +
 xcp_d/tests/test_interfaces_censoring.py     |   1 +
 xcp_d/tests/test_interfaces_concatenation.py |   1 +
 xcp_d/tests/test_interfaces_nilearn.py       |   1 +
 xcp_d/tests/test_interfaces_utils.py         |   1 +
 xcp_d/tests/test_smoothing.py                |   1 +
 xcp_d/tests/test_utils_atlas.py              |   1 +
 xcp_d/tests/test_utils_bids.py               |  31 ++--
 xcp_d/tests/test_utils_concatenation.py      |   1 +
 xcp_d/tests/test_utils_doc.py                |   1 +
 xcp_d/tests/test_utils_execsummary.py        |   1 +
 xcp_d/tests/test_utils_plotting.py           |   1 +
 xcp_d/tests/test_utils_qcmetrics.py          |   1 +
 xcp_d/tests/test_utils_utils.py              |   1 +
 xcp_d/tests/test_utils_write_save.py         |   1 +
 xcp_d/tests/test_workflows_anatomical.py     |   1 +
 xcp_d/tests/test_workflows_connectivity.py   |   1 +
 xcp_d/tests/test_workflows_execsummary.py    |   1 +
 xcp_d/tests/test_workflows_restingstate.py   |   1 +
 xcp_d/tests/utils.py                         |   1 +
 xcp_d/utils/bids.py                          | 116 ++++++--------
 xcp_d/utils/qcmetrics.py                     |   1 +
 xcp_d/utils/utils.py                         |   6 +-
 xcp_d/workflows/anatomical.py                | 134 ++++++----------
 xcp_d/workflows/concatenation.py             |   1 +
 xcp_d/workflows/plotting.py                  |   1 +
 44 files changed, 309 insertions(+), 180 deletions(-)

diff --git a/xcp_d/__main__.py b/xcp_d/__main__.py
index 383fe3109..396b7a298 100755
--- a/xcp_d/__main__.py
+++ b/xcp_d/__main__.py
@@ -1,4 +1,5 @@
 """A method for calling the command-line interface."""
+
 from xcp_d.cli.run import main
 
 if __name__ == "__main__":
diff --git a/xcp_d/cli/parser_utils.py b/xcp_d/cli/parser_utils.py
index b7d0abe65..a30fdacfd 100644
--- a/xcp_d/cli/parser_utils.py
+++ b/xcp_d/cli/parser_utils.py
@@ -1,4 +1,5 @@
 """Utility functions for xcp_d command-line interfaces."""
+
 import argparse
 import json
 import logging
diff --git a/xcp_d/ingression/__init__.py b/xcp_d/ingression/__init__.py
index 12c499679..5cd7f1b3e 100644
--- a/xcp_d/ingression/__init__.py
+++ b/xcp_d/ingression/__init__.py
@@ -1,4 +1,5 @@
 """Tools for converting derivatives from various pipelines to an fMRIPrep-like format."""
+
 from xcp_d.ingression import abcdbids, hcpya, ukbiobank, utils
 
 __all__ = [
diff --git a/xcp_d/ingression/ukbiobank.py b/xcp_d/ingression/ukbiobank.py
index 5f6890738..4f0d49130 100644
--- a/xcp_d/ingression/ukbiobank.py
+++ b/xcp_d/ingression/ukbiobank.py
@@ -1,4 +1,5 @@
 """Functions to convert preprocessed UK Biobank BOLD data to BIDS derivatives format."""
+
 import glob
 import json
 import os
diff --git a/xcp_d/interfaces/ants.py b/xcp_d/interfaces/ants.py
index de00737c9..88f1c03b5 100644
--- a/xcp_d/interfaces/ants.py
+++ b/xcp_d/interfaces/ants.py
@@ -1,4 +1,5 @@
 """ANTS interfaces."""
+
 import logging
 import os
 
diff --git a/xcp_d/interfaces/bids.py b/xcp_d/interfaces/bids.py
index 95b5ae7ef..06e1c18d9 100644
--- a/xcp_d/interfaces/bids.py
+++ b/xcp_d/interfaces/bids.py
@@ -1,9 +1,18 @@
 """Adapted interfaces from Niworkflows."""
+
 from json import loads
 from pathlib import Path
 
 from bids.layout import Config
 from nipype import logging
+from nipype.interfaces.base import (
+    BaseInterfaceInputSpec,
+    Directory,
+    File,
+    SimpleInterface,
+    TraitedSpec,
+    traits,
+)
 from niworkflows.interfaces.bids import DerivativesDataSink as BaseDerivativesDataSink
 from pkg_resources import resource_filename as pkgrf
 
@@ -33,3 +42,151 @@ class DerivativesDataSink(BaseDerivativesDataSink):
     _config_entities = config_entities
     _config_entities_dict = merged_entities
     _file_patterns = xcp_d_spec["default_path_patterns"]
+
+
+class _CollectRegistrationFilesInputSpec(BaseInterfaceInputSpec):
+    segmentation_dir = Directory(
+        exists=True,
+        required=True,
+        desc="Path to FreeSurfer or MCRIBS derivatives.",
+    )
+    software = traits.Enum(
+        "FreeSurfer",
+        "MCRIBS",
+        required=True,
+        desc="The software used for segmentation.",
+    )
+    hemisphere = traits.Enum(
+        "L",
+        "R",
+        required=True,
+        desc="The hemisphere being used.",
+    )
+    participant_id = traits.Str(
+        required=True,
+        desc="Participant ID. Used to select the subdirectory of the FreeSurfer derivatives.",
+    )
+
+
+class _CollectRegistrationFilesOutputSpec(TraitedSpec):
+    subject_sphere = File(
+        exists=True,
+        desc="Subject-space sphere.",
+    )
+    source_sphere = File(
+        exists=True,
+        desc="Source-space sphere (namely, fsaverage).",
+    )
+    target_sphere = File(
+        exists=True,
+        desc="Target-space sphere (fsLR for FreeSurfer, dHCP-in-fsLR for MCRIBS).",
+    )
+    sphere_to_sphere = File(
+        exists=True,
+        desc="Warp file going from source space to target space.",
+    )
+
+
+class CollectRegistrationFiles(SimpleInterface):
+    """Collect registration files for fsnative-to-fsLR transformation."""
+
+    input_spec = _CollectRegistrationFilesInputSpec
+    output_spec = _CollectRegistrationFilesOutputSpec
+
+    def _run_interface(self, runtime):
+        import os
+
+        from pkg_resources import resource_filename as pkgrf
+        from templateflow.api import get as get_template
+
+        hemisphere = self.inputs.hemisphere
+        hstr = f"{hemisphere.lower()}h"
+        participant_id = self.inputs.participant_id
+        if not participant_id.startswith("sub-"):
+            participant_id = f"sub-{participant_id}"
+
+        if self.inputs.software == "FreeSurfer":
+            # Find the subject's sphere in the FreeSurfer derivatives.
+            # TODO: Collect from the preprocessing derivatives if they're a compliant version.
+            # Namely, fMRIPrep >= 23.1.2, Nibabies >= 24.0.0a1.
+            self._results["subject_sphere"] = os.path.join(
+                self.inputs.segmentation_dir,
+                participant_id,
+                "surf",
+                f"{hstr}.sphere.reg",
+            )
+
+            # Load the fsaverage-164k sphere
+            # FreeSurfer: tpl-fsaverage_hemi-?_den-164k_sphere.surf.gii
+            self._results["source_sphere"] = str(
+                get_template(
+                    template="fsaverage",
+                    space=None,
+                    hemi=hemisphere,
+                    density="164k",
+                    desc=None,
+                    suffix="sphere",
+                )
+            )
+
+            # TODO: Collect from templateflow once it's uploaded.
+            # FreeSurfer: fs_?/fs_?-to-fs_LR_fsaverage.?_LR.spherical_std.164k_fs_?.surf.gii
+            self._results["sphere_to_sphere"] = pkgrf(
+                "xcp_d",
+                (
+                    f"data/standard_mesh_atlases/fs_{hemisphere}/"
+                    f"fs_{hemisphere}-to-fs_LR_fsaverage.{hemisphere}_LR.spherical_std."
+                    f"164k_fs_{hemisphere}.surf.gii"
+                ),
+            )
+
+            # FreeSurfer: tpl-fsLR_hemi-?_den-32k_sphere.surf.gii
+            self._results["target_sphere"] = str(
+                get_template(
+                    template="fsLR",
+                    space=None,
+                    hemi=hemisphere,
+                    density="32k",
+                    desc=None,
+                    suffix="sphere",
+                )
+            )
+
+        elif self.inputs.software == "MCRIBS":
+            # Find the subject's sphere in the MCRIBS derivatives.
+            # TODO: Collect from the preprocessing derivatives if they're a compliant version.
+            # Namely, fMRIPrep >= 23.1.2, Nibabies >= 24.0.0a1.
+            self._results["subject_sphere"] = os.path.join(
+                self.inputs.segmentation_dir,
+                participant_id,
+                "freesurfer",
+                participant_id,
+                "surf",
+                f"{hstr}.sphere.reg2",
+            )
+
+            # TODO: Collect from templateflow once it's uploaded.
+            # MCRIBS: tpl-fsaverage_hemi-?_den-41k_desc-reg_sphere.surf.gii
+            self._results["source_sphere"] = os.path.join(
+                self.inputs.segmentation_dir,
+                "templates_fsLR",
+                f"tpl-fsaverage_hemi-{hemisphere}_den-41k_desc-reg_sphere.surf.gii",
+            )
+
+            # TODO: Collect from templateflow once it's uploaded.
+            # MCRIBS: tpl-dHCP_space-fsaverage_hemi-?_den-41k_desc-reg_sphere.surf.gii
+            self._results["sphere_to_sphere"] = os.path.join(
+                self.inputs.segmentation_dir,
+                "templates_fsLR",
+                f"tpl-dHCP_space-fsaverage_hemi-{hemisphere}_den-41k_desc-reg_sphere.surf.gii",
+            )
+
+            # TODO: Collect from templateflow once it's uploaded.
+            # MCRIBS: tpl-dHCP_space-fsLR_hemi-?_den-32k_desc-week42_sphere.surf.gii
+            self._results["target_sphere"] = os.path.join(
+                self.inputs.segmentation_dir,
+                "templates_fsLR",
+                f"tpl-dHCP_space-fsLR_hemi-{hemisphere}_den-32k_desc-week42_sphere.surf.gii",
+            )
+
+        return runtime
diff --git a/xcp_d/interfaces/censoring.py b/xcp_d/interfaces/censoring.py
index 929b77a3b..a4ad519fa 100644
--- a/xcp_d/interfaces/censoring.py
+++ b/xcp_d/interfaces/censoring.py
@@ -1,4 +1,5 @@
 """Interfaces for the post-processing workflows."""
+
 import os
 
 import nibabel as nb
@@ -104,9 +105,9 @@ def _run_interface(self, runtime):
         if dummy_scans == 0:
             # write the output out
             self._results["bold_file_dropped_TR"] = self.inputs.bold_file
-            self._results[
-                "fmriprep_confounds_file_dropped_TR"
-            ] = self.inputs.fmriprep_confounds_file
+            self._results["fmriprep_confounds_file_dropped_TR"] = (
+                self.inputs.fmriprep_confounds_file
+            )
             self._results["confounds_file_dropped_TR"] = self.inputs.confounds_file
             self._results["motion_file_dropped_TR"] = self.inputs.motion_file
             self._results["temporal_mask_dropped_TR"] = self.inputs.temporal_mask
diff --git a/xcp_d/interfaces/concatenation.py b/xcp_d/interfaces/concatenation.py
index 4e00a4ca8..41e204750 100644
--- a/xcp_d/interfaces/concatenation.py
+++ b/xcp_d/interfaces/concatenation.py
@@ -1,4 +1,5 @@
 """Interfaces for the concatenation workflow."""
+
 import itertools
 import os
 import re
diff --git a/xcp_d/interfaces/nilearn.py b/xcp_d/interfaces/nilearn.py
index 81951551d..532a4ac48 100644
--- a/xcp_d/interfaces/nilearn.py
+++ b/xcp_d/interfaces/nilearn.py
@@ -1,4 +1,5 @@
 """Interfaces for Nilearn code."""
+
 import os
 
 from nilearn import maskers
diff --git a/xcp_d/interfaces/utils.py b/xcp_d/interfaces/utils.py
index 56a5be733..86c7821f8 100644
--- a/xcp_d/interfaces/utils.py
+++ b/xcp_d/interfaces/utils.py
@@ -1,4 +1,5 @@
 """Miscellaneous utility interfaces."""
+
 from nipype import logging
 from nipype.interfaces.base import (
     BaseInterfaceInputSpec,
diff --git a/xcp_d/interfaces/workbench.py b/xcp_d/interfaces/workbench.py
index f809db9c9..b28116cf2 100644
--- a/xcp_d/interfaces/workbench.py
+++ b/xcp_d/interfaces/workbench.py
@@ -1,4 +1,5 @@
 """Custom wb_command interfaces."""
+
 import os
 
 import nibabel as nb
diff --git a/xcp_d/tests/conftest.py b/xcp_d/tests/conftest.py
index 18786370f..20ea1ab11 100644
--- a/xcp_d/tests/conftest.py
+++ b/xcp_d/tests/conftest.py
@@ -1,4 +1,5 @@
 """Fixtures for the CircleCI tests."""
+
 import base64
 import os
 
diff --git a/xcp_d/tests/test_TR.py b/xcp_d/tests/test_TR.py
index c2a6c8317..858b9651b 100644
--- a/xcp_d/tests/test_TR.py
+++ b/xcp_d/tests/test_TR.py
@@ -5,6 +5,7 @@
 Arguments have to be passed to these functions because the data may be
 mounted in a container somewhere unintuitively.
 """
+
 import os.path as op
 
 import nibabel as nb
diff --git a/xcp_d/tests/test_cli.py b/xcp_d/tests/test_cli.py
index 1e7569b26..4880657fd 100644
--- a/xcp_d/tests/test_cli.py
+++ b/xcp_d/tests/test_cli.py
@@ -1,4 +1,5 @@
 """Command-line interface tests."""
+
 import os
 import shutil
 
diff --git a/xcp_d/tests/test_cli_run.py b/xcp_d/tests/test_cli_run.py
index a9a67dcfa..31ca80dde 100644
--- a/xcp_d/tests/test_cli_run.py
+++ b/xcp_d/tests/test_cli_run.py
@@ -1,4 +1,5 @@
 """Tests for functions in the cli.run module."""
+
 import logging
 import os
 from copy import deepcopy
diff --git a/xcp_d/tests/test_cli_utils.py b/xcp_d/tests/test_cli_utils.py
index d8d584d33..3bc5982da 100644
--- a/xcp_d/tests/test_cli_utils.py
+++ b/xcp_d/tests/test_cli_utils.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.cli.parser_utils module."""
+
 from argparse import ArgumentTypeError
 
 import pytest
diff --git a/xcp_d/tests/test_confounds.py b/xcp_d/tests/test_confounds.py
index 22a71765f..bb8306b4c 100644
--- a/xcp_d/tests/test_confounds.py
+++ b/xcp_d/tests/test_confounds.py
@@ -1,4 +1,5 @@
 """Test confounds handling."""
+
 import os
 
 import numpy as np
diff --git a/xcp_d/tests/test_despike.py b/xcp_d/tests/test_despike.py
index ee39e21c2..7dfe38e3b 100644
--- a/xcp_d/tests/test_despike.py
+++ b/xcp_d/tests/test_despike.py
@@ -6,6 +6,7 @@
 Arguments have to be passed to these functions because the data may be
 mounted in a container somewhere unintuitively.
 """
+
 import os
 
 import nibabel as nb
diff --git a/xcp_d/tests/test_filtering.py b/xcp_d/tests/test_filtering.py
index 18766b2cb..ee42ab8c9 100644
--- a/xcp_d/tests/test_filtering.py
+++ b/xcp_d/tests/test_filtering.py
@@ -1,4 +1,5 @@
 """Tests for filtering methods."""
+
 import re
 
 import numpy as np
diff --git a/xcp_d/tests/test_interfaces_censoring.py b/xcp_d/tests/test_interfaces_censoring.py
index 98cab51b7..f5fc3be1f 100644
--- a/xcp_d/tests/test_interfaces_censoring.py
+++ b/xcp_d/tests/test_interfaces_censoring.py
@@ -1,4 +1,5 @@
 """Tests for framewise displacement calculation."""
+
 import json
 import os
 
diff --git a/xcp_d/tests/test_interfaces_concatenation.py b/xcp_d/tests/test_interfaces_concatenation.py
index 1ec4953ac..5c1402acb 100644
--- a/xcp_d/tests/test_interfaces_concatenation.py
+++ b/xcp_d/tests/test_interfaces_concatenation.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.interfaces.concatenation module."""
+
 import os
 
 from nipype.interfaces.base import Undefined, isdefined
diff --git a/xcp_d/tests/test_interfaces_nilearn.py b/xcp_d/tests/test_interfaces_nilearn.py
index 6e4e90f50..4283b7a07 100644
--- a/xcp_d/tests/test_interfaces_nilearn.py
+++ b/xcp_d/tests/test_interfaces_nilearn.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.interfaces.nilearn module."""
+
 import os
 
 import nibabel as nb
diff --git a/xcp_d/tests/test_interfaces_utils.py b/xcp_d/tests/test_interfaces_utils.py
index 62601c926..c2dba02bb 100644
--- a/xcp_d/tests/test_interfaces_utils.py
+++ b/xcp_d/tests/test_interfaces_utils.py
@@ -1,4 +1,5 @@
 """Tests for xcp_d.interfaces.utils module."""
+
 import os
 
 import nibabel as nb
diff --git a/xcp_d/tests/test_smoothing.py b/xcp_d/tests/test_smoothing.py
index 8fe68e16d..b68efe7e9 100644
--- a/xcp_d/tests/test_smoothing.py
+++ b/xcp_d/tests/test_smoothing.py
@@ -1,4 +1,5 @@
 """Tests for smoothing methods."""
+
 import os
 import re
 import tempfile
diff --git a/xcp_d/tests/test_utils_atlas.py b/xcp_d/tests/test_utils_atlas.py
index c6ffeab58..32a252711 100644
--- a/xcp_d/tests/test_utils_atlas.py
+++ b/xcp_d/tests/test_utils_atlas.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.utils.atlas module."""
+
 import os
 
 import pytest
diff --git a/xcp_d/tests/test_utils_bids.py b/xcp_d/tests/test_utils_bids.py
index d8ef80530..21089caf7 100644
--- a/xcp_d/tests/test_utils_bids.py
+++ b/xcp_d/tests/test_utils_bids.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.utils.bids module."""
+
 import json
 import os
 
@@ -196,31 +197,25 @@ def test_get_tr(ds001419_data):
 
 
 def test_get_freesurfer_dir(datasets):
-    """Test get_freesurfer_dir and get_freesurfer_sphere."""
-    with pytest.raises(NotADirectoryError, match="No FreeSurfer derivatives found."):
+    """Test get_freesurfer_dir."""
+    with pytest.raises(NotADirectoryError, match="No FreeSurfer/MCRIBS derivatives found"):
         xbids.get_freesurfer_dir(".")
 
-    fs_dir = xbids.get_freesurfer_dir(datasets["nibabies"])
+    fs_dir, software = xbids.get_freesurfer_dir(datasets["nibabies"])
     assert os.path.isdir(fs_dir)
+    assert software == "FreeSurfer"
 
-    # Create fake FreeSurfer folder so there are two possible folders
-    tmp_fs_dir = os.path.join(os.path.dirname(fs_dir), "freesurfer-fail")
-    os.mkdir(tmp_fs_dir)
-    with pytest.raises(ValueError, match="More than one candidate"):
-        xbids.get_freesurfer_dir(datasets["nibabies"])
+    # Create fake FreeSurfer folder so there are two possible folders and it grabs the closest
+    tmp_fs_dir = os.path.join(datasets["nibabies"], "sourcedata/mcribs")
+    os.makedirs(tmp_fs_dir, exist_ok=True)
+    fs_dir, software = xbids.get_freesurfer_dir(datasets["nibabies"])
+    assert os.path.isdir(fs_dir)
+    assert software == "MCRIBS"
     os.rmdir(tmp_fs_dir)
 
-    fs_dir = xbids.get_freesurfer_dir(datasets["pnc"])
+    fs_dir, software = xbids.get_freesurfer_dir(datasets["pnc"])
     assert os.path.isdir(fs_dir)
-
-    sphere_file = xbids.get_freesurfer_sphere(fs_dir, "1648798153", "L")
-    assert os.path.isfile(sphere_file)
-
-    sphere_file = xbids.get_freesurfer_sphere(fs_dir, "sub-1648798153", "L")
-    assert os.path.isfile(sphere_file)
-
-    with pytest.raises(FileNotFoundError, match="Sphere file not found at"):
-        sphere_file = xbids.get_freesurfer_sphere(fs_dir, "fail", "L")
+    assert software == "FreeSurfer"
 
 
 def test_get_entity(datasets):
diff --git a/xcp_d/tests/test_utils_concatenation.py b/xcp_d/tests/test_utils_concatenation.py
index 6d4ea94f5..bbe6baf90 100644
--- a/xcp_d/tests/test_utils_concatenation.py
+++ b/xcp_d/tests/test_utils_concatenation.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.utils.concatenation module."""
+
 import os
 
 import nibabel as nb
diff --git a/xcp_d/tests/test_utils_doc.py b/xcp_d/tests/test_utils_doc.py
index 5413194e4..fb75d5a43 100644
--- a/xcp_d/tests/test_utils_doc.py
+++ b/xcp_d/tests/test_utils_doc.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.utils.doc module."""
+
 import os
 
 from xcp_d.utils import doc
diff --git a/xcp_d/tests/test_utils_execsummary.py b/xcp_d/tests/test_utils_execsummary.py
index 7902b4772..0557bea40 100644
--- a/xcp_d/tests/test_utils_execsummary.py
+++ b/xcp_d/tests/test_utils_execsummary.py
@@ -1,4 +1,5 @@
 """Test functions in xcp_d.utils.execsummary."""
+
 import os
 
 import matplotlib.pyplot as plt
diff --git a/xcp_d/tests/test_utils_plotting.py b/xcp_d/tests/test_utils_plotting.py
index 52aa82e09..9918d9a6f 100644
--- a/xcp_d/tests/test_utils_plotting.py
+++ b/xcp_d/tests/test_utils_plotting.py
@@ -1,4 +1,5 @@
 """Tests for xcp_d.utils.plotting module."""
+
 import os
 
 from xcp_d.utils import plotting
diff --git a/xcp_d/tests/test_utils_qcmetrics.py b/xcp_d/tests/test_utils_qcmetrics.py
index 87ebb1053..4ab5df4e9 100644
--- a/xcp_d/tests/test_utils_qcmetrics.py
+++ b/xcp_d/tests/test_utils_qcmetrics.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.utils.qcmetrics module."""
+
 import numpy as np
 
 from xcp_d.utils import qcmetrics
diff --git a/xcp_d/tests/test_utils_utils.py b/xcp_d/tests/test_utils_utils.py
index a2e673837..a8acb846d 100644
--- a/xcp_d/tests/test_utils_utils.py
+++ b/xcp_d/tests/test_utils_utils.py
@@ -1,4 +1,5 @@
 """Test functions in xcp_d.utils.utils."""
+
 import os
 
 import numpy as np
diff --git a/xcp_d/tests/test_utils_write_save.py b/xcp_d/tests/test_utils_write_save.py
index 4f6965aea..ef0bb0b0a 100644
--- a/xcp_d/tests/test_utils_write_save.py
+++ b/xcp_d/tests/test_utils_write_save.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.utils.write_save module."""
+
 import os
 
 import pytest
diff --git a/xcp_d/tests/test_workflows_anatomical.py b/xcp_d/tests/test_workflows_anatomical.py
index cb4e6e8d6..782939b5a 100644
--- a/xcp_d/tests/test_workflows_anatomical.py
+++ b/xcp_d/tests/test_workflows_anatomical.py
@@ -1,4 +1,5 @@
 """Tests for the xcp_d.workflows.anatomical module."""
+
 import os
 import shutil
 
diff --git a/xcp_d/tests/test_workflows_connectivity.py b/xcp_d/tests/test_workflows_connectivity.py
index f38bff27e..d98ffdf5d 100644
--- a/xcp_d/tests/test_workflows_connectivity.py
+++ b/xcp_d/tests/test_workflows_connectivity.py
@@ -1,4 +1,5 @@
 """Tests for connectivity matrix calculation."""
+
 import os
 import sys
 
diff --git a/xcp_d/tests/test_workflows_execsummary.py b/xcp_d/tests/test_workflows_execsummary.py
index 3128afc64..ba0a6321e 100644
--- a/xcp_d/tests/test_workflows_execsummary.py
+++ b/xcp_d/tests/test_workflows_execsummary.py
@@ -1,4 +1,5 @@
 """Test xcp_d.workflows.execsummary."""
+
 import os
 
 from nilearn import image
diff --git a/xcp_d/tests/test_workflows_restingstate.py b/xcp_d/tests/test_workflows_restingstate.py
index 194985e5f..62ce8049b 100644
--- a/xcp_d/tests/test_workflows_restingstate.py
+++ b/xcp_d/tests/test_workflows_restingstate.py
@@ -1,4 +1,5 @@
 """Test for alff."""
+
 import os
 import shutil
 
diff --git a/xcp_d/tests/utils.py b/xcp_d/tests/utils.py
index 2a88d035e..ba5740f07 100644
--- a/xcp_d/tests/utils.py
+++ b/xcp_d/tests/utils.py
@@ -1,4 +1,5 @@
 """Utility functions for tests."""
+
 import os
 import subprocess
 import tarfile
diff --git a/xcp_d/utils/bids.py b/xcp_d/utils/bids.py
index 492ab9d3b..926a3f270 100644
--- a/xcp_d/utils/bids.py
+++ b/xcp_d/utils/bids.py
@@ -737,9 +737,11 @@ def get_preproc_pipeline_info(input_type, fmri_dir):
 
     info_dict = {
         "name": dataset_dict["GeneratedBy"][0]["Name"],
-        "version": dataset_dict["GeneratedBy"][0]["Version"]
-        if "Version" in dataset_dict["GeneratedBy"][0].keys()
-        else "unknown",
+        "version": (
+            dataset_dict["GeneratedBy"][0]["Version"]
+            if "Version" in dataset_dict["GeneratedBy"][0].keys()
+            else "unknown"
+        ),
     }
     if input_type == "fmriprep":
         info_dict["references"] = "[@esteban2019fmriprep;@esteban2020analysis, RRID:SCR_016216]"
@@ -779,7 +781,7 @@ def _get_tr(img):
 
 
 def get_freesurfer_dir(fmri_dir):
-    """Find FreeSurfer derivatives associated with preprocessing pipeline.
+    """Find FreeSurfer or MCRIBS derivatives associated with preprocessing pipeline.
 
     NOTE: This is a Node function.
 
@@ -790,8 +792,9 @@ def get_freesurfer_dir(fmri_dir):
 
     Returns
     -------
-    freesurfer_path : :obj:`str`
-        Path to FreeSurfer derivatives.
+    seg_path : :obj:`str`
+        Path to FreeSurfer or MCRIBS derivatives.
+    seg
 
     Raises
     ------
@@ -800,78 +803,53 @@ def get_freesurfer_dir(fmri_dir):
     NotADirectoryError
         If no FreeSurfer derivatives are found.
     """
-    import glob
     import os
 
-    # for fMRIPrep/Nibabies versions >=20.2.1
-    freesurfer_paths = sorted(glob.glob(os.path.join(fmri_dir, "sourcedata/*freesurfer*")))
-    if len(freesurfer_paths) == 0:
-        # for fMRIPrep/Nibabies versions <20.2.1
-        freesurfer_paths = sorted(
-            glob.glob(os.path.join(os.path.dirname(fmri_dir), "*freesurfer*"))
-        )
-
-    if len(freesurfer_paths) == 1:
-        freesurfer_path = freesurfer_paths[0]
-
-    elif len(freesurfer_paths) > 1:
-        freesurfer_paths_str = "\n\t".join(freesurfer_paths)
-        raise ValueError(
-            "More than one candidate for FreeSurfer derivatives found. "
-            "We recommend mounting only one FreeSurfer directory in your Docker/Singularity "
-            "image. "
-            f"Detected candidates:\n\t{freesurfer_paths_str}"
-        )
-
-    else:
-        raise NotADirectoryError("No FreeSurfer derivatives found.")
-
-    return freesurfer_path
-
-
-def get_freesurfer_sphere(freesurfer_path, subject_id, hemisphere):
-    """Find FreeSurfer sphere file.
-
-    NOTE: This is a Node function.
-
-    Parameters
-    ----------
-    freesurfer_path : :obj:`str`
-        Path to the FreeSurfer derivatives.
-    subject_id : :obj:`str`
-        Subject ID. This may or may not be prefixed with "sub-".
-    hemisphere : {"L", "R"}
-        The hemisphere to grab.
+    from nipype import logging
 
-    Returns
-    -------
-    sphere_raw : :obj:`str`
-        Sphere file for the requested subject and hemisphere.
+    LOGGER = logging.getLogger("nipype.utils")
 
-    Raises
-    ------
-    FileNotFoundError
-        If the sphere file cannot be found.
-    """
-    import os
+    patterns = {
+        "Nibabies >= 24.0.0a1": (
+            os.path.join(fmri_dir, "sourcedata/mcribs"),
+            "MCRIBS",
+        ),
+        "fMRIPrep >= 20.2.1": (
+            os.path.join(fmri_dir, "sourcedata/freesurfer"),
+            "FreeSurfer",
+        ),
+        "Nibabies >= 21.0.0": (
+            os.path.join(fmri_dir, "sourcedata/infant-freesurfer"),
+            "FreeSurfer",
+        ),
+        "fMRIPrep < 20.2.1": (
+            os.path.join(os.path.dirname(fmri_dir), "freesurfer"),
+            "FreeSurfer",
+        ),
+        "Nibabies < 21.0.0": (
+            os.path.join(os.path.dirname(fmri_dir), "infant-freesurfer"),
+            "FreeSurfer",
+        ),
+    }
 
-    assert hemisphere in ("L", "R"), hemisphere
+    for desc, key in patterns.items():
+        pattern, software = key
+        if os.path.isdir(pattern):
+            LOGGER.info(
+                f"{software} derivatives associated with {desc} preprocessing derivatives found "
+                f"at {pattern}"
+            )
+            return pattern, software
 
-    if not subject_id.startswith("sub-"):
-        subject_id = f"sub-{subject_id}"
+        # Otherwise, continue to the next pattern
 
-    sphere_raw = os.path.join(
-        freesurfer_path,
-        subject_id,
-        "surf",
-        f"{hemisphere.lower()}h.sphere.reg",
+    seg_patterns = [pattern[0] for pattern in patterns.values()]
+    patterns_str = "\n\t".join(seg_patterns)
+    raise NotADirectoryError(
+        "No FreeSurfer/MCRIBS derivatives found in any of the following locations:"
+        f"\n\t{patterns_str}"
     )
 
-    if not os.path.isfile(sphere_raw):
-        raise FileNotFoundError(f"Sphere file not found at '{sphere_raw}'")
-
-    return sphere_raw
-
 
 def get_entity(filename, entity):
     """Extract a given entity from a BIDS filename via string manipulation.
diff --git a/xcp_d/utils/qcmetrics.py b/xcp_d/utils/qcmetrics.py
index 9619b8b1a..7fdc55e54 100644
--- a/xcp_d/utils/qcmetrics.py
+++ b/xcp_d/utils/qcmetrics.py
@@ -1,4 +1,5 @@
 """Quality control metrics."""
+
 import h5py
 import nibabel as nb
 import numpy as np
diff --git a/xcp_d/utils/utils.py b/xcp_d/utils/utils.py
index 4017716d9..5b11bf059 100644
--- a/xcp_d/utils/utils.py
+++ b/xcp_d/utils/utils.py
@@ -446,9 +446,9 @@ def denoise_with_nilearn(
                 f"Outlier volumes at beginning of run ({first_outliers[0]}-{first_outliers[1]}) "
                 "will be replaced with first non-outlier volume's values."
             )
-            interpolated_unfiltered_bold[
-                : first_outliers[1] + 1, :
-            ] = interpolated_unfiltered_bold[first_outliers[1] + 1, :]
+            interpolated_unfiltered_bold[: first_outliers[1] + 1, :] = (
+                interpolated_unfiltered_bold[first_outliers[1] + 1, :]
+            )
 
         # Replace outliers at end of run
         if last_outliers[1] == n_volumes - 1:
diff --git a/xcp_d/workflows/anatomical.py b/xcp_d/workflows/anatomical.py
index 59187628f..a968deba3 100644
--- a/xcp_d/workflows/anatomical.py
+++ b/xcp_d/workflows/anatomical.py
@@ -7,7 +7,6 @@
 from nipype.interfaces.freesurfer import MRIsConvert
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-from pkg_resources import resource_filename as pkgrf
 from templateflow.api import get as get_template
 
 from xcp_d.interfaces.ants import (
@@ -15,7 +14,7 @@
     CompositeInvTransformUtil,
     ConvertTransformFile,
 )
-from xcp_d.interfaces.bids import DerivativesDataSink
+from xcp_d.interfaces.bids import CollectRegistrationFiles, DerivativesDataSink
 from xcp_d.interfaces.c3 import C3d  # TM
 from xcp_d.interfaces.nilearn import BinaryMath, Merge
 from xcp_d.interfaces.workbench import (  # MB,TM
@@ -28,7 +27,7 @@
     SurfaceGenerateInflated,
     SurfaceSphereProjectUnproject,
 )
-from xcp_d.utils.bids import get_freesurfer_dir, get_freesurfer_sphere
+from xcp_d.utils.bids import get_freesurfer_dir
 from xcp_d.utils.doc import fill_doc
 from xcp_d.utils.utils import list_to_str
 from xcp_d.workflows.execsummary import (
@@ -414,6 +413,7 @@ def init_postprocess_surfaces_wf(
         ),
         name="inputnode",
     )
+    workflow.__desc__ = ""
 
     if dcan_qc and mesh_available:
         # Plot the white and pial surfaces on the brain in a brainsprite figure.
@@ -461,6 +461,10 @@ def init_postprocess_surfaces_wf(
         )
 
     if morphometry_files:
+        workflow.__desc__ += (
+            " fsLR-space morphometry surfaces were copied from the preprocessing derivatives to "
+            "the XCP-D derivatives."
+        )
         for morphometry_file in morphometry_files:
             # fmt:off
             workflow.connect([
@@ -471,6 +475,10 @@ def init_postprocess_surfaces_wf(
             # fmt:on
 
     if mesh_available:
+        workflow.__desc__ += (
+            " HCP-style midthickness, inflated, and very-inflated surfaces were generated from "
+            "the white-matter and pial surface meshes."
+        )
         # Generate and output HCP-style surface files.
         hcp_surface_wfs = {
             hemi: init_generate_hcp_surfaces_wf(
@@ -489,6 +497,10 @@ def init_postprocess_surfaces_wf(
         # fmt:on
 
     if mesh_available and standard_space_mesh:
+        workflow.__desc__ += (
+            " All surface files were already in fsLR space, and were copied to the output "
+            "directory."
+        )
         # Mesh files are already in fsLR.
         # fmt:off
         workflow.connect([
@@ -510,6 +522,7 @@ def init_postprocess_surfaces_wf(
         # fmt:on
 
     elif mesh_available:
+        workflow.__desc__ += " fsnative-space surfaces were then warped to fsLR space."
         # Mesh files are in fsnative and must be warped to fsLR.
         warp_surfaces_to_template_wf = init_warp_surfaces_to_template_wf(
             fmri_dir=fmri_dir,
@@ -658,7 +671,7 @@ def init_warp_surfaces_to_template_wf(
         Function(
             function=get_freesurfer_dir,
             input_names=["fmri_dir"],
-            output_names=["freesurfer_path"],
+            output_names=["freesurfer_path", "segmentation_software"],
         ),
         name="get_freesurfer_dir_node",
     )
@@ -712,6 +725,7 @@ def init_warp_surfaces_to_template_wf(
         workflow.connect([
             (get_freesurfer_dir_node, apply_transforms_wf, [
                 ("freesurfer_path", "inputnode.freesurfer_path"),
+                ("segmentation_software", "inputnode.segmentation_software"),
             ]),
             (update_xfm_wf, apply_transforms_wf, [
                 ("outputnode.merged_warpfield", "inputnode.merged_warpfield"),
@@ -1242,6 +1256,8 @@ def init_warp_one_hemisphere_wf(
     merged_inv_warpfield
     freesurfer_path
         Path to FreeSurfer derivatives. Used to load the subject's sphere file.
+    segmentation_software : {"FreeSurfer", "MCRIBS"}
+        The software used for the segmentation.
     participant_id
         Set from parameters.
 
@@ -1259,6 +1275,7 @@ def init_warp_one_hemisphere_wf(
                 "merged_warpfield",
                 "merged_inv_warpfield",
                 "freesurfer_path",
+                "segmentation_software",
                 "participant_id",
             ],
         ),
@@ -1266,46 +1283,19 @@ def init_warp_one_hemisphere_wf(
     )
     inputnode.inputs.participant_id = participant_id
 
-    # Load the fsaverage-164k sphere
-    # NOTE: Why do we need the fsaverage mesh?
-    fsaverage_mesh = str(
-        get_template(
-            template="fsaverage",
-            space=None,
-            hemi=hemisphere,
-            density="164k",
-            desc=None,
-            suffix="sphere",
-        )
-    )
-
-    # NOTE: Can we upload these to templateflow?
-    fs_hemisphere_to_fsLR = pkgrf(
-        "xcp_d",
-        (
-            f"data/standard_mesh_atlases/fs_{hemisphere}/"
-            f"fs_{hemisphere}-to-fs_LR_fsaverage.{hemisphere}_LR.spherical_std."
-            f"164k_fs_{hemisphere}.surf.gii"
-        ),
-    )
-    get_freesurfer_sphere_node = pe.Node(
-        Function(
-            function=get_freesurfer_sphere,
-            input_names=["freesurfer_path", "subject_id", "hemisphere"],
-            output_names=["sphere_raw"],
-        ),
-        name="get_freesurfer_sphere_node",
+    collect_registration_files = pe.Node(
+        CollectRegistrationFiles(hemisphere=hemisphere),
+        name="collect_registration_files",
+        mem_gb=0.1,
+        n_procs=1,
     )
-    get_freesurfer_sphere_node.inputs.hemisphere = hemisphere
-
-    # fmt:off
     workflow.connect([
-        (inputnode, get_freesurfer_sphere_node, [
-            ("freesurfer_path", "freesurfer_path"),
-            ("participant_id", "subject_id"),
-        ])
-    ])
-    # fmt:on
+        (inputnode, collect_registration_files, [
+            ("freesurfer_path", "segmentation_dir"),
+            ("participant_id", "participant_id"),
+            ("segmentation_software", "software"),
+        ]),
+    ])  # fmt:skip
 
     # NOTE: What does this step do?
     sphere_to_surf_gii = pe.Node(
@@ -1314,58 +1304,37 @@ def init_warp_one_hemisphere_wf(
         mem_gb=mem_gb,
         n_procs=omp_nthreads,
     )
-
-    # fmt:off
     workflow.connect([
-        (get_freesurfer_sphere_node, sphere_to_surf_gii, [("sphere_raw", "in_file")]),
-    ])
-    # fmt:on
+        (collect_registration_files, sphere_to_surf_gii, [("subject_sphere", "in_file")]),
+    ])  # fmt:skip
 
     # NOTE: What does this step do?
     surface_sphere_project_unproject = pe.Node(
-        SurfaceSphereProjectUnproject(
-            sphere_project_to=fsaverage_mesh,
-            sphere_unproject_from=fs_hemisphere_to_fsLR,
-        ),
+        SurfaceSphereProjectUnproject(),
         name="surface_sphere_project_unproject",
     )
-
-    # fmt:off
     workflow.connect([
+        (collect_registration_files, surface_sphere_project_unproject, [
+            ("source_sphere", "sphere_project_to"),
+            ("sphere_to_sphere", "sphere_unproject_from"),
+        ]),
         (sphere_to_surf_gii, surface_sphere_project_unproject, [("converted", "in_file")]),
-    ])
-    # fmt:on
-
-    fsLR_sphere = str(
-        get_template(
-            template="fsLR",
-            space=None,
-            hemi=hemisphere,
-            density="32k",
-            desc=None,
-            suffix="sphere",
-        )
-    )
+    ])  # fmt:skip
 
     # resample the surfaces to fsLR-32k
     # NOTE: Does that mean the data are in fsLR-164k before this?
     resample_to_fsLR32k = pe.MapNode(
-        CiftiSurfaceResample(
-            new_sphere=fsLR_sphere,
-            metric=" BARYCENTRIC ",
-        ),
+        CiftiSurfaceResample(metric="BARYCENTRIC"),
         name="resample_to_fsLR32k",
         mem_gb=mem_gb,
         n_procs=omp_nthreads,
         iterfield=["in_file"],
     )
-
-    # fmt:off
     workflow.connect([
         (inputnode, resample_to_fsLR32k, [("hemi_files", "in_file")]),
+        (collect_registration_files, resample_to_fsLR32k, [("target_sphere", "new_sphere")]),
         (surface_sphere_project_unproject, resample_to_fsLR32k, [("out_file", "current_sphere")]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     # apply affine to 32k surfs
     # NOTE: What does this step do? Aren't the data in fsLR-32k from resample_to_fsLR32k?
@@ -1376,13 +1345,10 @@ def init_warp_one_hemisphere_wf(
         n_procs=omp_nthreads,
         iterfield=["in_file"],
     )
-
-    # fmt:off
     workflow.connect([
-        (resample_to_fsLR32k, apply_affine_to_fsLR32k, [("out_file", "in_file")]),
         (inputnode, apply_affine_to_fsLR32k, [("world_xfm", "affine")]),
-    ])
-    # fmt:on
+        (resample_to_fsLR32k, apply_affine_to_fsLR32k, [("out_file", "in_file")]),
+    ])  # fmt:skip
 
     # apply FNIRT-format warpfield
     # NOTE: What does this step do?
@@ -1393,26 +1359,20 @@ def init_warp_one_hemisphere_wf(
         n_procs=omp_nthreads,
         iterfield=["in_file"],
     )
-
-    # fmt:off
     workflow.connect([
         (inputnode, apply_warpfield_to_fsLR32k, [
             ("merged_warpfield", "forward_warp"),
             ("merged_inv_warpfield", "warpfield"),
         ]),
         (apply_affine_to_fsLR32k, apply_warpfield_to_fsLR32k, [("out_file", "in_file")]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     outputnode = pe.Node(
         niu.IdentityInterface(fields=["warped_hemi_files"]),
         name="outputnode",
     )
-
-    # fmt:off
     workflow.connect([
         (apply_warpfield_to_fsLR32k, outputnode, [("out_file", "warped_hemi_files")]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     return workflow
diff --git a/xcp_d/workflows/concatenation.py b/xcp_d/workflows/concatenation.py
index ad9395c4f..09b0e8862 100644
--- a/xcp_d/workflows/concatenation.py
+++ b/xcp_d/workflows/concatenation.py
@@ -1,4 +1,5 @@
 """Workflows for concatenating postprocessed data."""
+
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
diff --git a/xcp_d/workflows/plotting.py b/xcp_d/workflows/plotting.py
index e19ebc503..26e719e94 100644
--- a/xcp_d/workflows/plotting.py
+++ b/xcp_d/workflows/plotting.py
@@ -1,4 +1,5 @@
 """Plotting workflows."""
+
 from nipype import Function
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe