junifer 0.0.3.dev188__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/markers/tests/test_parcel_aggregation.py

@@ -10,16 +10,17 @@ from pathlib import Path
 import nibabel as nib
 import numpy as np
 import pytest
-from nilearn import datasets
-from nilearn.image import concat_imgs, math_img, new_img_like, resample_to_img
+from nilearn.image import math_img, new_img_like
 from nilearn.maskers import NiftiLabelsMasker, NiftiMasker
 from nilearn.masking import compute_brain_mask
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 from scipy.stats import trim_mean
 
-from junifer.data import load_mask, load_parcellation, register_parcellation
+from junifer.data import get_mask, get_parcellation, register_parcellation
+from junifer.datareader import DefaultDataReader
 from junifer.markers.parcel_aggregation import ParcelAggregation
 from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
 def test_ParcelAggregation_input_output() -> None:
@@ -36,123 +37,145 @@ def test_ParcelAggregation_input_output() -> None:
 
 def test_ParcelAggregation_3D() -> None:
     """Test ParcelAggregation object on 3D images."""
-    # Get the testing parcellation (for nilearn)
-    parcellation = datasets.fetch_atlas_schaefer_2018(n_rois=100)
-
-    # Get the oasis VBM data
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
-    vbm = oasis_dataset.gray_matter_maps[0]
-    img = nib.load(vbm)
-
-    # Mask parcellation manually
-    parcellation_img_res = resample_to_img(
-        parcellation.maps,
-        img,
-        interpolation="nearest",
-    )
-    parcellation_bin = math_img(
-        "img != 0",
-        img=parcellation_img_res,
-    )
-
-    # Create NiftiMasker
-    masker = NiftiMasker(parcellation_bin, target_affine=img.affine)
-    data = masker.fit_transform(img)
-    parcellation_values = masker.transform(parcellation_img_res)
-    parcellation_values = np.squeeze(parcellation_values).astype(int)
-
-    # Compute the mean manually
-    manual = []
-    for t_v in sorted(np.unique(parcellation_values)):
-        t_values = np.mean(data[:, parcellation_values == t_v])
-        manual.append(t_values)
-    manual = np.array(manual)[np.newaxis, :]
-
-    # Create NiftiLabelsMasker
-    nifti_masker = NiftiLabelsMasker(labels_img=parcellation.maps)
-    auto = nifti_masker.fit_transform(img)
-
-    # Check that arrays are almost equal
-    assert_array_almost_equal(auto, manual)
-
-    # Use the ParcelAggregation object
-    marker = ParcelAggregation(
-        parcellation="Schaefer100x7",
-        method="mean",
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    jun_values3d_mean = marker.fit_transform(input)["VBM_GM"]["data"]
-
-    assert jun_values3d_mean.ndim == 2
-    assert jun_values3d_mean.shape[0] == 1
-    assert_array_equal(manual, jun_values3d_mean)
-
-    # Test using another function (std)
-    manual = []
-    for t_v in sorted(np.unique(parcellation_values)):
-        t_values = np.std(data[:, parcellation_values == t_v])
-        manual.append(t_values)
-    manual = np.array(manual)[np.newaxis, :]
-
-    # Use the ParcelAggregation object
-    marker = ParcelAggregation(parcellation="Schaefer100x7", method="std")
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    jun_values3d_std = marker.fit_transform(input)["VBM_GM"]["data"]
-
-    assert jun_values3d_std.ndim == 2
-    assert jun_values3d_std.shape[0] == 1
-    assert_array_equal(manual, jun_values3d_std)
-
-    # Test using another function with parameters
-    manual = []
-    for t_v in sorted(np.unique(parcellation_values)):
-        t_values = trim_mean(
-            data[:, parcellation_values == t_v],
-            proportiontocut=0.1,
-            axis=None,  # type: ignore
-        )
-        manual.append(t_values)
-    manual = np.array(manual)[np.newaxis, :]
-
-    # Use the ParcelAggregation object
-    marker = ParcelAggregation(
-        parcellation="Schaefer100x7",
-        method="trim_mean",
-        method_params={"proportiontocut": 0.1},
-    )
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    jun_values3d_tm = marker.fit_transform(input)["VBM_GM"]["data"]
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Create ParcelAggregation object
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            on="BOLD",
+        )
+        element_data["BOLD"]["data"] = element_data["BOLD"]["data"].slicer[
+            ..., 0:1
+        ]
+
+        # Compare with nilearn
+        # Load testing parcellation
+        testing_parcellation, _ = get_parcellation(
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+            target_data=element_data["BOLD"],
+        )
+        # Binarize parcellation
+        testing_parcellation_bin = math_img(
+            "img != 0",
+            img=testing_parcellation,
+        )
+        # Create NiftiMasker
+        masker = NiftiMasker(
+            testing_parcellation_bin,
+            target_affine=element_data["BOLD"]["data"].affine,
+        )
+        data = masker.fit_transform(element_data["BOLD"]["data"])
+        parcellation_values = np.squeeze(
+            masker.transform(testing_parcellation)
+        ).astype(int)
+        # Compute the mean manually
+        manual = []
+        for t_v in sorted(np.unique(parcellation_values)):
+            t_values = np.mean(data[:, parcellation_values == t_v])
+            manual.append(t_values)
+        manual = np.array(manual)[np.newaxis, :]
+
+        # Create NiftiLabelsMasker
+        nifti_labels_masker = NiftiLabelsMasker(
+            labels_img=testing_parcellation
+        )
+        nifti_labels_masked_bold = nifti_labels_masker.fit_transform(
+            element_data["BOLD"]["data"].slicer[..., 0:1]
+        )
 
-    assert jun_values3d_tm.ndim == 2
-    assert jun_values3d_tm.shape[0] == 1
-    assert_array_equal(manual, jun_values3d_tm)
+        parcel_agg_mean_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
+        # Check that arrays are almost equal
+        assert_array_equal(parcel_agg_mean_bold_data, manual)
+        assert_array_almost_equal(nifti_labels_masked_bold, manual)
+
+        # Check further
+        assert parcel_agg_mean_bold_data.ndim == 2
+        assert parcel_agg_mean_bold_data.shape[0] == 1
+        assert_array_equal(
+            nifti_labels_masked_bold.shape, parcel_agg_mean_bold_data.shape
+        )
+        assert_array_equal(nifti_labels_masked_bold, parcel_agg_mean_bold_data)
+
+        # Compute std manually
+        manual = []
+        for t_v in sorted(np.unique(parcellation_values)):
+            t_values = np.std(data[:, parcellation_values == t_v])
+            manual.append(t_values)
+        manual = np.array(manual)[np.newaxis, :]
+
+        # Create ParcelAggregation object
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="std",
+            on="BOLD",
+        )
+        parcel_agg_std_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
+        assert parcel_agg_std_bold_data.ndim == 2
+        assert parcel_agg_std_bold_data.shape[0] == 1
+        assert_array_equal(parcel_agg_std_bold_data, manual)
+
+        # Test using another function with parameters
+        manual = []
+        for t_v in sorted(np.unique(parcellation_values)):
+            t_values = trim_mean(
+                data[:, parcellation_values == t_v],
+                proportiontocut=0.1,
+                axis=None,  # type: ignore
+            )
+            manual.append(t_values)
+        manual = np.array(manual)[np.newaxis, :]
+
+        # Create ParcelAggregation object
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="trim_mean",
+            method_params={"proportiontocut": 0.1},
+            on="BOLD",
+        )
+        parcel_agg_trim_mean_bold_data = marker.fit_transform(element_data)[
+            "BOLD"
+        ]["data"]
+        assert parcel_agg_trim_mean_bold_data.ndim == 2
+        assert parcel_agg_trim_mean_bold_data.shape[0] == 1
+        assert_array_equal(parcel_agg_trim_mean_bold_data, manual)
 
 
 def test_ParcelAggregation_4D():
     """Test ParcelAggregation object on 4D images."""
-    # Get the testing parcellation (for nilearn)
-    parcellation = datasets.fetch_atlas_schaefer_2018(
-        n_rois=100, yeo_networks=7, resolution_mm=2
-    )
-
-    # Get the SPM auditory data:
-    subject_data = datasets.fetch_spm_auditory()
-    fmri_img = concat_imgs(subject_data.func)  # type: ignore
-
-    # Create NiftiLabelsMasker
-    nifti_masker = NiftiLabelsMasker(labels_img=parcellation.maps)
-    auto4d = nifti_masker.fit_transform(fmri_img)
-
-    # Create ParcelAggregation object
-    marker = ParcelAggregation(parcellation="Schaefer100x7", method="mean")
-    input = {"BOLD": {"data": fmri_img, "meta": {}}}
-    jun_values4d = marker.fit_transform(input)["BOLD"]["data"]
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Create ParcelAggregation object
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym", method="mean"
+        )
+        parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
+
+        # Compare with nilearn
+        # Load testing parcellation
+        testing_parcellation, _ = get_parcellation(
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+            target_data=element_data["BOLD"],
+        )
+        # Extract data
+        nifti_labels_masker = NiftiLabelsMasker(
+            labels_img=testing_parcellation
+        )
+        nifti_labels_masked_bold = nifti_labels_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
 
-    assert jun_values4d.ndim == 2
-    assert_array_equal(auto4d.shape, jun_values4d.shape)
-    assert_array_equal(auto4d, jun_values4d)
+        assert parcel_agg_bold_data.ndim == 2
+        assert_array_equal(
+            nifti_labels_masked_bold.shape, parcel_agg_bold_data.shape
+        )
+        assert_array_equal(nifti_labels_masked_bold, parcel_agg_bold_data)
 
 
 def test_ParcelAggregation_storage(tmp_path: Path) -> None:
@@ -164,130 +187,148 @@ def test_ParcelAggregation_storage(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    # Get the oasis VBM data
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
-    vbm = oasis_dataset.gray_matter_maps[0]
-    img = nib.load(vbm)
-    uri = tmp_path / "test_sphere_storage_3D.sqlite"
-
-    storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
-    meta = {
-        "element": {"subject": "sub-01", "session": "ses-01"},
-        "dependencies": {"nilearn", "nibabel"},
-    }
-    input = {"VBM_GM": {"data": img, "meta": meta}}
-    marker = ParcelAggregation(
-        parcellation="Schaefer100x7", method="mean", on="VBM_GM"
-    )
-
-    marker.fit_transform(input, storage=storage)
-
-    features = storage.list_features()
-    assert any(
-        x["name"] == "VBM_GM_ParcelAggregation" for x in features.values()
-    )
-
-    meta = {
-        "element": {"subject": "sub-01", "session": "ses-01"},
-        "dependencies": {"nilearn", "nibabel"},
-    }
-    # Get the SPM auditory data
-    subject_data = datasets.fetch_spm_auditory()
-    fmri_img = concat_imgs(subject_data.func)  # type: ignore
-    input = {"BOLD": {"data": fmri_img, "meta": meta}}
-    marker = ParcelAggregation(
-        parcellation="Schaefer100x7", method="mean", on="BOLD"
-    )
+    # Store 3D
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        storage = SQLiteFeatureStorage(
+            uri=tmp_path / "test_parcel_storage_3D.sqlite", upsert="ignore"
+        )
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            on="BOLD",
+        )
+        element_data["BOLD"]["data"] = element_data["BOLD"]["data"].slicer[
+            ..., 0:1
+        ]
+        marker.fit_transform(input=element_data, storage=storage)
+        features = storage.list_features()
+        assert any(
+            x["name"] == "BOLD_ParcelAggregation" for x in features.values()
+        )
 
-    marker.fit_transform(input, storage=storage)
-    features = storage.list_features()
-    assert any(
-        x["name"] == "BOLD_ParcelAggregation" for x in features.values()
-    )
+    # Store 4D
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        storage = SQLiteFeatureStorage(
+            uri=tmp_path / "test_parcel_storage_4D.sqlite", upsert="ignore"
+        )
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            on="BOLD",
+        )
+        marker.fit_transform(input=element_data, storage=storage)
+        features = storage.list_features()
+        assert any(
+            x["name"] == "BOLD_ParcelAggregation" for x in features.values()
+        )
 
 
 def test_ParcelAggregation_3D_mask() -> None:
     """Test ParcelAggregation object on 3D images with mask."""
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Create ParcelAggregation object
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            name="tian_mean",
+            on="BOLD",
+            masks="compute_brain_mask",
+        )
+        element_data["BOLD"]["data"] = element_data["BOLD"]["data"].slicer[
+            ..., 0:1
+        ]
+        parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
+
+        # Compare with nilearn
+        # Load testing parcellation
+        testing_parcellation, _ = get_parcellation(
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+            target_data=element_data["BOLD"],
+        )
+        # Load mask
+        mask_img = get_mask(
+            "compute_brain_mask", target_data=element_data["BOLD"]
+        )
+        # Extract data
+        nifti_labels_masker = NiftiLabelsMasker(
+            labels_img=testing_parcellation, mask_img=mask_img
+        )
+        nifti_labels_masked_bold = nifti_labels_masker.fit_transform(
+            element_data["BOLD"]["data"].slicer[..., 0:1]
+        )
 
-    # Get the testing parcellation (for nilearn)
-    parcellation = datasets.fetch_atlas_schaefer_2018(n_rois=100)
-
-    # Get one mask
-    mask_img, _ = load_mask("GM_prob0.2")
-
-    # Get the oasis VBM data
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
-    vbm = oasis_dataset.gray_matter_maps[0]
-    img = nib.load(vbm)
-
-    # Create NiftiLabelsMasker
-    nifti_masker = NiftiLabelsMasker(
-        labels_img=parcellation.maps, mask_img=mask_img
-    )
-    auto = nifti_masker.fit_transform(img)
-
-    # Use the ParcelAggregation object
-    marker = ParcelAggregation(
-        parcellation="Schaefer100x7",
-        method="mean",
-        masks="GM_prob0.2",
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    jun_values3d_mean = marker.fit_transform(input)["VBM_GM"]["data"]
-
-    assert jun_values3d_mean.ndim == 2
-    assert jun_values3d_mean.shape[0] == 1
-    assert_array_almost_equal(auto, jun_values3d_mean)
+        assert parcel_agg_bold_data.ndim == 2
+        assert_array_equal(
+            nifti_labels_masked_bold.shape, parcel_agg_bold_data.shape
+        )
+        assert_array_equal(nifti_labels_masked_bold, parcel_agg_bold_data)
 
 
 def test_ParcelAggregation_3D_mask_computed() -> None:
     """Test ParcelAggregation object on 3D images with computed masks."""
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        element_data["BOLD"]["data"] = element_data["BOLD"]["data"].slicer[
+            ..., 0:1
+        ]
+
+        # Compare with nilearn
+        # Load testing parcellation
+        testing_parcellation, _ = get_parcellation(
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+            target_data=element_data["BOLD"],
+        )
+        # Get a mask
+        mask_img = compute_brain_mask(
+            element_data["BOLD"]["data"], threshold=0.2
+        )
+        # Create NiftiLabelsMasker
+        nifti_labels_masker = NiftiLabelsMasker(
+            labels_img=testing_parcellation, mask_img=mask_img
+        )
+        nifti_labels_masked_bold_good = nifti_labels_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
 
-    # Get the testing parcellation (for nilearn)
-    parcellation = datasets.fetch_atlas_schaefer_2018(n_rois=100)
-
-    # Get the oasis VBM data
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
-    vbm = oasis_dataset.gray_matter_maps[0]
-    img = nib.load(vbm)
-
-    # Get one mask
-    mask_img = compute_brain_mask(img, threshold=0.2)
-
-    # Create NiftiLabelsMasker
-    nifti_masker = NiftiLabelsMasker(
-        labels_img=parcellation.maps, mask_img=mask_img
-    )
-    auto = nifti_masker.fit_transform(img)
-
-    # Get one mask
-    mask_img = compute_brain_mask(img, threshold=0.5)
-
-    # Create NiftiLabelsMasker
-    nifti_masker = NiftiLabelsMasker(
-        labels_img=parcellation.maps, mask_img=mask_img
-    )
-    auto_bad = nifti_masker.fit_transform(img)
-
-    # Use the ParcelAggregation object
-    marker = ParcelAggregation(
-        parcellation="Schaefer100x7",
-        method="mean",
-        masks={"compute_brain_mask": {"threshold": 0.2}},
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    jun_values3d_mean = marker.fit_transform(input)["VBM_GM"]["data"]
+        # Get another mask
+        mask_img = compute_brain_mask(
+            element_data["BOLD"]["data"], threshold=0.5
+        )
+        # Create NiftiLabelsMasker
+        nifti_labels_masker = NiftiLabelsMasker(
+            labels_img=testing_parcellation, mask_img=mask_img
+        )
+        nifti_labels_masked_bold_bad = nifti_labels_masker.fit_transform(
+            mask_img
+        )
 
-    assert jun_values3d_mean.ndim == 2
-    assert jun_values3d_mean.shape[0] == 1
-    assert_array_almost_equal(auto, jun_values3d_mean)
+        # Use the ParcelAggregation object
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            masks={"compute_brain_mask": {"threshold": 0.2}},
+            name="tian_mean",
+            on="BOLD",
+        )
+        parcel_agg_mean_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
+
+        assert parcel_agg_mean_bold_data.ndim == 2
+        assert parcel_agg_mean_bold_data.shape[0] == 1
+        assert_array_almost_equal(
+            nifti_labels_masked_bold_good, parcel_agg_mean_bold_data
+        )
 
-    with pytest.raises(AssertionError):
-        assert_array_almost_equal(jun_values3d_mean, auto_bad)
+        with pytest.raises(AssertionError):
+            assert_array_almost_equal(
+                parcel_agg_mean_bold_data, nifti_labels_masked_bold_bad
+            )
 
 
 def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
@@ -299,81 +340,93 @@ def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        element_data["BOLD"]["data"] = element_data["BOLD"]["data"].slicer[
+            ..., 0:1
+        ]
+
+        # Load testing parcellation
+        testing_parcellation, labels = get_parcellation(
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+            target_data=element_data["BOLD"],
+        )
 
-    # Get the testing parcellation
-    parcellation, labels, _ = load_parcellation("Schaefer100x7")
+        # Create two parcellations from it
+        parcellation_data = testing_parcellation.get_fdata()
+        parcellation1_data = parcellation_data.copy()
+        parcellation1_data[parcellation1_data > 8] = 0
+        parcellation2_data = parcellation_data.copy()
+        parcellation2_data[parcellation2_data <= 8] = 0
+        parcellation2_data[parcellation2_data > 0] -= 8
+        labels1 = labels[:8]
+        labels2 = labels[8:]
+
+        parcellation1_img = new_img_like(
+            testing_parcellation, parcellation1_data
+        )
+        parcellation2_img = new_img_like(
+            testing_parcellation, parcellation2_data
+        )
 
-    assert parcellation is not None
+        parcellation1_path = tmp_path / "parcellation1.nii.gz"
+        parcellation2_path = tmp_path / "parcellation2.nii.gz"
 
-    # Get the oasis VBM data
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
-    vbm = oasis_dataset.gray_matter_maps[0]
-    img = nib.load(vbm)
+        nib.save(parcellation1_img, parcellation1_path)
+        nib.save(parcellation2_img, parcellation2_path)
 
-    # Create two parcellations from it
-    parcellation_data = parcellation.get_fdata()
-    parcellation1_data = parcellation_data.copy()
-    parcellation1_data[parcellation1_data > 50] = 0
-    parcellation2_data = parcellation_data.copy()
-    parcellation2_data[parcellation2_data <= 50] = 0
-    parcellation2_data[parcellation2_data > 0] -= 50
-    labels1 = labels[:50]
-    labels2 = labels[50:]
+        register_parcellation(
+            name="TianxS1x3TxMNInonlinear2009cAsym_low",
+            parcellation_path=parcellation1_path,
+            parcels_labels=labels1,
+            space="MNI152NLin2009cAsym",
+            overwrite=True,
+        )
+        register_parcellation(
+            name="TianxS1x3TxMNInonlinear2009cAsym_high",
+            parcellation_path=parcellation2_path,
+            parcels_labels=labels2,
+            space="MNI152NLin2009cAsym",
+            overwrite=True,
+        )
 
-    parcellation1_img = new_img_like(parcellation, parcellation1_data)
-    parcellation2_img = new_img_like(parcellation, parcellation2_data)
+        # Use the ParcelAggregation object on the original parcellation
+        marker_original = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            name="tian_mean",
+            on="BOLD",
+        )
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
+
+        orig_mean_data = orig_mean["data"]
+        assert orig_mean_data.ndim == 2
+        assert orig_mean_data.shape == (1, 16)
+
+        # Use the ParcelAggregation object on the two parcellations
+        marker_split = ParcelAggregation(
+            parcellation=[
+                "TianxS1x3TxMNInonlinear2009cAsym_low",
+                "TianxS1x3TxMNInonlinear2009cAsym_high",
+            ],
+            method="mean",
+            name="tian_mean",
+            on="BOLD",
+        )
 
-    parcellation1_path = tmp_path / "parcellation1.nii.gz"
-    parcellation2_path = tmp_path / "parcellation2.nii.gz"
+        # No warnings should be raised
+        with warnings.catch_warnings():
+            warnings.simplefilter("error", category=UserWarning)
+            split_mean = marker_split.fit_transform(element_data)["BOLD"]
 
-    nib.save(parcellation1_img, parcellation1_path)
-    nib.save(parcellation2_img, parcellation2_path)
+        split_mean_data = split_mean["data"]
 
-    register_parcellation(
-        "Schaefer100x7_low", parcellation1_path, labels1, overwrite=True
-    )
-    register_parcellation(
-        "Schaefer100x7_high", parcellation2_path, labels2, overwrite=True
-    )
+        assert split_mean_data.ndim == 2
+        assert split_mean_data.shape == (1, 16)
 
-    # Use the ParcelAggregation object on the original parcellation
-    marker_original = ParcelAggregation(
-        parcellation="Schaefer100x7",
-        method="mean",
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    orig_mean = marker_original.fit_transform(input)["VBM_GM"]
-
-    orig_mean_data = orig_mean["data"]
-    assert orig_mean_data.ndim == 2
-    assert orig_mean_data.shape[0] == 1
-    assert orig_mean_data.shape[1] == 100
-    # assert_array_almost_equal(auto, jun_values3d_mean)
-
-    # Use the ParcelAggregation object on the two parcellations
-    marker_split = ParcelAggregation(
-        parcellation=["Schaefer100x7_low", "Schaefer100x7_high"],
-        method="mean",
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-
-    # No warnings should be raised
-    with warnings.catch_warnings():
-        warnings.simplefilter("error", category=UserWarning)
-        split_mean = marker_split.fit_transform(input)["VBM_GM"]
-    split_mean_data = split_mean["data"]
-
-    assert split_mean_data.ndim == 2
-    assert split_mean_data.shape[0] == 1
-    assert split_mean_data.shape[1] == 100
-
-    # Data and labels should be the same
-    assert_array_equal(orig_mean_data, split_mean_data)
-    assert orig_mean["col_names"] == split_mean["col_names"]
+        # Data and labels should be the same
+        assert_array_equal(orig_mean_data, split_mean_data)
+        assert orig_mean["col_names"] == split_mean["col_names"]
 
 
 def test_ParcelAggregation_3D_multiple_overlapping(tmp_path: Path) -> None:
@@ -385,87 +438,100 @@ def test_ParcelAggregation_3D_multiple_overlapping(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        element_data["BOLD"]["data"] = element_data["BOLD"]["data"].slicer[
+            ..., 0:1
+        ]
+
+        # Load testing parcellation
+        testing_parcellation, labels = get_parcellation(
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+            target_data=element_data["BOLD"],
+        )
 
-    # Get the testing parcellation
-    parcellation, labels, _ = load_parcellation("Schaefer100x7")
+        # Create two parcellations from it
+        parcellation_data = testing_parcellation.get_fdata()
+        parcellation1_data = parcellation_data.copy()
+        parcellation1_data[parcellation1_data > 8] = 0
+        parcellation2_data = parcellation_data.copy()
 
-    assert parcellation is not None
+        # Make the second parcellation overlap with the first
+        parcellation2_data[parcellation2_data <= 6] = 0
+        parcellation2_data[parcellation2_data > 0] -= 6
+        labels1 = [f"low_{x}" for x in labels[:8]]  # Change the labels
+        labels2 = [f"high_{x}" for x in labels[6:]]  # Change the labels
 
-    # Get the oasis VBM data
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
-    vbm = oasis_dataset.gray_matter_maps[0]
-    img = nib.load(vbm)
+        parcellation1_img = new_img_like(
+            testing_parcellation, parcellation1_data
+        )
+        parcellation2_img = new_img_like(
+            testing_parcellation, parcellation2_data
+        )
 
-    # Create two parcellations from it
-    parcellation_data = parcellation.get_fdata()
-    parcellation1_data = parcellation_data.copy()
-    parcellation1_data[parcellation1_data > 50] = 0
-    parcellation2_data = parcellation_data.copy()
+        parcellation1_path = tmp_path / "parcellation1.nii.gz"
+        parcellation2_path = tmp_path / "parcellation2.nii.gz"
 
-    # Make the second parcellation overlap with the first
-    parcellation2_data[parcellation2_data <= 45] = 0
-    parcellation2_data[parcellation2_data > 0] -= 45
-    labels1 = [f"low_{x}" for x in labels[:50]]  # Change the labels
-    labels2 = [f"high_{x}" for x in labels[45:]]  # Change the labels
+        nib.save(parcellation1_img, parcellation1_path)
+        nib.save(parcellation2_img, parcellation2_path)
 
-    parcellation1_img = new_img_like(parcellation, parcellation1_data)
-    parcellation2_img = new_img_like(parcellation, parcellation2_data)
+        register_parcellation(
+            name="TianxS1x3TxMNInonlinear2009cAsym_low",
+            parcellation_path=parcellation1_path,
+            parcels_labels=labels1,
+            space="MNI152NLin2009cAsym",
+            overwrite=True,
+        )
+        register_parcellation(
+            name="TianxS1x3TxMNInonlinear2009cAsym_high",
+            parcellation_path=parcellation2_path,
+            parcels_labels=labels2,
+            space="MNI152NLin2009cAsym",
+            overwrite=True,
+        )
 
-    parcellation1_path = tmp_path / "parcellation1.nii.gz"
-    parcellation2_path = tmp_path / "parcellation2.nii.gz"
+        # Use the ParcelAggregation object on the original parcellation
+        marker_original = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            name="tian_mean",
+            on="BOLD",
+        )
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
+
+        orig_mean_data = orig_mean["data"]
+        assert orig_mean_data.ndim == 2
+        assert orig_mean_data.shape == (1, 16)
+
+        # Use the ParcelAggregation object on the two parcellations
+        marker_split = ParcelAggregation(
+            parcellation=[
+                "TianxS1x3TxMNInonlinear2009cAsym_low",
+                "TianxS1x3TxMNInonlinear2009cAsym_high",
+            ],
+            method="mean",
+            name="tian_mean",
+            on="BOLD",
+        )
+        # Warning should be raised
+        with pytest.warns(RuntimeWarning, match="overlapping voxels"):
+            split_mean = marker_split.fit_transform(element_data)["BOLD"]
 
-    nib.save(parcellation1_img, parcellation1_path)
-    nib.save(parcellation2_img, parcellation2_path)
+        split_mean_data = split_mean["data"]
 
-    register_parcellation(
-        "Schaefer100x7_low2", parcellation1_path, labels1, overwrite=True
-    )
-    register_parcellation(
-        "Schaefer100x7_high2", parcellation2_path, labels2, overwrite=True
-    )
+        assert split_mean_data.ndim == 2
+        assert split_mean_data.shape == (1, 18)
+
+        # Overlapping voxels should be NaN
+        assert np.isnan(split_mean_data[:, 8:10]).all()
+
+        non_nan = split_mean_data[~np.isnan(split_mean_data)]
+        # Data should be the same
+        assert_array_equal(orig_mean_data, non_nan[None, :])
 
-    # Use the ParcelAggregation object on the original parcellation
-    marker_original = ParcelAggregation(
-        parcellation="Schaefer100x7",
-        method="mean",
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    orig_mean = marker_original.fit_transform(input)["VBM_GM"]
-
-    orig_mean_data = orig_mean["data"]
-    assert orig_mean_data.ndim == 2
-    assert orig_mean_data.shape[0] == 1
-    assert orig_mean_data.shape[1] == 100
-    # assert_array_almost_equal(auto, jun_values3d_mean)
-
-    # Use the ParcelAggregation object on the two parcellations
-    marker_split = ParcelAggregation(
-        parcellation=["Schaefer100x7_low2", "Schaefer100x7_high2"],
-        method="mean",
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    with pytest.warns(RuntimeWarning, match="overlapping voxels"):
-        split_mean = marker_split.fit_transform(input)["VBM_GM"]
-    split_mean_data = split_mean["data"]
-
-    assert split_mean_data.ndim == 2
-    assert split_mean_data.shape[0] == 1
-    assert split_mean_data.shape[1] == 105
-
-    # Overlapping voxels should be NaN
-    assert np.isnan(split_mean_data[:, 50:55]).all()
-
-    non_nan = split_mean_data[~np.isnan(split_mean_data)]
-    # Data should be the same
-    assert_array_equal(orig_mean_data, non_nan[None, :])
-
-    # Labels should be "low" for the first 50 and "high" for the second 50
-    assert all(x.startswith("low") for x in split_mean["col_names"][:50])
-    assert all(x.startswith("high") for x in split_mean["col_names"][50:])
+        # Labels should be "low" for the first 8 and "high" for the second 8
+        assert all(x.startswith("low") for x in split_mean["col_names"][:8])
+        assert all(x.startswith("high") for x in split_mean["col_names"][8:])
 
 
 def test_ParcelAggregation_3D_multiple_duplicated_labels(
@@ -479,127 +545,164 @@ def test_ParcelAggregation_3D_multiple_duplicated_labels(
         The path to the test directory.
 
     """
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        element_data["BOLD"]["data"] = element_data["BOLD"]["data"].slicer[
+            ..., 0:1
+        ]
+
+        # Load testing parcellation
+        testing_parcellation, labels = get_parcellation(
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+            target_data=element_data["BOLD"],
+        )
 
-    # Get the testing parcellation
-    parcellation, labels, _ = load_parcellation("Schaefer100x7")
+        # Create two parcellations from it
+        parcellation_data = testing_parcellation.get_fdata()
+        parcellation1_data = parcellation_data.copy()
+        parcellation1_data[parcellation1_data > 8] = 0
+        parcellation2_data = parcellation_data.copy()
+        parcellation2_data[parcellation2_data <= 8] = 0
+        parcellation2_data[parcellation2_data > 0] -= 8
+        labels1 = labels[:8]
+        labels2 = labels[7:-1]  # One label is duplicated
+
+        parcellation1_img = new_img_like(
+            testing_parcellation, parcellation1_data
+        )
+        parcellation2_img = new_img_like(
+            testing_parcellation, parcellation2_data
+        )
 
-    assert parcellation is not None
+        parcellation1_path = tmp_path / "parcellation1.nii.gz"
+        parcellation2_path = tmp_path / "parcellation2.nii.gz"
 
-    # Get the oasis VBM data
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
-    vbm = oasis_dataset.gray_matter_maps[0]
-    img = nib.load(vbm)
+        nib.save(parcellation1_img, parcellation1_path)
+        nib.save(parcellation2_img, parcellation2_path)
 
-    # Create two parcellations from it
-    parcellation_data = parcellation.get_fdata()
-    parcellation1_data = parcellation_data.copy()
-    parcellation1_data[parcellation1_data > 50] = 0
-    parcellation2_data = parcellation_data.copy()
-    parcellation2_data[parcellation2_data <= 50] = 0
-    parcellation2_data[parcellation2_data > 0] -= 50
-    labels1 = labels[:50]
-    labels2 = labels[49:-1]  # One label is duplicated
+        register_parcellation(
+            name="TianxS1x3TxMNInonlinear2009cAsym_low",
+            parcellation_path=parcellation1_path,
+            parcels_labels=labels1,
+            space="MNI152NLin2009cAsym",
+            overwrite=True,
+        )
+        register_parcellation(
+            name="TianxS1x3TxMNInonlinear2009cAsym_high",
+            parcellation_path=parcellation2_path,
+            parcels_labels=labels2,
+            space="MNI152NLin2009cAsym",
+            overwrite=True,
+        )
 
-    parcellation1_img = new_img_like(parcellation, parcellation1_data)
-    parcellation2_img = new_img_like(parcellation, parcellation2_data)
+        # Use the ParcelAggregation object on the original parcellation
+        marker_original = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            name="tian_mean",
+            on="BOLD",
+        )
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
+
+        orig_mean_data = orig_mean["data"]
+        assert orig_mean_data.ndim == 2
+        assert orig_mean_data.shape == (1, 16)
+
+        # Use the ParcelAggregation object on the two parcellations
+        marker_split = ParcelAggregation(
+            parcellation=[
+                "TianxS1x3TxMNInonlinear2009cAsym_low",
+                "TianxS1x3TxMNInonlinear2009cAsym_high",
+            ],
+            method="mean",
+            name="tian_mean",
+            on="BOLD",
+        )
 
-    parcellation1_path = tmp_path / "parcellation1.nii.gz"
-    parcellation2_path = tmp_path / "parcellation2.nii.gz"
+        # Warning should be raised
+        with pytest.warns(RuntimeWarning, match="duplicated labels."):
+            split_mean = marker_split.fit_transform(element_data)["BOLD"]
 
-    nib.save(parcellation1_img, parcellation1_path)
-    nib.save(parcellation2_img, parcellation2_path)
+        split_mean_data = split_mean["data"]
 
-    register_parcellation(
-        "Schaefer100x7_low", parcellation1_path, labels1, overwrite=True
-    )
-    register_parcellation(
-        "Schaefer100x7_high", parcellation2_path, labels2, overwrite=True
-    )
+        assert split_mean_data.ndim == 2
+        assert split_mean_data.shape == (1, 16)
 
-    # Use the ParcelAggregation object on the original parcellation
-    marker_original = ParcelAggregation(
-        parcellation="Schaefer100x7",
-        method="mean",
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-    orig_mean = marker_original.fit_transform(input)["VBM_GM"]
-
-    orig_mean_data = orig_mean["data"]
-    assert orig_mean_data.ndim == 2
-    assert orig_mean_data.shape[0] == 1
-    assert orig_mean_data.shape[1] == 100
-    # assert_array_almost_equal(auto, jun_values3d_mean)
-
-    # Use the ParcelAggregation object on the two parcellations
-    marker_split = ParcelAggregation(
-        parcellation=["Schaefer100x7_low", "Schaefer100x7_high"],
-        method="mean",
-        name="gmd_schaefer100x7_mean",
-        on="VBM_GM",
-    )  # Test passing "on" as a keyword argument
-    input = {"VBM_GM": {"data": img, "meta": {}}}
-
-    with pytest.warns(RuntimeWarning, match="duplicated labels."):
-        split_mean = marker_split.fit_transform(input)["VBM_GM"]
-    split_mean_data = split_mean["data"]
-
-    assert split_mean_data.ndim == 2
-    assert split_mean_data.shape[0] == 1
-    assert split_mean_data.shape[1] == 100
-
-    # Data should be the same
-    assert_array_equal(orig_mean_data, split_mean_data)
-
-    # Labels should be prefixed with the parcellation name
-    col_names = [f"Schaefer100x7_low_{x}" for x in labels1]
-    col_names += [f"Schaefer100x7_high_{x}" for x in labels2]
-    assert col_names == split_mean["col_names"]
+        # Data should be the same
+        assert_array_equal(orig_mean_data, split_mean_data)
+
+        # Labels should be prefixed with the parcellation name
+        col_names = [
+            f"TianxS1x3TxMNInonlinear2009cAsym_low_{x}" for x in labels1
+        ]
+        col_names += [
+            f"TianxS1x3TxMNInonlinear2009cAsym_high_{x}" for x in labels2
+        ]
+        assert col_names == split_mean["col_names"]
 
 
 def test_ParcelAggregation_4D_agg_time():
     """Test ParcelAggregation object on 4D images, aggregating time."""
-    # Get the testing parcellation (for nilearn)
-    parcellation = datasets.fetch_atlas_schaefer_2018(
-        n_rois=100, yeo_networks=7, resolution_mm=2
-    )
-
-    # Get the SPM auditory data:
-    subject_data = datasets.fetch_spm_auditory()
-    fmri_img = concat_imgs(subject_data.func)  # type: ignore
-
-    # Create NiftiLabelsMasker
-    nifti_masker = NiftiLabelsMasker(labels_img=parcellation.maps)
-    auto4d = nifti_masker.fit_transform(fmri_img)
-    auto_mean = auto4d.mean(axis=0)
-
-    # Create ParcelAggregation object
-    marker = ParcelAggregation(
-        parcellation="Schaefer100x7", method="mean", time_method="mean"
-    )
-    input = {"BOLD": {"data": fmri_img, "meta": {}}}
-    jun_values4d = marker.fit_transform(input)["BOLD"]["data"]
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Create ParcelAggregation object
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            time_method="mean",
+            on="BOLD",
+        )
+        parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
+
+        # Compare with nilearn
+        # Loading testing parcellation
+        testing_parcellation, _ = get_parcellation(
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+            target_data=element_data["BOLD"],
+        )
+        # Extract data
+        nifti_labels_masker = NiftiLabelsMasker(
+            labels_img=testing_parcellation
+        )
+        nifti_labels_masked_bold = nifti_labels_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
+        nifti_labels_masked_bold_mean = nifti_labels_masked_bold.mean(axis=0)
 
-    assert jun_values4d.ndim == 1
-    assert_array_equal(auto_mean.shape, jun_values4d.shape)
-    assert_array_almost_equal(auto_mean, jun_values4d, decimal=2)
+        assert parcel_agg_bold_data.ndim == 1
+        assert_array_equal(
+            nifti_labels_masked_bold_mean.shape, parcel_agg_bold_data.shape
+        )
+        assert_array_almost_equal(
+            nifti_labels_masked_bold_mean, parcel_agg_bold_data, decimal=2
+        )
 
-    auto_pick_0 = auto4d[:1, :]
-    marker = ParcelAggregation(
-        parcellation="Schaefer100x7",
-        method="mean",
-        time_method="select",
-        time_method_params={"pick": [0]},
-    )
+        # Test picking first time point
+        nifti_labels_masked_bold_pick_0 = nifti_labels_masked_bold[:1, :]
+        marker = ParcelAggregation(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            method="mean",
+            time_method="select",
+            time_method_params={"pick": [0]},
+            on="BOLD",
+        )
+        parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
 
-    input = {"BOLD": {"data": fmri_img, "meta": {}}}
-    jun_values4d = marker.fit_transform(input)["BOLD"]["data"]
+        assert parcel_agg_bold_data.ndim == 2
+        assert_array_equal(
+            nifti_labels_masked_bold_pick_0.shape, parcel_agg_bold_data.shape
+        )
+        assert_array_equal(
+            nifti_labels_masked_bold_pick_0, parcel_agg_bold_data
+        )
 
-    assert jun_values4d.ndim == 2
-    assert_array_equal(auto_pick_0.shape, jun_values4d.shape)
-    assert_array_equal(auto_pick_0, jun_values4d)
 
+def test_ParcelAggregation_errors() -> None:
+    """Test errors for ParcelAggregation."""
     with pytest.raises(ValueError, match="can only be used with BOLD data"):
         ParcelAggregation(
             parcellation="Schaefer100x7",
@@ -619,6 +722,22 @@ def test_ParcelAggregation_4D_agg_time():
             on="VBM_GM",
         )
 
-    with pytest.warns(RuntimeWarning, match="No time dimension to aggregate"):
-        input = {"BOLD": {"data": fmri_img.slicer[..., 0:1], "meta": {}}}
-        marker.fit_transform(input)
+
+def test_ParcelAggregation_warning() -> None:
+    """Test warning for ParcelAggregation."""
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        with pytest.warns(
+            RuntimeWarning, match="No time dimension to aggregate"
+        ):
+            marker = ParcelAggregation(
+                parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+                method="mean",
+                time_method="select",
+                time_method_params={"pick": [0]},
+                on="BOLD",
+            )
+            element_data["BOLD"]["data"] = element_data["BOLD"]["data"].slicer[
+                ..., 0:1
+            ]
+            marker.fit_transform(element_data)