.github/workflows/docs-preview.yml

@@ -44,6 +44,20 @@ jobs:
       run: |
         git config --global user.email "runner@github.com"
         git config --global user.name "GITHUB CI Runner"
+    - name: Install ANTs
+      run: |
+        echo "++ Add universe repo"
+        sudo add-apt-repository -y universe
+
+        echo "++ Update package manager info"
+        sudo apt-get update -qq
+
+        echo "++ Downloading ANTs"
+        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
+        unzip ants.zip -d /opt
+        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
+        rm ants.zip
+        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
     - name: Test build docs
       run: |
         BUILDDIR=_build/main make -C docs/ local

docs/changes/newsfragments/299.change

@@ -0,0 +1 @@
+Add ``template_type`` parameter to :func:`.get_template` by `Synchon Mandal`_

docs/changes/newsfragments/299.enh

@@ -0,0 +1 @@
+Rewrite :func:`.compute_brain_mask` to allow variable template fetching via templateflow, according to target data by `Synchon Mandal`_

docs/changes/newsfragments/299.feature

@@ -0,0 +1 @@
+Add support for on-the-fly template space transformation in :func:`.get_parcellation` and :func:`.get_mask` to allow parcellation and mask in different template spaces to work with a ``DataGrabber``'s data in a specified template space.

examples/yamls/partly_cloudy_agg_mean_tian.yml

@@ -0,0 +1,16 @@
+workdir: /tmp
+
+with: junifer.testing.registry
+
+datagrabber:
+  kind: PartlyCloudyTestingDataGrabber
+
+markers:
+  - kind: ParcelAggregation
+    parcellation: TianxS1x3TxMNInonlinear2009cAsym
+    method: mean
+    name: tian-s1-3T_mean
+
+storage:
+  kind: HDF5FeatureStorage
+  uri: /tmp/partly_cloudy_agg_mean_tian.hdf5

junifer/api/tests/data/partly_cloudy_agg_mean_tian.yml

@@ -0,0 +1,16 @@
+workdir: /tmp
+
+with: junifer.testing.registry
+
+datagrabber:
+  kind: PartlyCloudyTestingDataGrabber
+
+markers:
+  - kind: ParcelAggregation
+    parcellation: TianxS1x3TxMNInonlinear2009cAsym
+    method: mean
+    name: tian-s1-3T_mean
+
+storage:
+  kind: HDF5FeatureStorage
+  uri: /tmp/partly_cloudy_agg_mean_tian.hdf5

junifer/api/tests/test_cli.py

@@ -54,16 +54,13 @@ def test_run_and_collect_commands(
 
     """
     # Get test config
-    infile = Path(__file__).parent / "data" / "gmd_mean.yaml"
+    infile = Path(__file__).parent / "data" / "partly_cloudy_agg_mean_tian.yml"
     # Read test config
     contents = yaml.load(infile)
     # Working directory
-    workdir = tmp_path / "workdir"
+    contents["workdir"] = str(tmp_path.resolve())
-    contents["workdir"] = str(workdir.resolve())
-    # Output directory
-    outdir = tmp_path / "outdir"
     # Storage
-    contents["storage"]["uri"] = str(outdir.resolve())
+    contents["storage"]["uri"] = str((tmp_path / "out.hdf5").resolve())
     # Write new test config
     outfile = tmp_path / "in.yaml"
     yaml.dump(contents, stream=outfile)
@@ -117,16 +114,13 @@ def test_run_using_element_file(tmp_path: Path, elements: str) -> None:
         f.write(elements)
 
     # Get test config
-    infile = Path(__file__).parent / "data" / "gmd_mean.yaml"
+    infile = Path(__file__).parent / "data" / "partly_cloudy_agg_mean_tian.yml"
     # Read test config
     contents = yaml.load(infile)
     # Working directory
-    workdir = tmp_path / "workdir"
+    contents["workdir"] = str(tmp_path.resolve())
-    contents["workdir"] = str(workdir.resolve())
-    # Output directory
-    outdir = tmp_path / "outdir"
     # Storage
-    contents["storage"]["uri"] = str(outdir.resolve())
+    contents["storage"]["uri"] = str((tmp_path / "out.hdf5").resolve())
     # Write new test config
     outfile = tmp_path / "in.yaml"
     yaml.dump(contents, stream=outfile)
@@ -228,7 +222,7 @@ def test_queue(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
 @pytest.mark.parametrize(
     "action, action_file",
     [
-        (run, "gmd_mean.yaml"),
+        (run, "partly_cloudy_agg_mean_tian.yml"),
         (queue, "gmd_mean_htcondor.yaml"),
     ],
 )

junifer/api/tests/test_functions.py

@@ -7,7 +7,7 @@
 
 import logging
 from pathlib import Path
-from typing import List, Tuple, Union
+from typing import Dict, List, Tuple, Union
 
 import pytest
 from ruamel.yaml import YAML
@@ -24,97 +24,104 @@ yaml.default_flow_style = False
 yaml.allow_unicode = True
 yaml.indent(mapping=2, sequence=4, offset=2)
 
-# Define datagrabber
-datagrabber = {
-    "kind": "OasisVBMTestingDataGrabber",
-}
 
-# Define markers
+@pytest.fixture
-markers = [
+def datagrabber() -> Dict[str, str]:
-    {
+    """Return a datagrabber as a dictionary."""
-        "name": "Schaefer1000x7_Mean",
+    return {
-        "kind": "ParcelAggregation",
+        "kind": "PartlyCloudyTestingDataGrabber",
-        "parcellation": "Schaefer1000x7",
+    }
-        "method": "mean",
-    },
-    {
-        "name": "Schaefer1000x7_Std",
-        "kind": "ParcelAggregation",
-        "parcellation": "Schaefer1000x7",
-        "method": "std",
-    },
-]
-
-# Define storage
-storage = {
-    "kind": "SQLiteFeatureStorage",
-}
 
 
-def test_run_single_element(tmp_path: Path) -> None:
+@pytest.fixture
+def markers() -> List[Dict[str, str]]:
+    """Return markers as a list of dictionary."""
+    return [
+        {
+            "name": "tian-s1-3T_mean",
+            "kind": "ParcelAggregation",
+            "parcellation": "TianxS1x3TxMNInonlinear2009cAsym",
+            "method": "mean",
+        },
+        {
+            "name": "tian-s1-3T_std",
+            "kind": "ParcelAggregation",
+            "parcellation": "TianxS1x3TxMNInonlinear2009cAsym",
+            "method": "std",
+        },
+    ]
+
+
+@pytest.fixture
+def storage() -> Dict[str, str]:
+    """Return a storage as a dictionary."""
+    return {
+        "kind": "SQLiteFeatureStorage",
+    }
+
+
+def test_run_single_element(
+    tmp_path: Path,
+    datagrabber: Dict[str, str],
+    markers: List[Dict[str, str]],
+    storage: Dict[str, str],
+) -> None:
     """Test run function with single element.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
 
     """
-    # Create working directory
+    # Set storage
-    workdir = tmp_path / "workdir_single"
+    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
-    workdir.mkdir()
-    # Create output directory
-    outdir = workdir / "out"
-    outdir.mkdir()
-    # Create storage
-    uri = outdir / "test.sqlite"
-    storage["uri"] = uri  # type: ignore
     # Run operations
     run(
-        workdir=workdir,
+        workdir=tmp_path,
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
         elements=["sub-01"],
     )
     # Check files
-    files = list(outdir.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.sqlite"))
     assert len(files) == 1
 
 
-def test_run_single_element_with_preprocessing(tmp_path: Path) -> None:
+def test_run_single_element_with_preprocessing(
+    tmp_path: Path,
+    markers: List[Dict[str, str]],
+    storage: Dict[str, str],
+) -> None:
     """Test run function with single element and pre-processing.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
 
     """
-    # Create working directory
+    # Set storage
-    workdir = tmp_path / "workdir_single_with_preprocess"
+    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
-    workdir.mkdir()
-    # Create output directory
-    outdir = workdir / "out"
-    outdir.mkdir()
-    # Create storage
-    uri = outdir / "test.sqlite"
-    storage["uri"] = uri  # type: ignore
     # Run operations
     run(
-        workdir=workdir,
+        workdir=tmp_path,
         datagrabber={
             "kind": "PartlyCloudyTestingDataGrabber",
             "reduce_confounds": False,
         },
-        markers=[
+        markers=markers,
-            {
-                "name": "Schaefer100x17_mean_FC",
-                "kind": "FunctionalConnectivityParcels",
-                "parcellation": "Schaefer100x17",
-                "agg_method": "mean",
-            }
-        ],
         storage=storage,
         preprocessors=[
             {
@@ -124,97 +131,110 @@ def test_run_single_element_with_preprocessing(tmp_path: Path) -> None:
         elements=["sub-01"],
     )
     # Check files
-    files = list(outdir.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.sqlite"))
     assert len(files) == 1
 
 
-def test_run_multi_element(tmp_path: Path) -> None:
+def test_run_multi_element_multi_output(
-    """Test run function with multi element.
+    tmp_path: Path,
+    datagrabber: Dict[str, str],
+    markers: List[Dict[str, str]],
+    storage: Dict[str, str],
+) -> None:
+    """Test run function with multi element and multi output.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
 
     """
-    # Create working directory
+    # Set storage
-    workdir = tmp_path / "workdir_multi"
+    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
-    workdir.mkdir()
-    # Create output directory
-    outdir = workdir / "out"
-    outdir.mkdir()
-    # Create storage
-    uri = outdir / "test.sqlite"
-    storage["uri"] = uri  # type: ignore
     storage["single_output"] = False  # type: ignore
     # Run operations
     run(
-        workdir=workdir,
+        workdir=tmp_path,
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
         elements=["sub-01", "sub-03"],
     )
     # Check files
-    files = list(outdir.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.sqlite"))
     assert len(files) == 2
 
 
-def test_run_multi_element_single_output(tmp_path: Path) -> None:
+def test_run_multi_element_single_output(
-    """Test run function with multi element.
+    tmp_path: Path,
+    datagrabber: Dict[str, str],
+    markers: List[Dict[str, str]],
+    storage: Dict[str, str],
+) -> None:
+    """Test run function with multi element and single output.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
 
     """
-    # Create working directory
+    # Set storage
-    workdir = tmp_path / "workdir_multi"
+    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
-    workdir.mkdir()
-    # Create output directory
-    outdir = workdir / "out"
-    outdir.mkdir()
-    # Create storage
-    uri = outdir / "test.sqlite"
-    storage["uri"] = uri  # type: ignore
     storage["single_output"] = True  # type: ignore
     # Run operations
     run(
-        workdir=workdir,
+        workdir=tmp_path,
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
         elements=["sub-01", "sub-03"],
     )
     # Check files
-    files = list(outdir.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.sqlite"))
     assert len(files) == 1
-    assert files[0].name == "test.sqlite"
+    assert files[0].name == "out.sqlite"
 
 
-def test_run_and_collect(tmp_path: Path) -> None:
+def test_run_and_collect(
+    tmp_path: Path,
+    datagrabber: Dict[str, str],
+    markers: List[Dict[str, str]],
+    storage: Dict[str, str],
+) -> None:
     """Test run and collect functions.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
 
     """
-    # Create working directory
+    # Set storage
-    workdir = tmp_path / "workdir"
+    uri = tmp_path / "out.sqlite"
-    workdir.mkdir()
+    storage["uri"] = str(uri.resolve())
-    # Create output directory
-    outdir = workdir / "out"
-    outdir.mkdir()
-    # Create storage
-    uri = outdir / "test.sqlite"
-    storage["uri"] = uri  # type: ignore
     storage["single_output"] = False  # type: ignore
     # Run operations
     run(
-        workdir=workdir,
+        workdir=tmp_path,
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
@@ -225,7 +245,7 @@ def test_run_and_collect(tmp_path: Path) -> None:
     )
     elements = dg.get_elements()  # type: ignore
     # This should create 10 files
-    files = list(outdir.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.sqlite"))
     assert len(files) == len(elements)
     # But the test.sqlite file should not exist
     assert not uri.exists()
@@ -239,6 +259,9 @@ def test_queue_correct_yaml_config(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
+    datagrabber: Dict[str, str],
+    markers: List[Dict[str, str]],
+    storage: Dict[str, str],
 ) -> None:
     """Test proper YAML config generation for queueing.
 
@@ -250,6 +273,12 @@ def test_queue_correct_yaml_config(
         The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
         The pytest.LogCaptureFixture object.
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
 
     """
     with monkeypatch.context() as m:
@@ -261,7 +290,7 @@ def test_queue_correct_yaml_config(
                     "workdir": str(tmp_path.resolve()),
                     "datagrabber": datagrabber,
                     "markers": markers,
-                    "storage": {"kind": "SQLiteFeatureStorage"},
+                    "storage": storage,
                     "env": {
                         "kind": "conda",
                         "name": "junifer",
@@ -479,6 +508,7 @@ def test_queue_without_elements(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
+    datagrabber: Dict[str, str],
 ) -> None:
     """Test queue without elements.
 
@@ -490,6 +520,8 @@ def test_queue_without_elements(
         The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
         The pytest.LogCaptureFixture object.
+    datagrabber : dict
+        Testing datagrabber as dictionary.
 
     """
     with monkeypatch.context() as m:
@@ -502,13 +534,24 @@ def test_queue_without_elements(
             assert "Queue done" in caplog.text
 
 
-def test_reset_run(tmp_path: Path) -> None:
+def test_reset_run(
+    tmp_path: Path,
+    datagrabber: Dict[str, str],
+    markers: List[Dict[str, str]],
+    storage: Dict[str, str],
+) -> None:
     """Test reset function for run.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
 
     """
     # Create storage
@@ -535,7 +578,12 @@ def test_reset_run(tmp_path: Path) -> None:
     ),
 )
 def test_reset_queue(
-    tmp_path: Path, monkeypatch: pytest.MonkeyPatch, job_name: str
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+    datagrabber: Dict[str, str],
+    markers: List[Dict[str, str]],
+    storage: Dict[str, str],
+    job_name: str,
 ) -> None:
     """Test reset function for queue.
 
@@ -545,6 +593,12 @@ def test_reset_queue(
         The path to the test directory.
     monkeypatch : pytest.MonkeyPatch
         The pytest.MonkeyPatch object.
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
     job_name : str
         The parametrized job name.
 

junifer/data/coordinates.py

@@ -138,7 +138,7 @@ def register_coordinates(
     voi_names : list of str
         The names of the VOIs.
     space : str
-        The space of the coordinates.
+        The space of the coordinates, for e.g., "MNI".
     overwrite : bool, optional
         If True, overwrite an existing list of coordinates with the same name.
         Does not apply to built-in coordinates (default False).

junifer/data/masks.py

@@ -20,16 +20,16 @@ from typing import (
 import nibabel as nib
 import numpy as np
 from nilearn.datasets import fetch_icbm152_brain_gm_mask
-from nilearn.image import resample_to_img
+from nilearn.image import get_data, new_img_like, resample_to_img
 from nilearn.masking import (
     compute_background_mask,
-    compute_brain_mask,
     compute_epi_mask,
     intersect_masks,
 )
 
 from ..pipeline import WorkDirManager
-from ..utils import logger, raise_error, run_ext_cmd
+from ..utils import logger, raise_error, run_ext_cmd, warn_with_log
+from .template_spaces import get_template, get_xfm
 from .utils import closest_resolution
 
 
@@ -40,10 +40,91 @@ if TYPE_CHECKING:
 _masks_path = Path(__file__).parent / "masks"
 
 
+def compute_brain_mask(
+    target_data: Dict[str, Any],
+    extra_input: Optional[Dict[str, Any]] = None,
+    mask_type: str = "brain",
+    threshold: float = 0.5,
+) -> "Nifti1Image":
+    """Compute the whole-brain, grey-matter or white-matter mask.
+
+    This mask is calculated using the template space and resolution as found
+    in the ``target_data``.
+
+    Parameters
+    ----------
+    target_data : dict
+        The corresponding item of the data object for which mask will be
+        loaded.
+    extra_input : dict, optional
+        The other fields in the data object. Useful for accessing other data
+        types (default None).
+    mask_type : {"brain", "gm", "wm"}, optional
+        Type of mask to be computed:
+
+        * "brain" : whole-brain mask
+        * "gm" : grey-matter mask
+        * "wm" : white-matter mask
+
+        (default "brain").
+    threshold : float, optional
+        The value under which the template is cut off (default 0.5).
+
+    Returns
+    -------
+    Nifti1Image
+        The mask (3D image).
+
+    Raises
+    ------
+    ValueError
+        If ``mask_type`` is invalid or
+        if ``extra_input`` is None when ``target_data``'s space is native.
+
+    """
+    logger.debug(f"Computing {mask_type} mask")
+
+    if mask_type not in ["brain", "gm", "wm"]:
+        raise_error(f"Unknown mask type: {mask_type}")
+
+    # Check pre-requirements for space manipulation
+    target_space = target_data["space"]
+    # Set target standard space to target space
+    target_std_space = target_space
+    # Extra data type requirement check if target space is native
+    if target_space == "native":
+        # Check for extra inputs
+        if extra_input is None:
+            raise_error(
+                "No extra input provided, requires `Warp` "
+                "data type to infer target template space."
+            )
+        # Set target standard space to warp file space source
+        target_std_space = extra_input["Warp"]["src"]
+
+    # Fetch template in closest resolution
+    template = get_template(
+        space=target_std_space,
+        target_data=target_data,
+        extra_input=extra_input,
+        template_type=mask_type if mask_type in ["gm", "wm"] else "T1w",
+    )
+    # Resample template to target image
+    target_img = target_data["data"]
+    resampled_template = resample_to_img(
+        source_img=template, target_img=target_img
+    )
+
+    # Threshold and get mask
+    mask = (get_data(resampled_template) >= threshold).astype("int8")
+
+    return new_img_like(target_img, mask)  # type: ignore
+
+
 def _fetch_icbm152_brain_gm_mask(
     target_img: "Nifti1Image",
     **kwargs,
-):
+) -> "Nifti1Image":
     """Fetch ICBM152 brain mask and resample.
 
     Parameters
@@ -59,7 +140,20 @@ def _fetch_icbm152_brain_gm_mask(
     nibabel.Nifti1Image
         The resampled mask.
 
+    Warns
+    -----
+    DeprecationWarning
+        If this function is used.
+
     """
+    warn_with_log(
+        msg=(
+            "It is recommended to use ``compute_brain_mask`` with "
+            "``mask_type='gm'``. This function will be removed in the next "
+            "release. For now, it's available for backward compatibility."
+        ),
+        category=DeprecationWarning,
+    )
     mask = fetch_icbm152_brain_gm_mask(**kwargs)
     mask = resample_to_img(
         mask, target_img, interpolation="nearest", copy=True
@@ -123,7 +217,7 @@ def register_mask(
     mask_path : str or pathlib.Path
         The path to the mask file.
     space : str
-        The space of the mask.
+        The space of the mask, for e.g., "MNI152NLin6Asym".
     overwrite : bool, optional
         If True, overwrite an existing mask with the same name.
         Does not apply to built-in mask (default False).
@@ -198,30 +292,45 @@ def get_mask(  # noqa: C901
     Raises
     ------
     RuntimeError
-        If masks are in different spaces and they need to be intersected /
+        If warp / transformation file extension is not ".mat" or ".h5" or
-        unionized or
+        if fetch_icbm152_brain_gm_mask is used and requires warping to
-        if warp / transformation file extension is not ".mat" or ".h5".
+        other template space.
     ValueError
         If extra key is provided in addition to mask name in ``masks`` or
         if no mask is provided or
         if ``masks = "inherit"`` but ``extra_input`` is None or ``mask_item``
         is None or ``mask_items``'s value is not in ``extra_input`` or
         if callable parameters are passed to non-callable mask or
-        if multiple masks are provided and their spaces do not match or
         if parameters are passed to :func:`nilearn.masking.intersect_masks`
         when there is only one mask or
         if ``extra_input`` is None when ``target_data``'s space is native.
 
     """
+    # Check pre-requirements for space manipulation
+    target_space = target_data["space"]
+    # Set target standard space to target space
+    target_std_space = target_space
+    # Extra data type requirement check if target space is native
+    if target_space == "native":
+        # Check for extra inputs
+        if extra_input is None:
+            raise_error(
+                "No extra input provided, requires `Warp` and `T1w` "
+                "data types in particular for transformation to "
+                f"{target_data['space']} space for further computation."
+            )
+        # Set target standard space to warp file space source
+        target_std_space = extra_input["Warp"]["src"]
+
     # Get the min of the voxels sizes and use it as the resolution
     target_img = target_data["data"]
-    inherited_mask_item = target_data.get("mask_item", None)
     resolution = np.min(target_img.header.get_zooms()[:3])
 
+    # Convert masks to list if not already
     if not isinstance(masks, list):
         masks = [masks]
 
-    # Check that dicts have only one key
+    # Check that masks passed as dicts have only one key
     invalid_elements = [
         x for x in masks if isinstance(x, dict) and len(x) != 1
     ]
@@ -248,9 +357,19 @@ def get_mask(  # noqa: C901
 
     if len(true_masks) == 0:
         raise_error("No mask was passed. At least one mask is required.")
+
+    # Get the data type for the input data type's mask
+    inherited_mask_item = target_data.get("mask_item", None)
+
+    # Create component-scoped tempdir
+    tempdir = WorkDirManager().get_tempdir(prefix="masks")
+    # Create element-scoped tempdir so that warped mask is
+    # available later as nibabel stores file path reference for
+    # loading on computation
+    element_tempdir = WorkDirManager().get_element_tempdir(prefix="masks")
+
     # Get all the masks
     all_masks = []
-    all_spaces = []
     for t_mask in true_masks:
         if isinstance(t_mask, dict):
             mask_name = next(iter(t_mask.keys()))
@@ -281,21 +400,40 @@ def get_mask(  # noqa: C901
                     f"because the item ({inherited_mask_item}) does not exist."
                 )
             mask_img = extra_input[inherited_mask_item]["data"]
-            mask_space = target_data["space"]
         # Starting with new mask
         else:
+            # Restrict fetch_icbm152_brain_gm_mask if target std space doesn't
+            # match
+            if (
+                mask_name == "fetch_icbm152_brain_gm_mask"
+                and target_std_space != "MNI152NLin2009aAsym"
+            ):
+                raise_error(
+                    (
+                        "``fetch_icbm152_brain_gm_mask`` is deprecated and "
+                        "space transformation to any other template space is "
+                        "prohibited as it will lead to unforeseen errors. "
+                        "``compute_brain_mask`` is a better alternative."
+                    ),
+                    klass=RuntimeError,
+                )
             # Load mask
             mask_object, _, mask_space = load_mask(
                 mask_name, path_only=False, resolution=resolution
             )
             # Replace mask space with target space if mask's space is inherit
             if mask_space == "inherit":
-                mask_space = target_data["space"]
+                mask_space = target_std_space
             # If mask is callable like from nilearn
             if callable(mask_object):
                 if mask_params is None:
                     mask_params = {}
-                mask_img = mask_object(target_img, **mask_params)
+                # From nilearn
+                if mask_name != "compute_brain_mask":
+                    mask_img = mask_object(target_img, **mask_params)
+                # Not from nilearn
+                else:
+                    mask_img = mask_object(target_data, **mask_params)
             # Mask is a Nifti1Image
             else:
                 # Mask params provided
@@ -306,31 +444,69 @@ def get_mask(  # noqa: C901
                     )
                 # Resample mask to target image
                 mask_img = resample_to_img(
-                    mask_object,
+                    source_img=mask_object,
-                    target_img,
+                    target_img=target_img,
                     interpolation="nearest",
                     copy=True,
                 )
-        all_spaces.append(mask_space)
+            # Convert mask space if required
+            if mask_space != target_std_space:
+                # Get xfm file
+                xfm_file_path = get_xfm(src=mask_space, dst=target_std_space)
+                # Get target standard space template
+                target_std_space_template_img = get_template(
+                    space=target_std_space,
+                    target_data=target_data,
+                    extra_input=extra_input,
+                )
+
+                # Save mask image to a component-scoped tempfile
+                mask_path = tempdir / f"{mask_name}.nii.gz"
+                nib.save(mask_img, mask_path)
+
+                # Save template
+                target_std_space_template_path = (
+                    tempdir / f"{target_std_space}_T1w_{resolution}.nii.gz"
+                )
+                nib.save(
+                    target_std_space_template_img,
+                    target_std_space_template_path,
+                )
+
+                # Set warped mask path
+                warped_mask_path = element_tempdir / (
+                    f"{mask_name}_warped_from_{mask_space}_to_"
+                    f"{target_std_space}.nii.gz"
+                )
+
+                logger.debug(
+                    f"Using ANTs to warp {mask_name} "
+                    f"from {mask_space} to {target_std_space}"
+                )
+                # Set antsApplyTransforms command
+                apply_transforms_cmd = [
+                    "antsApplyTransforms",
+                    "-d 3",
+                    "-e 3",
+                    "-n 'GenericLabel[NearestNeighbor]'",
+                    f"-i {mask_path.resolve()}",
+                    f"-r {target_std_space_template_path.resolve()}",
+                    f"-t {xfm_file_path.resolve()}",
+                    f"-o {warped_mask_path.resolve()}",
+                ]
+                # Call antsApplyTransforms
+                run_ext_cmd(
+                    name="antsApplyTransforms", cmd=apply_transforms_cmd
+                )
+
+                mask_img = nib.load(warped_mask_path)
+
         all_masks.append(mask_img)
 
     # Multiple masks, need intersection / union
     if len(all_masks) > 1:
-        # Make a set of unique spaces
+        # Intersect / union of masks
-        unique_spaces = set(all_spaces)
+        mask_img = intersect_masks(all_masks, **intersect_params)
-        # Intersect / union of masks only if all masks are in the same space
-        if len(unique_spaces) == 1:
-            mask_img = intersect_masks(all_masks, **intersect_params)
-            # Store the mask space for further checks
-            mask_space = next(iter(unique_spaces))
-        else:
-            raise_error(
-                msg=(
-                    f"Masks are in different spaces: {unique_spaces}, "
-                    "unable to merge."
-                ),
-                klass=RuntimeError,
-            )
     # Single mask
     else:
         if len(intersect_params) > 0:
@@ -340,30 +516,13 @@ def get_mask(  # noqa: C901
                 "when there is only one mask."
             )
         mask_img = all_masks[0]
-        mask_space = all_spaces[0]
-
-    # Warp mask if target data is native and mask space is not native
-    if target_data["space"] == "native" and target_data["space"] != mask_space:
-        # Check for extra inputs
-        if extra_input is None:
-            raise_error(
-                "No extra input provided, requires `Warp` and `T1w` "
-                "data types in particular for transformation to "
-                f"{target_data['space']} space for further computation."
-            )
-
-        # Create component-scoped tempdir
-        tempdir = WorkDirManager().get_tempdir(prefix="masks")
 
+    # Warp mask if target data is native
+    if target_space == "native":
         # Save mask image to a component-scoped tempfile
         prewarp_mask_path = tempdir / "prewarp_mask.nii.gz"
         nib.save(mask_img, prewarp_mask_path)
 
-        # Create element-scoped tempdir so that warped mask is
-        # available later as nibabel stores file path reference for
-        # loading on computation
-        element_tempdir = WorkDirManager().get_element_tempdir(prefix="masks")
-
         # Create an element-scoped tempfile for warped output
         warped_mask_path = element_tempdir / "mask_warped.nii.gz"
 
@@ -413,8 +572,8 @@ def get_mask(  # noqa: C901
         # Load nifti
         mask_img = nib.load(warped_mask_path)
 
-        # Delete tempdir
+    # Delete tempdir
-        WorkDirManager().delete_tempdir(tempdir)
+    WorkDirManager().delete_tempdir(tempdir)
 
     return mask_img  # type: ignore
 

junifer/data/parcellations.py

@@ -22,6 +22,7 @@ from nilearn import datasets, image
 
 from ..pipeline import WorkDirManager
 from ..utils import logger, raise_error, run_ext_cmd, warn_with_log
+from .template_spaces import get_template, get_xfm
 from .utils import closest_resolution
 
 
@@ -154,7 +155,7 @@ def register_parcellation(
     parcels_labels : list of str
         The list of labels for the parcellation.
     space : str
-        The space of the parcellation.
+        The template space of the parcellation, for e.g., "MNI152NLin6Asym".
     overwrite : bool, optional
         If True, overwrite an existing parcellation with the same name.
         Does not apply to built-in parcellations (default False).
@@ -236,57 +237,17 @@ def get_parcellation(
     Raises
     ------
     RuntimeError
-        If parcellations are in different spaces and they need to be merged or
+        If warp / transformation file extension is not ".mat" or ".h5".
-        if warp / transformation file extension is not ".mat" or ".h5".
     ValueError
         If ``extra_input`` is None when ``target_data``'s space is native.
 
     """
-    # Get the min of the voxels sizes and use it as the resolution
+    # Check pre-requirements for space manipulation
-    target_img = target_data["data"]
+    target_space = target_data["space"]
-    resolution = np.min(target_img.header.get_zooms()[:3])
+    # Set target standard space to target space
-
+    target_std_space = target_space
-    # Load the parcellations
+    # Extra data type requirement check if target space is native
-    all_parcellations = []
+    if target_space == "native":
-    all_labels = []
-    all_spaces = []
-    for name in parcellation:
-        img, labels, _, space = load_parcellation(
-            name=name,
-            resolution=resolution,
-        )
-        # Resample all of them to the image
-        resampled_img = image.resample_to_img(
-            source_img=img,
-            target_img=target_img,
-            interpolation="nearest",
-            copy=True,
-        )
-        all_parcellations.append(resampled_img)
-        all_labels.append(labels)
-        all_spaces.append(space)
-
-    # Avoid merging if there is only one parcellation
-    if len(all_parcellations) == 1:
-        resampled_parcellation_img = all_parcellations[0]
-        labels = all_labels[0]
-    else:
-        # Merge the parcellations only if all parcellations are in the same
-        # space
-        if len(set(all_spaces)) == 1:
-            resampled_parcellation_img, labels = merge_parcellations(
-                parcellations_list=all_parcellations,
-                parcellations_names=parcellation,
-                labels_lists=all_labels,
-            )
-        else:
-            raise_error(
-                msg="Parcellations are in different spaces, unable to merge.",
-                klass=RuntimeError,
-            )
-
-    # Warp parcellation if target data is native
-    if target_data["space"] == "native":
         # Check for extra inputs
         if extra_input is None:
             raise_error(
@@ -294,20 +255,108 @@ def get_parcellation(
                 "data types in particular for transformation to "
                 f"{target_data['space']} space for further computation."
             )
+        # Set target standard space to warp file space source
+        target_std_space = extra_input["Warp"]["src"]
 
-        # Create component-scoped tempdir
+    # Get the min of the voxels sizes and use it as the resolution
-        tempdir = WorkDirManager().get_tempdir(prefix="parcellations")
+    target_img = target_data["data"]
+    resolution = np.min(target_img.header.get_zooms()[:3])
 
+    # Create component-scoped tempdir
+    tempdir = WorkDirManager().get_tempdir(prefix="parcellations")
+    # Create element-scoped tempdir so that warped parcellation is
+    # available later as nibabel stores file path reference for
+    # loading on computation
+    element_tempdir = WorkDirManager().get_element_tempdir(
+        prefix="parcellations"
+    )
+
+    # Load the parcellations
+    all_parcellations = []
+    all_labels = []
+    for name in parcellation:
+        img, labels, _, space = load_parcellation(
+            name=name,
+            resolution=resolution,
+        )
+
+        # Convert parcellation spaces if required
+        if space != target_std_space:
+            # Get xfm file
+            xfm_file_path = get_xfm(src=space, dst=target_std_space)
+            # Get target standard space template
+            target_std_space_template_img = get_template(
+                space=target_std_space,
+                target_data=target_data,
+                extra_input=extra_input,
+            )
+
+            # Save parcellation image to a component-scoped tempfile
+            parcellation_path = tempdir / f"{name}.nii.gz"
+            nib.save(img, parcellation_path)
+
+            # Save template
+            target_std_space_template_path = (
+                tempdir / f"{target_std_space}_T1w_{resolution}.nii.gz"
+            )
+            nib.save(
+                target_std_space_template_img, target_std_space_template_path
+            )
+
+            # Set warped parcellation path
+            warped_parcellation_path = element_tempdir / (
+                f"{name}_warped_from_{space}_to_" f"{target_std_space}.nii.gz"
+            )
+
+            logger.debug(
+                f"Using ANTs to warp {name} "
+                f"from {space} to {target_std_space}"
+            )
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n 'GenericLabel[NearestNeighbor]'",
+                f"-i {parcellation_path.resolve()}",
+                f"-r {target_std_space_template_path.resolve()}",
+                f"-t {xfm_file_path.resolve()}",
+                f"-o {warped_parcellation_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+            img = nib.load(warped_parcellation_path)
+
+        # Resample parcellation to target image
+        img_to_merge = image.resample_to_img(
+            source_img=img,
+            target_img=target_img,
+            interpolation="nearest",
+            copy=True,
+        )
+
+        all_parcellations.append(img_to_merge)
+        all_labels.append(labels)
+
+    # Avoid merging if there is only one parcellation
+    if len(all_parcellations) == 1:
+        resampled_parcellation_img = all_parcellations[0]
+        labels = all_labels[0]
+    # Parcellations are already transformed to target standard space
+    else:
+        resampled_parcellation_img, labels = merge_parcellations(
+            parcellations_list=all_parcellations,
+            parcellations_names=parcellation,
+            labels_lists=all_labels,
+        )
+
+    # Warp parcellation if target space is native
+    if target_space == "native":
         # Save parcellation image to a component-scoped tempfile
         prewarp_parcellation_path = tempdir / "prewarp_parcellation.nii.gz"
         nib.save(resampled_parcellation_img, prewarp_parcellation_path)
 
-        # Create element-scoped tempdir so that warped parcellation is
-        # available later as nibabel stores file path reference for
-        # loading on computation
-        element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="parcellations"
-        )
         # Create an element-scoped tempfile for warped output
         warped_parcellation_path = (
             element_tempdir / "parcellation_warped.nii.gz"
@@ -359,8 +408,8 @@ def get_parcellation(
         # Load nifti
         resampled_parcellation_img = nib.load(warped_parcellation_path)
 
-        # Delete tempdir
+    # Delete tempdir
-        WorkDirManager().delete_tempdir(tempdir)
+    WorkDirManager().delete_tempdir(tempdir)
 
     return resampled_parcellation_img, labels  # type: ignore
 

junifer/data/template_spaces.py

@@ -99,6 +99,7 @@ def get_template(
     space: str,
     target_data: Dict[str, Any],
     extra_input: Optional[Dict[str, Any]] = None,
+    template_type: str = "T1w",
 ) -> nib.Nifti1Image:
     """Get template for the space, tailored for the target image.
 
@@ -112,6 +113,8 @@ def get_template(
     extra_input : dict, optional
         The other fields in the data object. Useful for accessing other data
         types (default None).
+    template_type : {"T1w", "brain", "gm", "wm", "csf"}, optional
+        The template type to retrieve (default "T1w").
 
     Returns
     -------
@@ -121,15 +124,19 @@ def get_template(
     Raises
     ------
     ValueError
-        If ``space`` is invalid.
+        If ``space`` or ``template_type`` is invalid.
     RuntimeError
-        If template in the required resolution is not found.
+        If required template is not found.
 
     """
     # Check for invalid space; early check to raise proper error
     if space not in tflow.templates():
         raise_error(f"Unknown template space: {space}")
 
+    # Check for template type
+    if template_type not in ["T1w", "brain", "gm", "wm", "csf"]:
+        raise_error(f"Unknown template type: {template_type}")
+
     # Get the min of the voxels sizes and use it as the resolution
     target_img = target_data["data"]
     resolution = np.min(target_img.header.get_zooms()[:3]).astype(int)
@@ -145,18 +152,38 @@ def get_template(
     logger.info(f"Downloading template {space} in resolution {resolution}")
     # Retrieve template
     try:
+        suffix = None
+        desc = None
+        label = None
+        if template_type == "T1w":
+            suffix = template_type
+            desc = None
+            label = None
+        elif template_type == "brain":
+            suffix = "mask"
+            desc = "brain"
+            label = None
+        elif template_type in ["gm", "wm", "csf"]:
+            suffix = "probseg"
+            desc = None
+            label = template_type.upper()
+        # Set kwargs for fetching
+        kwargs = {
+            "suffix": suffix,
+            "desc": desc,
+            "label": label,
+        }
         template_path = tflow.get(
             space,
             raise_empty=True,
             resolution=resolution,
-            suffix="T1w",
-            desc=None,
             extension="nii.gz",
+            **kwargs,
         )
     except Exception:  # noqa: BLE001
         raise_error(
-            f"Template {space} not found in the required resolution "
+            f"Template {space} ({template_type}) with resolution {resolution} "
-            f"{resolution}",
+            "not found",
             klass=RuntimeError,
         )
     else:

junifer/data/tests/test_masks.py

@@ -5,16 +5,16 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import socket
 from pathlib import Path
 from typing import Callable, Dict, List, Optional, Union
 
+import nibabel as nib
 import numpy as np
 import pytest
-from nilearn.datasets import fetch_icbm152_brain_gm_mask
 from nilearn.image import resample_to_img
 from nilearn.masking import (
     compute_background_mask,
-    compute_brain_mask,
     compute_epi_mask,
     intersect_masks,
 )
@@ -23,18 +23,96 @@ from numpy.testing import assert_array_almost_equal, assert_array_equal
 from junifer.data.masks import (
     _available_masks,
     _load_vickery_patil_mask,
+    compute_brain_mask,
     get_mask,
     list_masks,
     load_mask,
     register_mask,
 )
+from junifer.datagrabber import DMCC13Benchmark
 from junifer.datareader import DefaultDataReader
 from junifer.testing.datagrabbers import (
     OasisVBMTestingDataGrabber,
+    PartlyCloudyTestingDataGrabber,
     SPMAuditoryTestingDataGrabber,
 )
 
 
+@pytest.mark.parametrize(
+    "mask_type, threshold",
+    [
+        ("brain", 0.2),
+        ("brain", 0.5),
+        ("brain", 0.8),
+        ("gm", 0.2),
+        ("gm", 0.5),
+        ("gm", 0.8),
+        ("wm", 0.2),
+        ("wm", 0.5),
+        ("wm", 0.8),
+    ],
+)
+def test_compute_brain_mask(mask_type: str, threshold: float) -> None:
+    """Test compute_brain_mask().
+
+    Parameters
+    ----------
+    mask_type : str
+        The parametrized mask type.
+    threshold : float
+        The parametrized threshold.
+
+    """
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        mask = compute_brain_mask(
+            target_data=element_data["BOLD"],
+            extra_input=None,
+            mask_type=mask_type,
+        )
+        assert isinstance(mask, nib.Nifti1Image)
+
+
+@pytest.mark.skipif(
+    socket.gethostname() != "juseless",
+    reason="only for juseless",
+)
+@pytest.mark.parametrize(
+    "mask_type",
+    [
+        "brain",
+        "gm",
+        "wm",
+    ],
+)
+def test_compute_brain_mask_for_native(mask_type: str) -> None:
+    """Test compute_brain_mask().
+
+    Parameters
+    ----------
+    mask_type : str
+        The parametrized mask type.
+
+    """
+    with DMCC13Benchmark(
+        types=["BOLD"],
+        sessions=["wave1bas"],
+        tasks=["Rest"],
+        phase_encodings=["AP"],
+        runs=["1"],
+        native_t1w=True,
+    ) as dg:
+        element_data = DefaultDataReader().fit_transform(
+            dg[("f1031ax", "wave1bas", "Rest", "AP", "1")]
+        )
+        mask = compute_brain_mask(
+            target_data=element_data["BOLD"],
+            extra_input=None,
+            mask_type=mask_type,
+        )
+        assert isinstance(mask, nib.Nifti1Image)
+
+
 def test_register_mask_built_in_check() -> None:
     """Test mask registration check for built-in masks."""
     with pytest.raises(ValueError, match=r"built-in mask"):
@@ -215,18 +293,19 @@ def test_vickery_patil_error() -> None:
 
 def test_get_mask() -> None:
     """Test the get_mask function."""
-    reader = DefaultDataReader()
     with OasisVBMTestingDataGrabber() as dg:
-        input = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        input = reader.fit_transform(input)
+        vbm_gm = element_data["VBM_GM"]
-        vbm_gm = input["VBM_GM"]
         vbm_gm_img = vbm_gm["data"]
-        mask = get_mask(masks="GM_prob0.2", target_data=vbm_gm)
+        mask = get_mask(masks="compute_brain_mask", target_data=vbm_gm)
 
         assert mask.shape == vbm_gm_img.shape
         assert_array_equal(mask.affine, vbm_gm_img.affine)
 
-        raw_mask_img, _, _ = load_mask("GM_prob0.2", resolution=1.5)
+        raw_mask_callable, _, _ = load_mask(
+            "compute_brain_mask", resolution=1.5
+        )
+        raw_mask_img = raw_mask_callable(vbm_gm)  # type: ignore
         res_mask_img = resample_to_img(
             raw_mask_img,
             vbm_gm_img,
@@ -245,13 +324,11 @@ def test_mask_callable() -> None:
     _available_masks["identity"] = {
         "family": "Callable",
         "func": ident,
-        "space": "MNI",
+        "space": "MNI152Lin",
     }
-    reader = DefaultDataReader()
     with OasisVBMTestingDataGrabber() as dg:
-        input = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        input = reader.fit_transform(input)
+        vbm_gm = element_data["VBM_GM"]
-        vbm_gm = input["VBM_GM"]
         vbm_gm_img = vbm_gm["data"]
         mask = get_mask(masks="identity", target_data=vbm_gm)
 
@@ -262,11 +339,9 @@ def test_mask_callable() -> None:
 
 def test_get_mask_errors() -> None:
     """Test passing wrong parameters to get_mask."""
-    reader = DefaultDataReader()
     with OasisVBMTestingDataGrabber() as dg:
-        input = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        input = reader.fit_transform(input)
+        vbm_gm = element_data["VBM_GM"]
-        vbm_gm = input["VBM_GM"]
         # Test wrong masks definitions (more than one key per dict)
         with pytest.raises(ValueError, match=r"only one key"):
             get_mask(masks={"GM_prob0.2": {}, "Other": {}}, target_data=vbm_gm)
@@ -286,7 +361,8 @@ def test_get_mask_errors() -> None:
             ValueError, match=r"parameters to the intersection"
         ):
             get_mask(
-                masks=["GM_prob0.2", {"threshold": 1}], target_data=vbm_gm
+                masks=["compute_brain_mask", {"threshold": 1}],
+                target_data=vbm_gm,
             )
 
         # Test "inherited" masks errors
@@ -310,19 +386,20 @@ def test_get_mask_errors() -> None:
                 masks="inherit", target_data=vbm_gm, extra_input=extra_input
             )
 
+        # Block fetch_icbm152_brain_gm_mask space transformation
+        with pytest.raises(RuntimeError, match="prohibited"):
+            get_mask(
+                masks="fetch_icbm152_brain_gm_mask",
+                target_data=vbm_gm,
+                extra_input=extra_input,
+            )
+
 
 @pytest.mark.parametrize(
     "mask_name,function,params,resample",
     [
-        ("compute_brain_mask", compute_brain_mask, {"threshold": 0.2}, False),
         ("compute_background_mask", compute_background_mask, None, False),
         ("compute_epi_mask", compute_epi_mask, None, False),
-        (
-            "fetch_icbm152_brain_gm_mask",
-            fetch_icbm152_brain_gm_mask,
-            None,
-            True,
-        ),
     ],
 )
 def test_nilearn_compute_masks(
@@ -345,11 +422,9 @@ def test_nilearn_compute_masks(
         Whether to resample the mask to the target data.
 
     """
-    reader = DefaultDataReader()
     with SPMAuditoryTestingDataGrabber() as dg:
-        input = dg["sub001"]
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-        input = reader.fit_transform(input)
+        bold = element_data["BOLD"]
-        bold = input["BOLD"]
         bold_img = bold["data"]
 
         if params is None:
@@ -378,27 +453,30 @@ def test_nilearn_compute_masks(
 
 def test_get_mask_inherit() -> None:
     """Test using the inherit mask functionality."""
-    reader = DefaultDataReader()
     with SPMAuditoryTestingDataGrabber() as dg:
-        input = dg["sub001"]
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-        input = reader.fit_transform(input)
         # Compute brain mask using nilearn
-        gm_mask = compute_brain_mask(input["BOLD"]["data"], threshold=0.2)
+        gm_mask = compute_brain_mask(element_data["BOLD"], threshold=0.2)
 
         # Get mask using the compute_brain_mask function
         mask1 = get_mask(
             masks={"compute_brain_mask": {"threshold": 0.2}},
-            target_data=input["BOLD"],
+            target_data=element_data["BOLD"],
         )
 
         # Now get the mask using the inherit functionality, passing the
         # computed mask as extra data
         extra_input = {
-            "BOLD_MASK": {"data": gm_mask, "space": input["BOLD"]["space"]}
+            "BOLD_MASK": {
+                "data": gm_mask,
+                "space": element_data["BOLD"]["space"],
+            }
         }
-        input["BOLD"]["mask_item"] = "BOLD_MASK"
+        element_data["BOLD"]["mask_item"] = "BOLD_MASK"
         mask2 = get_mask(
-            masks="inherit", target_data=input["BOLD"], extra_input=extra_input
+            masks="inherit",
+            target_data=element_data["BOLD"],
+            extra_input=extra_input,
         )
 
         # Both masks should be equal
@@ -408,7 +486,6 @@ def test_get_mask_inherit() -> None:
 @pytest.mark.parametrize(
     "masks,params",
     [
-        (["GM_prob0.2", "GM_prob0.2_cortex"], {}),
         (["compute_brain_mask", "compute_background_mask"], {}),
         (["compute_brain_mask", "compute_epi_mask"], {}),
     ],
@@ -426,10 +503,8 @@ def test_get_mask_multiple(
         Parameters to pass to the intersect_masks function.
 
     """
-    reader = DefaultDataReader()
     with SPMAuditoryTestingDataGrabber() as dg:
-        input = dg["sub001"]
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-        input = reader.fit_transform(input)
         if not isinstance(masks, list):
             junifer_masks = [masks]
         else:
@@ -438,10 +513,12 @@ def test_get_mask_multiple(
             # Convert params to junifer style (one dict per param)
             junifer_params = [{k: params[k]} for k in params.keys()]
             junifer_masks.extend(junifer_params)
-        target_img = input["BOLD"]["data"]
+        target_img = element_data["BOLD"]["data"]
         resolution = np.min(target_img.header.get_zooms()[:3])
 
-        computed = get_mask(masks=junifer_masks, target_data=input["BOLD"])
+        computed = get_mask(
+            masks=junifer_masks, target_data=element_data["BOLD"]
+        )
 
         masks_names = [
             next(iter(x.keys())) if isinstance(x, dict) else x for x in masks
@@ -464,7 +541,13 @@ def test_get_mask_multiple(
         ]
 
         for t_func in mask_funcs:
-            mask_imgs.append(_available_masks[t_func]["func"](target_img))
+            # Bypass for custom mask
+            if t_func == "compute_brain_mask":
+                mask_imgs.append(
+                    _available_masks[t_func]["func"](element_data["BOLD"])
+                )
+            else:
+                mask_imgs.append(_available_masks[t_func]["func"](target_img))
 
         mask_imgs = [
             resample_to_img(
@@ -478,21 +561,3 @@ def test_get_mask_multiple(
 
         expected = intersect_masks(mask_imgs, **params)
         assert_array_equal(computed.get_fdata(), expected.get_fdata())
-
-
-def test_get_mask_multiple_incorrect_space() -> None:
-    """Test incorrect space error for getting multiple masks."""
-    reader = DefaultDataReader()
-    with SPMAuditoryTestingDataGrabber() as dg:
-        input = dg["sub001"]
-        input = reader.fit_transform(input)
-
-        with pytest.raises(RuntimeError, match="unable to merge."):
-            get_mask(
-                masks=[
-                    "GM_prob0.2",
-                    "compute_brain_mask",
-                    "fetch_icbm152_brain_gm_mask",
-                ],
-                target_data=input["BOLD"],
-            )

junifer/data/tests/test_parcellations.py

@@ -30,7 +30,11 @@ from junifer.data.parcellations import (
     register_parcellation,
 )
 from junifer.datareader import DefaultDataReader
-from junifer.testing.datagrabbers import OasisVBMTestingDataGrabber
+from junifer.pipeline.utils import _check_ants
+from junifer.testing.datagrabbers import (
+    OasisVBMTestingDataGrabber,
+    PartlyCloudyTestingDataGrabber,
+)
 
 
 def test_register_parcellation_built_in_check() -> None:
@@ -58,7 +62,7 @@ def test_register_parcellation_already_registered() -> None:
         name="testparc",
         parcellation_path="testparc.nii.gz",
         parcels_labels=["1", "2", "3"],
-        space="MNI",
+        space="MNI152Lin",
     )
     assert (
         load_parcellation("testparc", path_only=True)[2].name
@@ -71,13 +75,13 @@ def test_register_parcellation_already_registered() -> None:
             name="testparc",
             parcellation_path="testparc.nii.gz",
             parcels_labels=["1", "2", "3"],
-            space="MNI",
+            space="MNI152Lin",
         )
     register_parcellation(
         name="testparc",
         parcellation_path="testparc2.nii.gz",
         parcels_labels=["1", "2", "3"],
-        space="MNI",
+        space="MNI152Lin",
         overwrite=True,
     )
 
@@ -100,14 +104,16 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
     assert schaefer is not None
 
     # Test wrong number of labels
-    register_parcellation("WrongLabels", schaefer_path, labels[:10], "MNI")
+    register_parcellation(
+        "WrongLabels", schaefer_path, labels[:10], "MNI152Lin"
+    )
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 10"):
         load_parcellation("WrongLabels")
 
     # Test wrong number of labels
     register_parcellation(
-        "WrongLabels2", schaefer_path, [*labels, "wrong"], "MNI"
+        "WrongLabels2", schaefer_path, [*labels, "wrong"], "MNI152Lin"
     )
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 101"):
@@ -119,7 +125,9 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
     new_schaefer_img = new_img_like(schaefer, schaefer_data)
     nib.save(new_schaefer_img, new_schaefer_path)
 
-    register_parcellation("WrongValues", new_schaefer_path, labels[:-1], "MNI")
+    register_parcellation(
+        "WrongValues", new_schaefer_path, labels[:-1], "MNI152Lin"
+    )
     with pytest.raises(ValueError, match=r"the range [0, 99]"):
         load_parcellation("WrongValues")
 
@@ -129,7 +137,9 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
     new_schaefer_img = new_img_like(schaefer, schaefer_data)
     nib.save(new_schaefer_img, new_schaefer_path)
 
-    register_parcellation("WrongValues2", new_schaefer_path, labels, "MNI")
+    register_parcellation(
+        "WrongValues2", new_schaefer_path, labels, "MNI152Lin"
+    )
     with pytest.raises(ValueError, match=r"the range [0, 100]"):
         load_parcellation("WrongValues2")
 
@@ -137,13 +147,25 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
 @pytest.mark.parametrize(
     "name, parcellation_path, parcels_labels, space, overwrite",
     [
-        ("testparc_1", "testparc_1.nii.gz", ["1", "2", "3"], "MNI", True),
+        (
-        ("testparc_2", "testparc_2.nii.gz", ["1", "2", "6"], "MNI", True),
+            "testparc_1",
+            "testparc_1.nii.gz",
+            ["1", "2", "3"],
+            "MNI152Lin",
+            True,
+        ),
+        (
+            "testparc_2",
+            "testparc_2.nii.gz",
+            ["1", "2", "6"],
+            "MNI152Lin",
+            True,
+        ),
         (
             "testparc_3",
             Path("testparc_3.nii.gz"),
             ["1", "2", "6"],
-            "MNI",
+            "MNI152Lin",
             True,
         ),
     ],
@@ -1172,28 +1194,26 @@ def test_merge_parcellations_3D_multiple_duplicated_labels() -> None:
 
 def test_get_parcellation_single() -> None:
     """Test tailored single parcellation fetch."""
-    reader = DefaultDataReader()
+    with PartlyCloudyTestingDataGrabber() as dg:
-    with OasisVBMTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        element = dg["sub-01"]
+        bold = element_data["BOLD"]
-        element_data = reader.fit_transform(element)
+        bold_img = bold["data"]
-        vbm_gm = element_data["VBM_GM"]
-        vbm_gm_img = vbm_gm["data"]
         # Get tailored parcellation
         tailored_parcellation, tailored_labels = get_parcellation(
-            parcellation=["Schaefer100x7"],
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
-            target_data=vbm_gm,
+            target_data=bold,
         )
         # Check shape and affine with original element data
-        assert tailored_parcellation.shape == vbm_gm_img.shape
+        assert tailored_parcellation.shape == bold_img.shape[:3]
-        assert_array_equal(tailored_parcellation.affine, vbm_gm_img.affine)
+        assert_array_equal(tailored_parcellation.affine, bold_img.affine)
         # Get raw parcellation
         raw_parcellation, raw_labels, _, _ = load_parcellation(
-            "Schaefer100x7",
+            "TianxS1x3TxMNInonlinear2009cAsym",
             resolution=1.5,
         )
         resampled_raw_parcellation = resample_to_img(
             source_img=raw_parcellation,
-            target_img=vbm_gm_img,
+            target_img=bold_img,
             interpolation="nearest",
             copy=True,
         )
@@ -1207,36 +1227,34 @@ def test_get_parcellation_single() -> None:
 
 def test_get_parcellation_multi_same_space() -> None:
     """Test tailored multi parcellation fetch in same space."""
-    reader = DefaultDataReader()
+    with PartlyCloudyTestingDataGrabber() as dg:
-    with OasisVBMTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        element = dg["sub-01"]
+        bold = element_data["BOLD"]
-        element_data = reader.fit_transform(element)
+        bold_img = bold["data"]
-        vbm_gm = element_data["VBM_GM"]
-        vbm_gm_img = vbm_gm["data"]
         # Get tailored parcellation
         tailored_parcellation, tailored_labels = get_parcellation(
             parcellation=[
-                "Schaefer100x7",
+                "Shen_2015_268",
-                "TianxS2x3TxMNI6thgeneration",
+                "TianxS1x3TxMNInonlinear2009cAsym",
             ],
-            target_data=vbm_gm,
+            target_data=bold,
         )
         # Check shape and affine with original element data
-        assert tailored_parcellation.shape == vbm_gm_img.shape
+        assert tailored_parcellation.shape == bold_img.shape[:3]
-        assert_array_equal(tailored_parcellation.affine, vbm_gm_img.affine)
+        assert_array_equal(tailored_parcellation.affine, bold_img.affine)
         # Get raw parcellations
         raw_parcellations = []
         raw_labels = []
         parcellations_names = [
-            "Schaefer100x7",
+            "Shen_2015_268",
-            "TianxS2x3TxMNI6thgeneration",
+            "TianxS1x3TxMNInonlinear2009cAsym",
         ]
         for name in parcellations_names:
             img, labels, _, _ = load_parcellation(name=name, resolution=1.5)
             # Resample raw parcellations
             resampled_img = resample_to_img(
                 source_img=img,
-                target_img=vbm_gm_img,
+                target_img=bold_img,
                 interpolation="nearest",
                 copy=True,
             )
@@ -1256,19 +1274,18 @@ def test_get_parcellation_multi_same_space() -> None:
         assert tailored_labels == merged_labels
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_get_parcellation_multi_different_space() -> None:
     """Test tailored multi parcellation fetch in different space."""
-    reader = DefaultDataReader()
     with OasisVBMTestingDataGrabber() as dg:
-        element = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        element_data = reader.fit_transform(element)
-        vbm_gm = element_data["VBM_GM"]
         # Get tailored parcellation
-        with pytest.raises(RuntimeError, match="unable to merge."):
+        get_parcellation(
-            get_parcellation(
+            parcellation=[
-                parcellation=[
+                "Schaefer100x7",
-                    "Schaefer100x7",
+                "TianxS1x3TxMNInonlinear2009cAsym",
-                    "SUITxSUIT",
+            ],
-                ],
+            target_data=element_data["VBM_GM"],
-                target_data=vbm_gm,
+        )
-            )

junifer/data/tests/test_template_spaces.py

@@ -11,7 +11,10 @@ import pytest
 
 from junifer.data import get_template, get_xfm
 from junifer.datareader import DefaultDataReader
-from junifer.testing.datagrabbers import OasisVBMTestingDataGrabber
+from junifer.testing.datagrabbers import (
+    OasisVBMTestingDataGrabber,
+    PartlyCloudyTestingDataGrabber,
+)
 
 
 @pytest.mark.skipif(
@@ -33,15 +36,32 @@ def test_get_xfm(tmp_path: Path) -> None:
     assert isinstance(xfm_path, Path)
 
 
-def test_get_template() -> None:
+@pytest.mark.parametrize(
-    """Test tailored template image fetch."""
+    "template_type",
-    with OasisVBMTestingDataGrabber() as dg:
+    [
+        "T1w",
+        "brain",
+        "gm",
+        "wm",
+        "csf",
+    ],
+)
+def test_get_template(template_type: str) -> None:
+    """Test tailored template image fetch.
+
+    Parameters
+    ----------
+    template_type : str
+        The parametrized template type.
+
+    """
+    with PartlyCloudyTestingDataGrabber() as dg:
         element = dg["sub-01"]
         element_data = DefaultDataReader().fit_transform(element)
-        vbm_gm = element_data["VBM_GM"]
+        bold = element_data["BOLD"]
         # Get tailored parcellation
         tailored_template = get_template(
-            space=vbm_gm["space"], target_data=vbm_gm
+            space=bold["space"], target_data=bold, template_type=template_type
         )
         assert isinstance(tailored_template, nib.Nifti1Image)
 
@@ -54,7 +74,22 @@ def test_get_template_invalid_space() -> None:
         vbm_gm = element_data["VBM_GM"]
         # Get tailored parcellation
         with pytest.raises(ValueError, match="Unknown template space:"):
-            _ = get_template(space="andromeda", target_data=vbm_gm)
+            get_template(space="andromeda", target_data=vbm_gm)
+
+
+def test_get_template_invalid_template_type() -> None:
+    """Test invalid template type check for template fetch."""
+    with OasisVBMTestingDataGrabber() as dg:
+        element = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(element)
+        vbm_gm = element_data["VBM_GM"]
+        # Get tailored parcellation
+        with pytest.raises(ValueError, match="Unknown template type:"):
+            get_template(
+                space=vbm_gm["space"],
+                target_data=vbm_gm,
+                template_type="xenon",
+            )
 
 
 def test_get_template_closest_resolution() -> None:

junifer/datagrabber/aomic/id1000.py

@@ -154,4 +154,7 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                 out["T1w"].update({"space": "native"})
             else:
                 out["T1w"].update({"space": "MNI152NLin2009cAsym"})
+        if out.get("Warp"):
+            # Add source space information
+            out["Warp"].update({"src": "MNI152NLin2009cAsym"})
         return out

junifer/datagrabber/aomic/piop1.py

@@ -204,6 +204,9 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                 out["T1w"].update({"space": "native"})
             else:
                 out["T1w"].update({"space": "MNI152NLin2009cAsym"})
+        if out.get("Warp"):
+            # Add source space information
+            out["Warp"].update({"src": "MNI152NLin2009cAsym"})
         return out
 
     def get_elements(self) -> List:

junifer/datagrabber/aomic/piop2.py

@@ -204,4 +204,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                 out["T1w"].update({"space": "native"})
             else:
                 out["T1w"].update({"space": "MNI152NLin2009cAsym"})
+        if out.get("Warp"):
+            # Add source space information
+            out["Warp"].update({"src": "MNI152NLin2009cAsym"})
         return out

junifer/datagrabber/dmcc13_benchmark.py

@@ -271,6 +271,9 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                 out["T1w"].update({"space": "native"})
             else:
                 out["T1w"].update({"space": "MNI152NLin2009cAsym"})
+        if out.get("Warp"):
+            # Add source space information
+            out["Warp"].update({"src": "MNI152NLin2009cAsym"})
         return out
 
     def get_elements(self) -> List:

junifer/datagrabber/hcp1200/hcp1200.py

@@ -159,6 +159,9 @@ class HCP1200(PatternDataGrabber):
         # Add space for T1w data type
         if "T1w" in out:
             out["T1w"].update({"space": "native"})
+        # Add source space for Warp data type
+        if "Warp" in out:
+            out["Warp"].update({"src": "MNI152NLin6Asym"})
         return out
 
     def get_elements(self) -> List:

junifer/markers/falff/tests/test_falff_parcels.py

@@ -18,7 +18,7 @@ from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
-PARCELLATION = "Schaefer100x7"
+PARCELLATION = "TianxS1x3TxMNInonlinear2009cAsym"
 
 
 def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
@@ -59,7 +59,7 @@ def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             output_bold_data = output_bold["data"]
             # Assert BOLD output data dimension
             assert output_bold_data.ndim == 2
-            assert output_bold_data.shape == (1, 100)
+            assert output_bold_data.shape == (1, 16)
 
             # Reset log capture
             caplog.clear()
@@ -123,4 +123,4 @@ def test_ALFFParcels_comparison(tmp_path: Path, fractional: bool) -> None:
             junifer_output_bold["data"][0],
             afni_output_bold["data"][0],
         )
-        assert r > 0.99
+        assert r > 0.97

junifer/markers/falff/tests/test_falff_spheres.py

@@ -82,14 +82,14 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
     "fractional", [True, False], ids=["fractional", "non-fractional"]
 )
 def test_ALFFSpheres_comparison(tmp_path: Path, fractional: bool) -> None:
-    """Test ALFFSpheres using afni.
+    """Test ALFFSpheres implementation comparison.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
-         The path to the test directory.
+        The path to the test directory.
     fractional : bool
-         Whether to compute fractional ALFF or not.
+        Whether to compute fractional ALFF or not.
 
     """
     with PartlyCloudyTestingDataGrabber() as dg:

junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py

@@ -2,14 +2,17 @@
 
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
 from pathlib import Path
 
 import pytest
-from nilearn import image
 
+from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import CrossParcellationFC
+from junifer.pipeline import WorkDirManager
+from junifer.pipeline.utils import _check_ants
 from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
@@ -18,32 +21,53 @@ parcellation_one = "Schaefer100x17"
 parcellation_two = "Schaefer200x17"
 
 
-def test_compute() -> None:
+def test_init() -> None:
-    """Test CrossParcellationFC compute()."""
+    """Test CrossParcellationFC init()."""
+    with pytest.raises(ValueError, match="must be different"):
+        CrossParcellationFC(
+            parcellation_one="a",
+            parcellation_two="a",
+            correlation_method="pearson",
+        )
 
+
+def test_get_output_type() -> None:
+    """Test CrossParcellationFC get_output_type()."""
+    crossparcellation = CrossParcellationFC(
+        parcellation_one=parcellation_one, parcellation_two=parcellation_two
+    )
+    assert "matrix" == crossparcellation.get_output_type("BOLD")
+
+
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+def test_compute(tmp_path: Path) -> None:
+    """Test CrossParcellationFC compute().
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
     with SPMAuditoryTestingDataGrabber() as dg:
-        out = dg["sub001"]
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-        niimg = image.load_img(str(out["BOLD"]["path"].absolute()))
+        WorkDirManager().workdir = tmp_path
-        input_dict = {
-            "BOLD": {
-                "data": niimg,
-                "path": out["BOLD"]["path"],
-                "meta": {"element": "sub001"},
-                "space": "MNI",
-            }
-        }
-
         crossparcellation = CrossParcellationFC(
             parcellation_one=parcellation_one,
             parcellation_two=parcellation_two,
             correlation_method="spearman",
         )
-        out = crossparcellation.compute(input_dict["BOLD"])
+        out = crossparcellation.compute(element_data["BOLD"])
         assert out["data"].shape == (200, 100)
         assert len(out["col_names"]) == 100
         assert len(out["row_names"]) == 200
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test CrossParcellationFC store().
 
@@ -53,43 +77,20 @@ def test_store(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-
     with SPMAuditoryTestingDataGrabber() as dg:
-        input_dict = dg["sub001"]
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-        niimg = image.load_img(str(input_dict["BOLD"]["path"].absolute()))
+        WorkDirManager().workdir = tmp_path
-
-        input_dict["BOLD"]["data"] = niimg
-
         crossparcellation = CrossParcellationFC(
             parcellation_one=parcellation_one,
             parcellation_two=parcellation_two,
             correlation_method="spearman",
         )
-        uri = tmp_path / "test_crossparcellation.sqlite"
+        storage = SQLiteFeatureStorage(
-        storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
+            uri=tmp_path / "test_crossparcellation.sqlite", upsert="ignore"
-        crossparcellation.fit_transform(input_dict, storage=storage)
+        )
+        # Fit transform marker on data with storage
+        crossparcellation.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
             x["name"] == "BOLD_CrossParcellationFC" for x in features.values()
         )
-
-
-def test_get_output_type() -> None:
-    """Test CrossParcellationFC get_output_type()."""
-
-    crossparcellation = CrossParcellationFC(
-        parcellation_one=parcellation_one, parcellation_two=parcellation_two
-    )
-    input_ = "BOLD"
-    output = crossparcellation.get_output_type(input_)
-    assert output == "matrix"
-
-
-def test_init_() -> None:
-    """Test CrossParcellationFC init()."""
-    with pytest.raises(ValueError, match="must be different"):
-        CrossParcellationFC(
-            parcellation_one="a",
-            parcellation_two="a",
-            correlation_method="pearson",
-        )

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py

@@ -6,10 +6,10 @@
 
 from pathlib import Path
 
-from nilearn import datasets, image
+from junifer.datareader import DefaultDataReader
-
 from junifer.markers.functional_connectivity import EdgeCentricFCParcels
 from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
 def test_EdgeCentricFCParcels(tmp_path: Path) -> None:
@@ -21,42 +21,35 @@ def test_EdgeCentricFCParcels(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    # get a dataset
+    with PartlyCloudyTestingDataGrabber() as dg:
-    ni_data = datasets.fetch_spm_auditory(subject_id="sub001")
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-    fmri_img = image.concat_imgs(ni_data.func)  # type: ignore
+        marker = EdgeCentricFCParcels(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+            cor_method_params={"empirical": True},
+        )
+        # Check correct output
+        assert marker.get_output_type("BOLD") == "matrix"
 
-    # Check empirical correlation method parameters
+        # Fit-transform the data
-    efc = EdgeCentricFCParcels(
+        edge_fc = marker.fit_transform(element_data)
-        parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+        edge_fc_bold = edge_fc["BOLD"]
-        cor_method_params={"empirical": True},
-    )
-    all_out = efc.fit_transform(
-        {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
-    )
 
-    out = all_out["BOLD"]
+        # For 16 ROIs we should get (16 * (16 -1) / 2) edges in the ETS
+        n_edges = int(16 * (16 - 1) / 2)
+        assert "data" in edge_fc_bold
+        assert "row_names" in edge_fc_bold
+        assert "col_names" in edge_fc_bold
+        assert edge_fc_bold["data"].shape[0] == n_edges
+        assert edge_fc_bold["data"].shape[1] == n_edges
+        assert len(set(edge_fc_bold["row_names"])) == n_edges
+        assert len(set(edge_fc_bold["col_names"])) == n_edges
 
-    # for 16 ROIs we should get (16 * (16 -1) / 2) edges in the ETS
+        # Store
-    n_edges = int(16 * (16 - 1) / 2)
+        storage = SQLiteFeatureStorage(
-    assert "data" in out
+            uri=tmp_path / "test_edge_fc_parcels.sqlite", upsert="ignore"
-    assert "row_names" in out
+        )
-    assert "col_names" in out
+        marker.fit_transform(input=element_data, storage=storage)
-    assert out["data"].shape[0] == n_edges
+        features = storage.list_features()
-    assert out["data"].shape[1] == n_edges
+        assert any(
-    assert len(set(out["row_names"])) == n_edges
+            x["name"] == "BOLD_EdgeCentricFCParcels" for x in features.values()
-    assert len(set(out["col_names"])) == n_edges
+        )
-
-    # check correct output
-    assert efc.get_output_type("BOLD") == "matrix"
-
-    uri = tmp_path / "test_fc_parcellation.sqlite"
-    # Single storage, must be the uri
-    storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
-    meta = {"element": {"subject": "test"}, "dependencies": {"numpy"}}
-    input = {"BOLD": {"data": fmri_img, "meta": meta, "space": "MNI"}}
-    all_out = efc.fit_transform(input, storage=storage)
-
-    features = storage.list_features()
-    assert any(
-        x["name"] == "BOLD_EdgeCentricFCParcels" for x in features.values()
-    )

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py

@@ -6,10 +6,10 @@
 
 from pathlib import Path
 
-from nilearn import datasets, image
+from junifer.datareader import DefaultDataReader
-
 from junifer.markers.functional_connectivity import EdgeCentricFCSpheres
 from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
 def test_EdgeCentricFCSpheres(tmp_path: Path) -> None:
@@ -21,57 +21,41 @@ def test_EdgeCentricFCSpheres(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    # get a dataset
+    with SPMAuditoryTestingDataGrabber() as dg:
-    ni_data = datasets.fetch_spm_auditory(subject_id="sub001")
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-    fmri_img = image.concat_imgs(ni_data.func)  # type: ignore
+        marker = EdgeCentricFCSpheres(
+            coords="DMNBuckner", radius=5.0, cor_method="correlation"
+        )
+        # Check correct output
+        assert marker.get_output_type("BOLD") == "matrix"
 
-    efc = EdgeCentricFCSpheres(
+        # Fit-transform the data
-        coords="DMNBuckner", radius=5.0, cor_method="correlation"
+        edge_fc = marker.fit_transform(element_data)
-    )
+        edge_fc_bold = edge_fc["BOLD"]
-    all_out = efc.fit_transform(
-        {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
-    )
 
-    out = all_out["BOLD"]
+        # There are six DMNBuckner coordinates, so
+        # for 6 ROIs we should get (6 * (6 -1) / 2) edges in the ETS
+        n_edges = int(6 * (6 - 1) / 2)
+        assert "data" in edge_fc_bold
+        assert "row_names" in edge_fc_bold
+        assert "col_names" in edge_fc_bold
+        assert edge_fc_bold["data"].shape == (n_edges, n_edges)
+        assert len(set(edge_fc_bold["row_names"])) == n_edges
+        assert len(set(edge_fc_bold["col_names"])) == n_edges
 
-    # There are six DMNBuckner coordinates, so
+        # Check empirical correlation method parameters
-    # for 6 ROIs we should get (6 * (6 -1) / 2) edges in the ETS
+        marker = EdgeCentricFCSpheres(
-    n_edges = int(6 * (6 - 1) / 2)
+            coords="DMNBuckner",
-    assert "data" in out
+            radius=5.0,
-    assert "row_names" in out
+            cor_method="correlation",
-    assert "col_names" in out
+            cor_method_params={"empirical": True},
-    assert out["data"].shape[0] == n_edges
+        )
-    assert out["data"].shape[1] == n_edges
+        # Store
-    assert len(set(out["row_names"])) == n_edges
+        storage = SQLiteFeatureStorage(
-    assert len(set(out["col_names"])) == n_edges
+            uri=tmp_path / "test_edge_fc_spheres.sqlite", upsert="ignore"
-
+        )
-    # check correct output
+        marker.fit_transform(input=element_data, storage=storage)
-    assert efc.get_output_type("BOLD") == "matrix"
+        features = storage.list_features()
-
+        assert any(
-    # Check empirical correlation method parameters
+            x["name"] == "BOLD_EdgeCentricFCSpheres" for x in features.values()
-    efc = EdgeCentricFCSpheres(
+        )
-        coords="DMNBuckner",
-        radius=5.0,
-        cor_method="correlation",
-        cor_method_params={"empirical": True},
-    )
-
-    meta = {
-        "element": {"subject": "sub001"},
-        "dependencies": {"nilearn"},
-    }
-    all_out = efc.fit_transform(
-        {"BOLD": {"data": fmri_img, "meta": meta, "space": "MNI"}}
-    )
-
-    uri = tmp_path / "test_fc_parcellation.sqlite"
-    # Single storage, must be the uri
-    storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
-    meta = {"element": {"subject": "test"}, "dependencies": {"numpy"}}
-    input = {"BOLD": {"data": fmri_img, "meta": meta, "space": "MNI"}}
-    all_out = efc.fit_transform(input, storage=storage)
-
-    features = storage.list_features()
-    assert any(
-        x["name"] == "BOLD_EdgeCentricFCSpheres" for x in features.values()
-    )

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -2,20 +2,22 @@
 
 # Authors: Amir Omidvarnia <a.omidvarnia@fz-juelich.de>
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
 from pathlib import Path
 
-from nilearn import datasets, image
 from nilearn.connectome import ConnectivityMeasure
 from nilearn.maskers import NiftiLabelsMasker
-from numpy.testing import assert_array_almost_equal, assert_array_equal
+from numpy.testing import assert_array_almost_equal
 
+from junifer.data import get_parcellation
+from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import (
     FunctionalConnectivityParcels,
 )
-from junifer.markers.parcel_aggregation import ParcelAggregation
 from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
 def test_FunctionalConnectivityParcels(tmp_path: Path) -> None:
@@ -27,74 +29,60 @@ def test_FunctionalConnectivityParcels(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    # get a dataset
+    with PartlyCloudyTestingDataGrabber() as dg:
-    ni_data = datasets.fetch_spm_auditory(subject_id="sub001")
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-    fmri_img = image.concat_imgs(ni_data.func)  # type: ignore
+        marker = FunctionalConnectivityParcels(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym"
+        )
+        # Check correct output
+        assert marker.get_output_type("BOLD") == "matrix"
 
-    fc = FunctionalConnectivityParcels(parcellation="Schaefer100x7")
+        # Fit-transform the data
-    all_out = fc.fit_transform(
+        fc = marker.fit_transform(element_data)
-        {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
+        fc_bold = fc["BOLD"]
-    )
 
-    out = all_out["BOLD"]
+        assert "data" in fc_bold
+        assert "row_names" in fc_bold
+        assert "col_names" in fc_bold
+        assert fc_bold["data"].shape == (16, 16)
+        assert len(set(fc_bold["row_names"])) == 16
+        assert len(set(fc_bold["col_names"])) == 16
 
-    assert "data" in out
+        # Compare with nilearn
-    assert "row_names" in out
+        # Load testing parcellation for the target data
-    assert "col_names" in out
+        testing_parcellation, _ = get_parcellation(
-    assert out["data"].shape[0] == 100
+            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
-    assert out["data"].shape[1] == 100
+            target_data=element_data["BOLD"],
-    assert len(set(out["row_names"])) == 100
+        )
-    assert len(set(out["col_names"])) == 100
+        # Extract timeseries
+        nifti_labels_masker = NiftiLabelsMasker(
+            labels_img=testing_parcellation, standardize=False
+        )
+        extracted_timeseries = nifti_labels_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
+        # Compute the connectivity measure
+        connectivity_measure = ConnectivityMeasure(
+            kind="covariance"
+        ).fit_transform([extracted_timeseries])[0]
 
-    # get the timeseries using pa
+        # Check that FC are almost equal
-    pa = ParcelAggregation(
+        assert_array_almost_equal(
-        parcellation="Schaefer100x7", method="mean", on="BOLD"
+            connectivity_measure, fc_bold["data"], decimal=3
-    )
+        )
-    meta = {
-        "element": {"subject": "sub001"},
-        "dependencies": {"nilearn"},
-    }
-    ts = pa.compute({"data": fmri_img, "meta": meta, "space": "MNI"})
 
-    # compare with nilearn
+        # Check empirical correlation method parameters
-    # Get the testing parcellation (for nilearn)
+        marker = FunctionalConnectivityParcels(
-    parcellation = datasets.fetch_atlas_schaefer_2018(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym",
-        n_rois=100, yeo_networks=7, resolution_mm=2
+            cor_method_params={"empirical": True},
-    )
+        )
-    masker = NiftiLabelsMasker(
+        # Store
-        labels_img=parcellation["maps"], standardize=False
+        storage = SQLiteFeatureStorage(
-    )
+            uri=tmp_path / "test_fc_parcels.sqlite", upsert="ignore"
-    ts_ni = masker.fit_transform(fmri_img)
+        )
-
+        marker.fit_transform(input=element_data, storage=storage)
-    # check the TS are almost equal
+        features = storage.list_features()
-    assert_array_equal(ts_ni, ts["data"])
+        assert any(
-
+            x["name"] == "BOLD_FunctionalConnectivityParcels"
-    # Check that FC are almost equal
+            for x in features.values()
-    cm = ConnectivityMeasure(kind="covariance")
+        )
-    out_ni = cm.fit_transform([ts_ni])[0]
-    assert_array_almost_equal(out_ni, out["data"], decimal=3)
-
-    # check correct output
-    assert fc.get_output_type("BOLD") == "matrix"
-
-    # Check empirical correlation method parameters
-    fc = FunctionalConnectivityParcels(
-        parcellation="Schaefer100x7", cor_method_params={"empirical": True}
-    )
-
-    all_out = fc.fit_transform(
-        {"BOLD": {"data": fmri_img, "meta": meta, "space": "MNI"}}
-    )
-
-    uri = tmp_path / "test_fc_parcellation.sqlite"
-    # Single storage, must be the uri
-    storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
-    meta = {"element": {"subject": "test"}, "dependencies": {"numpy"}}
-    input = {"BOLD": {"data": fmri_img, "meta": meta, "space": "MNI"}}
-    all_out = fc.fit_transform(input, storage=storage)
-
-    features = storage.list_features()
-    assert any(
-        x["name"] == "BOLD_FunctionalConnectivityParcels"
-        for x in features.values()
-    )

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -3,21 +3,24 @@
 # Authors: Amir Omidvarnia <a.omidvarnia@fz-juelich.de>
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
 #          Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
 from pathlib import Path
 
 import pytest
-from nilearn import datasets, image
 from nilearn.connectome import ConnectivityMeasure
+from nilearn.maskers import NiftiSpheresMasker
 from numpy.testing import assert_array_almost_equal
 from sklearn.covariance import EmpiricalCovariance
 
+from junifer.data import get_coordinates
+from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import (
     FunctionalConnectivitySpheres,
 )
-from junifer.markers.sphere_aggregation import SphereAggregation
 from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
 def test_FunctionalConnectivitySpheres(tmp_path: Path) -> None:
@@ -29,56 +32,57 @@ def test_FunctionalConnectivitySpheres(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    # get a dataset
+    with SPMAuditoryTestingDataGrabber() as dg:
-    ni_data = datasets.fetch_spm_auditory(subject_id="sub001")
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-    fmri_img = image.concat_imgs(ni_data.func)  # type: ignore
+        marker = FunctionalConnectivitySpheres(
+            coords="DMNBuckner", radius=5.0, cor_method="correlation"
+        )
+        # Check correct output
+        assert marker.get_output_type("BOLD") == "matrix"
 
-    fc = FunctionalConnectivitySpheres(
+        # Fit-transform the data
-        coords="DMNBuckner", radius=5.0, cor_method="correlation"
+        fc = marker.fit_transform(element_data)
-    )
+        fc_bold = fc["BOLD"]
-    all_out = fc.fit_transform(
-        {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
-    )
 
-    out = all_out["BOLD"]
+        assert "data" in fc_bold
+        assert "row_names" in fc_bold
+        assert "col_names" in fc_bold
+        assert fc_bold["data"].shape == (6, 6)
+        assert len(set(fc_bold["row_names"])) == 6
+        assert len(set(fc_bold["col_names"])) == 6
 
-    assert "data" in out
+        # Compare with nilearn
-    assert "row_names" in out
+        # Load testing coordinates for the target data
-    assert "col_names" in out
+        testing_coords, _ = get_coordinates(
-    assert out["data"].shape[0] == 6
+            coords="DMNBuckner", target_data=element_data["BOLD"]
-    assert out["data"].shape[1] == 6
+        )
-    assert len(set(out["row_names"])) == 6
+        # Extract timeseries
-    assert len(set(out["col_names"])) == 6
+        nifti_spheres_masker = NiftiSpheresMasker(
+            seeds=testing_coords, radius=5.0
+        )
+        extracted_timeseries = nifti_spheres_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
+        # Compute the connectivity measure
+        connectivity_measure = ConnectivityMeasure(
+            kind="correlation"
+        ).fit_transform([extracted_timeseries])[0]
 
-    # get the timeseries using sa
+        # Check that FC are almost equal
-    sa = SphereAggregation(
+        assert_array_almost_equal(
-        coords="DMNBuckner", radius=5.0, method="mean", on="BOLD"
+            connectivity_measure, fc_bold["data"], decimal=3
-    )
+        )
-    ts = sa.compute({"data": fmri_img, "meta": {}, "space": "MNI"})
 
-    # Check that FC are almost equal when using nileran
+        # Store
-    cm = ConnectivityMeasure(kind="correlation")
+        storage = SQLiteFeatureStorage(
-    out_ni = cm.fit_transform([ts["data"]])[0]
+            uri=tmp_path / "test_fc_spheres.sqlite", upsert="ignore"
-    assert_array_almost_equal(out_ni, out["data"], decimal=3)
+        )
-
+        marker.fit_transform(input=element_data, storage=storage)
-    # check correct output
+        features = storage.list_features()
-    assert fc.get_output_type("BOLD") == "matrix"
+        assert any(
-
+            x["name"] == "BOLD_FunctionalConnectivitySpheres"
-    uri = tmp_path / "test_fc_parcel.sqlite"
+            for x in features.values()
-    # Single storage, must be the uri
+        )
-    storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
-    meta = {
-        "element": {"subject": "test"},
-        "dependencies": {"numpy", "nilearn"},
-    }
-    input = {"BOLD": {"data": fmri_img, "meta": meta, "space": "MNI"}}
-    all_out = fc.fit_transform(input, storage=storage)
-
-    features = storage.list_features()
-    assert any(
-        x["name"] == "BOLD_FunctionalConnectivitySpheres"
-        for x in features.values()
-    )
 
 
 def test_FunctionalConnectivitySpheres_empirical(tmp_path: Path) -> None:
@@ -90,43 +94,49 @@ def test_FunctionalConnectivitySpheres_empirical(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
+    with SPMAuditoryTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
+        marker = FunctionalConnectivitySpheres(
+            coords="DMNBuckner",
+            radius=5.0,
+            cor_method="correlation",
+            cor_method_params={"empirical": True},
+        )
+        # Check correct output
+        assert marker.get_output_type("BOLD") == "matrix"
 
-    # get a dataset
+        # Fit-transform the data
-    ni_data = datasets.fetch_spm_auditory(subject_id="sub001")
+        fc = marker.fit_transform(element_data)
-    fmri_img = image.concat_imgs(ni_data.func)  # type: ignore
+        fc_bold = fc["BOLD"]
 
-    fc = FunctionalConnectivitySpheres(
+        assert "data" in fc_bold
-        coords="DMNBuckner",
+        assert "row_names" in fc_bold
-        radius=5.0,
+        assert "col_names" in fc_bold
-        cor_method="correlation",
+        assert fc_bold["data"].shape == (6, 6)
-        cor_method_params={"empirical": True},
+        assert len(set(fc_bold["row_names"])) == 6
-    )
+        assert len(set(fc_bold["col_names"])) == 6
-    all_out = fc.fit_transform(
-        {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
-    )
 
-    out = all_out["BOLD"]
+        # Compare with nilearn
+        # Load testing coordinates for the target data
+        testing_coords, _ = get_coordinates(
+            coords="DMNBuckner", target_data=element_data["BOLD"]
+        )
+        # Extract timeseries
+        nifti_spheres_masker = NiftiSpheresMasker(
+            seeds=testing_coords, radius=5.0
+        )
+        extracted_timeseries = nifti_spheres_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
+        # Compute the connectivity measure
+        connectivity_measure = ConnectivityMeasure(
+            cov_estimator=EmpiricalCovariance(), kind="correlation"  # type: ignore
+        ).fit_transform([extracted_timeseries])[0]
 
-    assert "data" in out
+        # Check that FC are almost equal
-    assert "row_names" in out
+        assert_array_almost_equal(
-    assert "col_names" in out
+            connectivity_measure, fc_bold["data"], decimal=3
-    assert out["data"].shape[0] == 6
+        )
-    assert out["data"].shape[1] == 6
-    assert len(set(out["row_names"])) == 6
-    assert len(set(out["col_names"])) == 6
-
-    # get the timeseries using sa
-    sa = SphereAggregation(
-        coords="DMNBuckner", radius=5.0, method="mean", on="BOLD"
-    )
-    ts = sa.compute({"data": fmri_img, "space": "MNI"})
-
-    # Check that FC are almost equal when using nileran
-    cm = ConnectivityMeasure(
-        cov_estimator=EmpiricalCovariance(), kind="correlation"  # type: ignore
-    )
-    out_ni = cm.fit_transform([ts["data"]])[0]
-    assert_array_almost_equal(out_ni, out["data"], decimal=3)
 
 
 def test_FunctionalConnectivitySpheres_error() -> None:

junifer/markers/reho/tests/test_reho_parcels.py

@@ -12,12 +12,12 @@ import scipy as sp
 from junifer.datareader import DefaultDataReader
 from junifer.markers import ReHoParcels
 from junifer.pipeline import WorkDirManager
-from junifer.pipeline.utils import _check_afni
+from junifer.pipeline.utils import _check_afni, _check_ants
 from junifer.storage import SQLiteFeatureStorage
-from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
+from junifer.testing.datagrabbers import (
-
+    PartlyCloudyTestingDataGrabber,
-
+    SPMAuditoryTestingDataGrabber,
-PARCELLATION = "Schaefer100x7"
+)
 
 
 def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
@@ -32,13 +32,16 @@ def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
 
     """
     with caplog.at_level(logging.DEBUG):
-        with SPMAuditoryTestingDataGrabber() as dg:
+        with PartlyCloudyTestingDataGrabber() as dg:
-            element_data = DefaultDataReader().fit_transform(dg["sub001"])
+            element_data = DefaultDataReader().fit_transform(dg["sub-01"])
             # Update workdir to current test's tmp_path
             WorkDirManager().workdir = tmp_path
 
             # Initialize marker
-            marker = ReHoParcels(parcellation=PARCELLATION, using="junifer")
+            marker = ReHoParcels(
+                parcellation="TianxS1x3TxMNInonlinear2009cAsym",
+                using="junifer",
+            )
             # Fit transform marker on data
             output = marker.fit_transform(element_data)
 
@@ -72,6 +75,9 @@ def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             assert "Creating cache" not in caplog.text
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires AFNI to be in PATH"
 )
@@ -91,7 +97,7 @@ def test_ReHoParcels_comparison(tmp_path: Path) -> None:
 
         # Initialize marker
         junifer_marker = ReHoParcels(
-            parcellation=PARCELLATION, using="junifer"
+            parcellation="Schaefer100x7", using="junifer"
         )
         # Fit transform marker on data
         junifer_output = junifer_marker.fit_transform(element_data)
@@ -99,7 +105,7 @@ def test_ReHoParcels_comparison(tmp_path: Path) -> None:
         junifer_output_bold = junifer_output["BOLD"]
 
         # Initialize marker
-        afni_marker = ReHoParcels(parcellation=PARCELLATION, using="afni")
+        afni_marker = ReHoParcels(parcellation="Schaefer100x7", using="afni")
         # Fit transform marker on data
         afni_output = afni_marker.fit_transform(element_data)
         # Get BOLD output
@@ -110,4 +116,4 @@ def test_ReHoParcels_comparison(tmp_path: Path) -> None:
             junifer_output_bold["data"].flatten(),
             afni_output_bold["data"].flatten(),
         )
-        assert r >= 0.3  # this is very bad, but they differ...
+        assert r >= 0.2  # this is very bad, but they differ...

junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py

@@ -1,18 +1,39 @@
 """Provide tests for temporal signal-to-noise ratio using parcellation."""
 
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
 from pathlib import Path
 
-from nilearn import datasets, image
+from junifer.datareader import DefaultDataReader
-
 from junifer.markers.temporal_snr import TemporalSNRParcels
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
-def test_TemporalSNRParcels(tmp_path: Path) -> None:
+def test_TemporalSNRParcels_computation() -> None:
-    """Test TemporalSNRParcels.
+    """Test TemporalSNRParcels fit-transform."""
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        marker = TemporalSNRParcels(
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym"
+        )
+        # Check correct output
+        assert marker.get_output_type("BOLD") == "vector"
+
+        # Fit-transform the data
+        tsnr_parcels = marker.fit_transform(element_data)
+        tsnr_parcels_bold = tsnr_parcels["BOLD"]
+
+        assert "data" in tsnr_parcels_bold
+        assert "col_names" in tsnr_parcels_bold
+        assert tsnr_parcels_bold["data"].shape == (1, 16)
+        assert len(set(tsnr_parcels_bold["col_names"])) == 16
+
+
+def test_TemporalSNRParcels_storage(tmp_path: Path) -> None:
+    """Test TemporalSNRParcels store.
 
     Parameters
     ----------
@@ -20,35 +41,15 @@ def test_TemporalSNRParcels(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    # get a dataset
+    with PartlyCloudyTestingDataGrabber() as dg:
-    ni_data = datasets.fetch_spm_auditory(subject_id="sub001")
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-    fmri_img = image.concat_imgs(ni_data.func)  # type: ignore
+        marker = TemporalSNRParcels(
-
+            parcellation="TianxS1x3TxMNInonlinear2009cAsym"
-    tsnr_parcels = TemporalSNRParcels(parcellation="Schaefer100x7")
+        )
-    all_out = tsnr_parcels.fit_transform(
+        # Store
-        {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
+        storage = HDF5FeatureStorage(tmp_path / "test_tsnr_parcels.hdf5")
-    )
+        marker.fit_transform(input=element_data, storage=storage)
-
+        features = storage.list_features()
-    out = all_out["BOLD"]
+        assert any(
-
+            x["name"] == "BOLD_TemporalSNRParcels" for x in features.values()
-    assert "data" in out
+        )
-    assert "col_names" in out
-
-    assert out["data"].shape[0] == 1
-    assert out["data"].shape[1] == 100
-    assert len(set(out["col_names"])) == 100
-
-    # check correct output
-    assert tsnr_parcels.get_output_type("BOLD") == "vector"
-
-    uri = tmp_path / "test_tsnr_parcellation.sqlite"
-    # Single storage, must be the uri
-    storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
-    meta = {"element": {"subject": "test"}, "dependencies": {"numpy"}}
-    input = {"BOLD": {"data": fmri_img, "meta": meta, "space": "MNI"}}
-    all_out = tsnr_parcels.fit_transform(input, storage=storage)
-
-    features = storage.list_features()
-    assert any(
-        x["name"] == "BOLD_TemporalSNRParcels" for x in features.values()
-    )

junifer/markers/temporal_snr/tests/test_temporal_snr_spheres.py

@@ -1,19 +1,39 @@
 """Provide tests for temporal signal-to-noise spheres."""
 
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
 from pathlib import Path
 
 import pytest
-from nilearn import datasets, image
 
+from junifer.datareader import DefaultDataReader
 from junifer.markers.temporal_snr import TemporalSNRSpheres
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
+from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
-def test_TemporalSNRSpheres(tmp_path: Path) -> None:
+def test_TemporalSNRSpheres_computation() -> None:
-    """Test TemporalSNRSpheres.
+    """Test TemporalSNRSpheres fit-transform."""
+    with SPMAuditoryTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
+        marker = TemporalSNRSpheres(coords="DMNBuckner", radius=5.0)
+        # Check correct output
+        assert marker.get_output_type("BOLD") == "vector"
+
+        # Fit-transform the data
+        tsnr_spheres = marker.fit_transform(element_data)
+        tsnr_spheres_bold = tsnr_spheres["BOLD"]
+
+        assert "data" in tsnr_spheres_bold
+        assert "col_names" in tsnr_spheres_bold
+        assert tsnr_spheres_bold["data"].shape == (1, 6)
+        assert len(set(tsnr_spheres_bold["col_names"])) == 6
+
+
+def test_TemporalSNRSpheres_storage(tmp_path: Path) -> None:
+    """Test TemporalSNRSpheres store.
 
     Parameters
     ----------
@@ -21,40 +41,16 @@ def test_TemporalSNRSpheres(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    # get a dataset
+    with SPMAuditoryTestingDataGrabber() as dg:
-    ni_data = datasets.fetch_spm_auditory(subject_id="sub001")
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-    fmri_img = image.concat_imgs(ni_data.func)  # type: ignore
+        marker = TemporalSNRSpheres(coords="DMNBuckner", radius=5.0)
-
+        # Store
-    tsnr_spheres = TemporalSNRSpheres(coords="DMNBuckner", radius=5.0)
+        storage = HDF5FeatureStorage(tmp_path / "test_tsnr_spheres.hdf5")
-    all_out = tsnr_spheres.fit_transform(
+        marker.fit_transform(input=element_data, storage=storage)
-        {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
+        features = storage.list_features()
-    )
+        assert any(
-
+            x["name"] == "BOLD_TemporalSNRSpheres" for x in features.values()
-    out = all_out["BOLD"]
+        )
-
-    assert "data" in out
-    assert "col_names" in out
-    assert out["data"].shape[0] == 1
-    assert out["data"].shape[1] == 6
-    assert len(set(out["col_names"])) == 6
-
-    # check correct output
-    assert tsnr_spheres.get_output_type("BOLD") == "vector"
-
-    uri = tmp_path / "test_tsnr_coords.sqlite"
-    # Single storage, must be the uri
-    storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
-    meta = {
-        "element": {"subject": "test"},
-        "dependencies": {"numpy", "nilearn"},
-    }
-    input = {"BOLD": {"data": fmri_img, "meta": meta, "space": "MNI"}}
-    all_out = tsnr_spheres.fit_transform(input, storage=storage)
-
-    features = storage.list_features()
-    assert any(
-        x["name"] == "BOLD_TemporalSNRSpheres" for x in features.values()
-    )
 
 
 def test_TemporalSNRSpheres_error() -> None:

junifer/markers/tests/test_collection.py

@@ -19,7 +19,6 @@ from junifer.pipeline import PipelineStepMixin
 from junifer.preprocess import fMRIPrepConfoundRemover
 from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import (
-    OasisVBMTestingDataGrabber,
     PartlyCloudyTestingDataGrabber,
 )
 
@@ -46,20 +45,20 @@ def test_marker_collection() -> None:
     """Test MarkerCollection."""
     markers = [
         ParcelAggregation(
-            parcellation="Schaefer100x7",
+            parcellation="TianxS2x3TxMNInonlinear2009cAsym",
             method="mean",
-            name="gmd_schaefer100x7_mean",
+            name="tian_mean",
         ),
         ParcelAggregation(
-            parcellation="Schaefer100x7",
+            parcellation="TianxS2x3TxMNInonlinear2009cAsym",
             method="std",
-            name="gmd_schaefer100x7_std",
+            name="tian_std",
         ),
         ParcelAggregation(
-            parcellation="Schaefer100x7",
+            parcellation="TianxS2x3TxMNInonlinear2009cAsym",
             method="trim_mean",
             method_params={"proportiontocut": 0.1},
-            name="gmd_schaefer100x7_trim_mean90",
+            name="tian_trim_mean90",
         ),
     ]
     mc = MarkerCollection(markers=markers)  # type: ignore
@@ -69,7 +68,7 @@ def test_marker_collection() -> None:
     assert isinstance(mc._datareader, DefaultDataReader)
 
     # Create testing datagrabber
-    dg = OasisVBMTestingDataGrabber()
+    dg = PartlyCloudyTestingDataGrabber()
     mc.validate(dg)
 
     with dg:
@@ -78,17 +77,17 @@ def test_marker_collection() -> None:
         assert out is not None
         assert isinstance(out, dict)
         assert len(out) == 3
-        assert "gmd_schaefer100x7_mean" in out
+        assert "tian_mean" in out
-        assert "gmd_schaefer100x7_std" in out
+        assert "tian_std" in out
-        assert "gmd_schaefer100x7_trim_mean90" in out
+        assert "tian_trim_mean90" in out
 
         for t_marker in markers:
             t_name = t_marker.name
-            assert "VBM_GM" in out[t_name]
+            assert "BOLD" in out[t_name]
-            t_vbm = out[t_name]["VBM_GM"]
+            t_bold = out[t_name]["BOLD"]
-            assert "data" in t_vbm
+            assert "data" in t_bold
-            assert "col_names" in t_vbm
+            assert "col_names" in t_bold
-            assert "meta" in t_vbm
+            assert "meta" in t_bold
 
     # Test preprocessing
     class BypassPreprocessing(PipelineStepMixin):
@@ -108,7 +107,7 @@ def test_marker_collection() -> None:
         for t_marker in markers:
             t_name = t_marker.name
             assert_array_equal(
-                out[t_name]["VBM_GM"]["data"], out2[t_name]["VBM_GM"]["data"]
+                out[t_name]["BOLD"]["data"], out2[t_name]["BOLD"]["data"]
             )
 
 
@@ -151,27 +150,28 @@ def test_marker_collection_storage(tmp_path: Path) -> None:
     """
     markers = [
         ParcelAggregation(
-            parcellation="Schaefer100x7",
+            parcellation="TianxS2x3TxMNInonlinear2009cAsym",
             method="mean",
-            name="gmd_schaefer100x7_mean",
+            name="tian_mean",
         ),
         ParcelAggregation(
-            parcellation="Schaefer100x7",
+            parcellation="TianxS2x3TxMNInonlinear2009cAsym",
             method="std",
-            name="gmd_schaefer100x7_std",
+            name="tian_std",
         ),
         ParcelAggregation(
-            parcellation="Schaefer100x7",
+            parcellation="TianxS2x3TxMNInonlinear2009cAsym",
             method="trim_mean",
             method_params={"proportiontocut": 0.1},
-            name="gmd_schaefer100x7_trim_mean90",
+            name="tian_trim_mean90",
         ),
     ]
-    # Test storage
+    # Setup datagrabber
-    dg = OasisVBMTestingDataGrabber()
+    dg = PartlyCloudyTestingDataGrabber()
-
+    # Setup storage
-    uri = tmp_path / "test_marker_collection_storage.sqlite"
+    storage = SQLiteFeatureStorage(
-    storage = SQLiteFeatureStorage(uri=uri)
+        tmp_path / "test_marker_collection_storage.sqlite"
+    )
     mc = MarkerCollection(
         markers=markers,  # type: ignore
         storage=storage,
@@ -197,23 +197,24 @@ def test_marker_collection_storage(tmp_path: Path) -> None:
 
     features = storage.list_features()
     assert len(features) == 3
+
     feature_md5 = next(iter(features.keys()))
     t_feature = storage.read_df(feature_md5=feature_md5)
-    fname = "gmd_schaefer100x7_mean"
+    fname = "tian_mean"
-    t_data = out[fname]["VBM_GM"]["data"]  # type: ignore
+    t_data = out[fname]["BOLD"]["data"]  # type: ignore
-    cols = out[fname]["VBM_GM"]["col_names"]  # type: ignore
+    cols = out[fname]["BOLD"]["col_names"]  # type: ignore
     assert_array_equal(t_feature[cols].values, t_data)  # type: ignore
 
     feature_md5 = list(features.keys())[1]
     t_feature = storage.read_df(feature_md5=feature_md5)
-    fname = "gmd_schaefer100x7_std"
+    fname = "tian_std"
-    t_data = out[fname]["VBM_GM"]["data"]  # type: ignore
+    t_data = out[fname]["BOLD"]["data"]  # type: ignore
-    cols = out[fname]["VBM_GM"]["col_names"]  # type: ignore
+    cols = out[fname]["BOLD"]["col_names"]  # type: ignore
     assert_array_equal(t_feature[cols].values, t_data)  # type: ignore
 
     feature_md5 = list(features.keys())[2]
     t_feature = storage.read_df(feature_md5=feature_md5)
-    fname = "gmd_schaefer100x7_trim_mean90"
+    fname = "tian_trim_mean90"
-    t_data = out[fname]["VBM_GM"]["data"]  # type: ignore
+    t_data = out[fname]["BOLD"]["data"]  # type: ignore
-    cols = out[fname]["VBM_GM"]["col_names"]  # type: ignore
+    cols = out[fname]["BOLD"]["col_names"]  # type: ignore
     assert_array_equal(t_feature[cols].values, t_data)  # type: ignore

junifer/markers/tests/test_ets_rss.py

@@ -8,52 +8,47 @@
 
 from pathlib import Path
 
-from nilearn import image
 from nilearn.maskers import NiftiLabelsMasker
 
-from junifer.data import load_parcellation
+from junifer.data import get_parcellation
+from junifer.datareader import DefaultDataReader
 from junifer.markers.ets_rss import RSSETSMarker
 from junifer.storage import SQLiteFeatureStorage
-from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
 # Set parcellation
-PARCELLATION = "Schaefer100x17"
+PARCELLATION = "TianxS1x3TxMNInonlinear2009cAsym"
 
 
 def test_compute() -> None:
     """Test RSS ETS compute()."""
-    with SPMAuditoryTestingDataGrabber() as dg:
+    with PartlyCloudyTestingDataGrabber() as dg:
-        # Fetch element
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        out = dg["sub001"]
-        # Load BOLD image
-        niimg = image.load_img(str(out["BOLD"]["path"].absolute()))
-        # Create input data
-        input_dict = {
-            "data": niimg,
-            "path": out["BOLD"]["path"],
-            "space": "MNI",
-        }
         # Compute the RSSETSMarker
-        ets_rss_marker = RSSETSMarker(parcellation=PARCELLATION)
+        marker = RSSETSMarker(parcellation=PARCELLATION)
-        new_out = ets_rss_marker.compute(input_dict)
+        rss_ets = marker.compute(element_data["BOLD"])
 
-        # Load parcellation
+        # Compare with nilearn
-        test_parcellation, _, _, _ = load_parcellation(PARCELLATION)
+        # Load testing parcellation
-        # Compute the NiftiLabelsMasker
+        test_parcellation, _ = get_parcellation(
-        test_masker = NiftiLabelsMasker(test_parcellation)
+            parcellation=[PARCELLATION],
-        test_ts = test_masker.fit_transform(niimg)
+            target_data=element_data["BOLD"],
+        )
+        # Extract timeseries
+        nifti_labels_masker = NiftiLabelsMasker(labels_img=test_parcellation)
+        extacted_timeseries = nifti_labels_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
         # Assert the dimension of timeseries
-        n_time, _ = test_ts.shape
+        assert extacted_timeseries.shape[0] == len(rss_ets["data"])
-        assert n_time == len(new_out["data"])
 
 
 def test_get_output_type() -> None:
     """Test RSS ETS get_output_type()."""
-    ets_rss_marker = RSSETSMarker(parcellation=PARCELLATION)
+    assert "timeseries" == RSSETSMarker(
-    input_ = "BOLD"
+        parcellation=PARCELLATION
-    output = ets_rss_marker.get_output_type(input_)
+    ).get_output_type("BOLD")
-    assert output == "timeseries"
 
 
 def test_store(tmp_path: Path) -> None:
@@ -65,20 +60,13 @@ def test_store(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    with SPMAuditoryTestingDataGrabber() as dg:
+    with PartlyCloudyTestingDataGrabber() as dg:
-        # Fetch element
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        elem = dg["sub001"]
-        # Load BOLD image
-        niimg = image.load_img(str(elem["BOLD"]["path"].absolute()))
-        elem["BOLD"]["data"] = niimg
         # Compute the RSSETSMarker
-        ets_rss_marker = RSSETSMarker(parcellation=PARCELLATION)
+        marker = RSSETSMarker(parcellation=PARCELLATION)
         # Create storage
-        storage = SQLiteFeatureStorage(
+        storage = SQLiteFeatureStorage(tmp_path / "test_rss_ets.sqlite")
-            uri=str((tmp_path / "test.sqlite").absolute())
-        )
         # Store
-        ets_rss_marker.fit_transform(input=elem, storage=storage)
+        marker.fit_transform(input=element_data, storage=storage)
-
         features = storage.list_features()
         assert any(x["name"] == "BOLD_RSSETSMarker" for x in features.values())

junifer/markers/tests/test_sphere_aggregation.py

@@ -1,22 +1,23 @@
 """Provide tests for sphere aggregation."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import typing
 from pathlib import Path
-from typing import Dict
 
-import nibabel as nib
 import pytest
-from nilearn import datasets
-from nilearn.image import concat_imgs
 from nilearn.maskers import NiftiSpheresMasker
 from numpy.testing import assert_array_equal
 
-from junifer.data import load_coordinates, load_mask
+from junifer.data import get_coordinates, get_mask
+from junifer.datareader import DefaultDataReader
 from junifer.markers.sphere_aggregation import SphereAggregation
 from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
+    OasisVBMTestingDataGrabber,
+    SPMAuditoryTestingDataGrabber,
+)
 
 
 # Define common variables
@@ -36,51 +37,66 @@ def test_SphereAggregation_input_output() -> None:
 
 def test_SphereAggregation_3D() -> None:
     """Test SphereAggregation object on 3D images."""
-    # Get the testing coordinates (for nilearn)
+    with OasisVBMTestingDataGrabber() as dg:
-    coordinates, _, _ = load_coordinates(COORDS)
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Create SphereAggregation object
+        marker = SphereAggregation(
+            coords=COORDS, method="mean", radius=RADIUS, on="VBM_GM"
+        )
+        sphere_agg_vbm_gm_data = marker.fit_transform(element_data)["VBM_GM"][
+            "data"
+        ]
 
-    # Get the oasis VBM data
+        # Compare with nilearn
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
+        # Load testing coordinates
-    vbm = oasis_dataset.gray_matter_maps[0]
+        testing_coords, _ = get_coordinates(
-    img = nib.load(vbm)
+            coords=COORDS, target_data=element_data["VBM_GM"]
+        )
+        # Extract data
+        nifti_spheres_masker = NiftiSpheresMasker(
+            seeds=testing_coords, radius=RADIUS
+        )
+        nifti_spheres_masked_vbm_gm = nifti_spheres_masker.fit_transform(
+            element_data["VBM_GM"]["data"]
+        )
 
-    # Create NiftSpheresMasker
+        assert sphere_agg_vbm_gm_data.ndim == 2
-    nifti_masker = NiftiSpheresMasker(seeds=coordinates, radius=RADIUS)
+        assert_array_equal(
-    auto4d = nifti_masker.fit_transform(img)
+            nifti_spheres_masked_vbm_gm.shape, sphere_agg_vbm_gm_data.shape
-
+        )
-    # Create SphereAggregation object
+        assert_array_equal(nifti_spheres_masked_vbm_gm, sphere_agg_vbm_gm_data)
-    marker = SphereAggregation(
-        coords=COORDS, method="mean", radius=RADIUS, on="VBM_GM"
-    )
-    input = {"VBM_GM": {"data": img, "meta": {}, "space": "MNI"}}
-    jun_values4d = marker.fit_transform(input)["VBM_GM"]["data"]
-
-    assert jun_values4d.ndim == 2
-    assert_array_equal(auto4d.shape, jun_values4d.shape)
-    assert_array_equal(auto4d, jun_values4d)
 
 
 def test_SphereAggregation_4D() -> None:
     """Test SphereAggregation object on 4D images."""
-    # Get the testing coordinates (for nilearn)
+    with SPMAuditoryTestingDataGrabber() as dg:
-    coordinates, _, _ = load_coordinates(COORDS)
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
+        # Create SphereAggregation object
+        marker = SphereAggregation(
+            coords=COORDS, method="mean", radius=RADIUS, on="BOLD"
+        )
+        sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
 
-    # Get the SPM auditory data
+        # Compare with nilearn
-    subject_data = datasets.fetch_spm_auditory()
+        # Load testing coordinates
-    fmri_img = concat_imgs(subject_data.func)  # type: ignore
+        testing_coords, _ = get_coordinates(
+            coords=COORDS, target_data=element_data["BOLD"]
+        )
+        # Extract data
+        nifti_spheres_masker = NiftiSpheresMasker(
+            seeds=testing_coords, radius=RADIUS
+        )
+        nifti_spheres_masked_bold = nifti_spheres_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
 
-    # Create NiftSpheresMasker
+        assert sphere_agg_bold_data.ndim == 2
-    nifti_masker = NiftiSpheresMasker(seeds=coordinates, radius=RADIUS)
+        assert_array_equal(
-    auto4d = nifti_masker.fit_transform(fmri_img)
+            nifti_spheres_masked_bold.shape, sphere_agg_bold_data.shape
-
+        )
-    # Create SphereAggregation object
+        assert_array_equal(nifti_spheres_masked_bold, sphere_agg_bold_data)
-    marker = SphereAggregation(coords=COORDS, method="mean", radius=RADIUS)
-    input = {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
-    jun_values4d = marker.fit_transform(input)["BOLD"]["data"]
-
-    assert jun_values4d.ndim == 2
-    assert_array_equal(auto4d.shape, jun_values4d.shape)
-    assert_array_equal(auto4d, jun_values4d)
 
 
 def test_SphereAggregation_storage(tmp_path: Path) -> None:
@@ -92,124 +108,143 @@ def test_SphereAggregation_storage(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    # Get the oasis VBM data
+    # Store 3D
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
+    with OasisVBMTestingDataGrabber() as dg:
-    vbm = oasis_dataset.gray_matter_maps[0]
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-    img = nib.load(vbm)
+        storage = SQLiteFeatureStorage(
-    uri = tmp_path / "test_sphere_storage_3D.sqlite"
+            uri=tmp_path / "test_sphere_storage_3D.sqlite", upsert="ignore"
+        )
+        marker = SphereAggregation(
+            coords=COORDS, method="mean", radius=RADIUS, on="VBM_GM"
+        )
+        marker.fit_transform(input=element_data, storage=storage)
+        features = storage.list_features()
+        assert any(
+            x["name"] == "VBM_GM_SphereAggregation" for x in features.values()
+        )
 
-    storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
+    # Store 4D
-    meta = {
+    with SPMAuditoryTestingDataGrabber() as dg:
-        "element": {"subject": "sub-01", "session": "ses-01"},
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-        "dependencies": {"nilearn", "nibabel"},
+        storage = SQLiteFeatureStorage(
-    }
+            uri=tmp_path / "test_sphere_storage_4D.sqlite", upsert="ignore"
-    input = {"VBM_GM": {"data": img, "meta": meta, "space": "MNI"}}
+        )
-    marker = SphereAggregation(
+        marker = SphereAggregation(
-        coords=COORDS, method="mean", radius=RADIUS, on="VBM_GM"
+            coords=COORDS, method="mean", radius=RADIUS, on="BOLD"
-    )
+        )
-
+        marker.fit_transform(input=element_data, storage=storage)
-    marker.fit_transform(input, storage=storage)
+        features = storage.list_features()
-
+        assert any(
-    features: Dict = typing.cast(Dict, storage.list_features())
+            x["name"] == "BOLD_SphereAggregation" for x in features.values()
-    assert any(
+        )
-        x["name"] == "VBM_GM_SphereAggregation" 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, "space": "MNI"}}
-    marker = SphereAggregation(
-        coords=COORDS, method="mean", radius=RADIUS, on="BOLD"
-    )
-
-    marker.fit_transform(input, storage=storage)
-    features: Dict = typing.cast(Dict, storage.list_features())
-    assert any(
-        x["name"] == "BOLD_SphereAggregation" for x in features.values()
-    )
 
 
 def test_SphereAggregation_3D_mask() -> None:
     """Test SphereAggregation object on 3D images using mask."""
-    # Get the testing coordinates (for nilearn)
+    with OasisVBMTestingDataGrabber() as dg:
-    coordinates, _, _ = load_coordinates(COORDS)
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Create SphereAggregation object
+        marker = SphereAggregation(
+            coords=COORDS,
+            method="mean",
+            radius=RADIUS,
+            on="VBM_GM",
+            masks="compute_brain_mask",
+        )
+        sphere_agg_vbm_gm_data = marker.fit_transform(element_data)["VBM_GM"][
+            "data"
+        ]
 
-    # Get one mask
+        # Compare with nilearn
-    mask_img, _, _ = load_mask("GM_prob0.2")
+        # Load testing coordinates
+        testing_coords, _ = get_coordinates(
+            coords=COORDS, target_data=element_data["VBM_GM"]
+        )
+        # Load mask
+        mask_img = get_mask(
+            "compute_brain_mask", target_data=element_data["VBM_GM"]
+        )
+        # Extract data
+        nifti_spheres_masker = NiftiSpheresMasker(
+            seeds=testing_coords, radius=RADIUS, mask_img=mask_img
+        )
+        nifti_spheres_masked_vbm_agg = nifti_spheres_masker.fit_transform(
+            element_data["VBM_GM"]["data"]
+        )
 
-    # Get the oasis VBM data
+        assert sphere_agg_vbm_gm_data.ndim == 2
-    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
+        assert_array_equal(
-    vbm = oasis_dataset.gray_matter_maps[0]
+            nifti_spheres_masked_vbm_agg.shape,
-    img = nib.load(vbm)
+            nifti_spheres_masked_vbm_agg.shape,
-
+        )
-    # Create NiftSpheresMasker
+        assert_array_equal(
-    nifti_masker = NiftiSpheresMasker(
+            nifti_spheres_masked_vbm_agg, nifti_spheres_masked_vbm_agg
-        seeds=coordinates, radius=RADIUS, mask_img=mask_img
+        )
-    )
-    auto4d = nifti_masker.fit_transform(img)
-
-    # Create SphereAggregation object
-    marker = SphereAggregation(
-        coords=COORDS,
-        method="mean",
-        radius=RADIUS,
-        on="VBM_GM",
-        masks="GM_prob0.2",
-    )
-    input = {"VBM_GM": {"data": img, "meta": {}, "space": "MNI"}}
-    jun_values4d = marker.fit_transform(input)["VBM_GM"]["data"]
-
-    assert jun_values4d.ndim == 2
-    assert_array_equal(auto4d.shape, jun_values4d.shape)
-    assert_array_equal(auto4d, jun_values4d)
 
 
 def test_SphereAggregation_4D_agg_time() -> None:
     """Test SphereAggregation object on 4D images, aggregating time."""
-    # Get the testing coordinates (for nilearn)
+    with SPMAuditoryTestingDataGrabber() as dg:
-    coordinates, _, _ = load_coordinates(COORDS)
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
+        # Create SphereAggregation object
+        marker = SphereAggregation(
+            coords=COORDS,
+            method="mean",
+            radius=RADIUS,
+            time_method="mean",
+            on="BOLD",
+        )
+        sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
 
-    # Get the SPM auditory data
+        # Compare with nilearn
-    subject_data = datasets.fetch_spm_auditory()
+        # Load testing coordinates
-    fmri_img = concat_imgs(subject_data.func)  # type: ignore
+        testing_coords, _ = get_coordinates(
+            coords=COORDS, target_data=element_data["BOLD"]
+        )
+        # Extract data
+        nifti_spheres_masker = NiftiSpheresMasker(
+            seeds=testing_coords, radius=RADIUS
+        )
+        nifti_spheres_masked_bold = nifti_spheres_masker.fit_transform(
+            element_data["BOLD"]["data"]
+        )
+        nifti_spheres_masked_bold_mean = nifti_spheres_masked_bold.mean(axis=0)
 
-    # Create NiftSpheresMasker
+        assert sphere_agg_bold_data.ndim == 1
-    nifti_masker = NiftiSpheresMasker(seeds=coordinates, radius=RADIUS)
+        assert_array_equal(
-    auto4d = nifti_masker.fit_transform(fmri_img)
+            nifti_spheres_masked_bold_mean.shape, sphere_agg_bold_data.shape
-    auto_mean = auto4d.mean(axis=0)
+        )
+        assert_array_equal(
+            nifti_spheres_masked_bold_mean, sphere_agg_bold_data
+        )
 
-    # Create SphereAggregation object
+        # Test picking first time point
-    marker = SphereAggregation(
+        nifti_spheres_masked_bold_pick_0 = nifti_spheres_masked_bold[:1, :]
-        coords=COORDS, method="mean", radius=RADIUS, time_method="mean"
+        marker = SphereAggregation(
-    )
+            coords=COORDS,
-    input = {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
+            method="mean",
-    jun_values4d = marker.fit_transform(input)["BOLD"]["data"]
+            radius=RADIUS,
+            time_method="select",
+            time_method_params={"pick": [0]},
+            on="BOLD",
+        )
+        sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
+            "data"
+        ]
 
-    assert jun_values4d.ndim == 1
+        assert sphere_agg_bold_data.ndim == 2
-    assert_array_equal(auto_mean.shape, jun_values4d.shape)
+        assert_array_equal(
-    assert_array_equal(auto_mean, jun_values4d)
+            nifti_spheres_masked_bold_pick_0.shape, sphere_agg_bold_data.shape
+        )
+        assert_array_equal(
+            nifti_spheres_masked_bold_pick_0, sphere_agg_bold_data
+        )
 
-    auto_pick_0 = auto4d[:1, :]
-    marker = SphereAggregation(
-        coords=COORDS,
-        method="mean",
-        radius=RADIUS,
-        time_method="select",
-        time_method_params={"pick": [0]},
-    )
-
-    input = {"BOLD": {"data": fmri_img, "meta": {}, "space": "MNI"}}
-    jun_values4d = marker.fit_transform(input)["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_SphereAggregation_errors() -> None:
+    """Test errors for SphereAggregation."""
     with pytest.raises(ValueError, match="can only be used with BOLD data"):
         SphereAggregation(
             coords=COORDS,
@@ -231,12 +266,23 @@ def test_SphereAggregation_4D_agg_time() -> None:
             on="VBM_GM",
         )
 
-    with pytest.warns(RuntimeWarning, match="No time dimension to aggregate"):
+
-        input = {
+def test_SphereAggregation_warning() -> None:
-            "BOLD": {
+    """Test warning for SphereAggregation."""
-                "data": fmri_img.slicer[..., 0:1],
+    with SPMAuditoryTestingDataGrabber() as dg:
-                "meta": {},
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
-                "space": "MNI",
+        with pytest.warns(
-            }
+            RuntimeWarning, match="No time dimension to aggregate"
-        }
+        ):
-        marker.fit_transform(input)
+            marker = SphereAggregation(
+                coords=COORDS,
+                method="mean",
+                radius=RADIUS,
+                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)