docs/builtin.rst

@@ -515,7 +515,7 @@ Available
    * - Name
      - Keys
      - Version added
-     - Publication
+     - Description - Publication
    * - Vickery-Patil (Gray Matter)
      - | ``GM_prob0.2``
      - 0.0.1
@@ -528,6 +528,29 @@ Available
      - | Vickery, Sam, & Patil, Kaustubh. (2022).
        | Chimpanzee and Human Gray Matter Masks [Data set]. Zenodo.
        | https://doi.org/10.5281/zenodo.6463123
+   * - Nilearn's MNI152 1mm-resolution mask
+     - | ``compute_brain_mask``
+     - 0.0.2
+     - | Compute the whole-brain mask. This mask is calculated using MNI152 1mm-resolution template mask onto the 
+       | target image. See :func:`nilearn.masking.compute_brain_mask`
+   * - Nilearn's mask computed from FMRI data
+     - | ``compute_epi_mask``
+     - 0.0.2
+     - | Compute a brain mask from fMRI data. This is based on an heuristic proposed by T.Nichols: find the least 
+       | dense point of the histogram, between fractions ``lower_cutoff`` and ``upper_cutoff`` of the total image 
+       | histogram. See :func:`nilearn.masking.compute_epi_mask`
+   * - Nilearn's background mask
+     - | ``compute_background_mask``
+     - 0.0.2
+     - | Compute a brain mask for the images by guessing the value of the background from the border of the image.
+       | See :func:`nilearn.masking.compute_background_mask`
+
+   * - Nilearn's ICBM152 template gray-matter mask
+     - | ``fetch_icbm152_brain_gm_mask``
+     - 0.0.2
+     - | Compute a gray-matter mask from the asymmetrical ICBM152 2009 template, release a.
+       | See :func:`nilearn.datasets.fetch_icbm152_brain_gm_mask`
+
 
 Planned
 ~~~~~~~

docs/changes/latest.inc

@@ -37,6 +37,9 @@ Enhancements
 
 - Change HCP datagrabber tests to decrease CI running time (:gh:`155` by `Fede Raimondo`_).
 
+- Add support for nilearn computed masks (``compute_epi_mask``, ``compute_brain_mask``, ``compute_background_mask``,
+  ``fetch_icbm152_brain_gm_mask``) (:gh:`175` by `Fede Raimondo`_).
+
 Bugs
 ~~~~
 

junifer/data/__init__.py

@@ -19,6 +19,7 @@ from .masks import (
     list_masks,
     load_mask,
     register_mask,
+    get_mask,
 )
 
 from . import utils

junifer/data/masks.py

@@ -4,9 +4,27 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Union
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Union,
+    Callable,
+)
+
+import numpy as np
 
 import nibabel as nib
+from nilearn.masking import (
+    compute_brain_mask,
+    compute_background_mask,
+    compute_epi_mask,
+)
+from nilearn.datasets import fetch_icbm152_brain_gm_mask
+from nilearn.image import resample_to_img
 
 from ..utils.logging import logger, raise_error
 from .utils import closest_resolution
@@ -18,6 +36,30 @@ if TYPE_CHECKING:
 # Path to the VOIs
 _masks_path = Path(__file__).parent / "masks"
 
+
+def _fetch_icbm152_brain_gm_mask(target_img: "Nifti1Image", **kwargs):
+    """Fetch ICBM152 brain mask and resample.
+
+    Parameters
+    ----------
+    target_img : nibabel.Nifti1Image
+        The image to which the mask will be resampled.
+    **kwargs : dict
+        Keyword arguments to be passed to
+        :func:`nilearn.datasets.fetch_icbm152_brain_gm_mask`.
+
+    Returns
+    -------
+    nibabel.Nifti1Image
+        The resampled mask.
+    """
+    mask = fetch_icbm152_brain_gm_mask(**kwargs)
+    mask = resample_to_img(
+        mask, target_img, interpolation="nearest", copy=True
+    )
+    return mask
+
+
 """
 A dictionary containing all supported masks and their respective file or
 data.
@@ -28,6 +70,22 @@ data/masks directory. The user can also register their own masks.
 _available_masks: Dict[str, Dict[str, Any]] = {
     "GM_prob0.2": {"family": "Vickery-Patil"},
     "GM_prob0.2_cortex": {"family": "Vickery-Patil"},
+    "compute_brain_mask": {
+        "family": "Callable",
+        "func": compute_brain_mask,
+    },
+    "compute_background_mask": {
+        "family": "Callable",
+        "func": compute_background_mask,
+    },
+    "compute_epi_mask": {
+        "family": "Callable",
+        "func": compute_epi_mask,
+    },
+    "fetch_icbm152_brain_gm_mask": {
+        "family": "Callable",
+        "func": _fetch_icbm152_brain_gm_mask,
+    },
 }
 
 
@@ -88,11 +146,67 @@ def list_masks() -> List[str]:
     return sorted(_available_masks.keys())
 
 
+def get_mask(
+    mask: Union[str, Dict],
+    target_data: Dict[str, Any],
+) -> "Nifti1Image":
+    """Get mask, tailored for the target image.
+
+    Parameters
+    ----------
+    masks : str or dict
+        The name of the mask, or the name of a callable mask and the parameters
+        of the mask.
+    target_data : dict
+        The corresponding item of the data object to which the mask will be
+        applied.
+
+    Returns
+    -------
+    Nifti1Image
+        The mask image.
+    """
+    # 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])
+
+    if isinstance(mask, dict):
+        if len(mask) != 1:
+            raise_error(
+                "The mask dictionary must have only one key, "
+                "the name of the mask."
+            )
+        mask_name = list(mask.keys())[0]
+        mask_params = mask[mask_name]
+    else:
+        mask_name = mask
+        mask_params = None
+
+    mask_object, _ = load_mask(
+        mask_name, path_only=False, resolution=resolution
+    )
+    if callable(mask_object):
+        if mask_params is None:
+            mask_params = {}
+        mask_img = mask_object(target_img, **mask_params)
+    else:  # Mask is a Nifti1Image
+        if mask_params is not None:
+            raise_error("Cannot pass callable params to a non-callable mask.")
+        mask_img = resample_to_img(
+            mask_object,
+            target_img,
+            interpolation="nearest",
+            copy=True,
+        )
+
+    return mask_img
+
+
 def load_mask(
     name: str,
     resolution: Optional[float] = None,
     path_only: bool = False,
-) -> Tuple[Optional["Nifti1Image"], Path]:
+) -> Tuple[Optional[Union["Nifti1Image", Callable]], Optional[Path]]:
     """Load mask.
 
     Parameters
@@ -109,11 +223,12 @@ def load_mask(
 
     Returns
     -------
-    Nifti1Image or None
+    Nifti1Image, Callable or None
         Loaded mask image.
-    pathlib.Path
+    pathlib.Path or None
         File path to the mask image.
     """
+    mask_img = None
     if name not in _available_masks:
         raise_error(
             f"Mask {name} not found. " f"Valid options are: {list_masks()}"
@@ -126,14 +241,16 @@ def load_mask(
         mask_fname = Path(mask_definition["path"])
     elif t_family == "Vickery-Patil":
         mask_fname = _load_vickery_patil_mask(name, resolution)
+    elif t_family == "Callable":
+        mask_img = mask_definition["func"]
+        mask_fname = None
     else:
         raise_error(f"I don't know about the {t_family} mask family.")
 
-    logger.info(f"Loading mask {mask_fname.absolute()}")
-
-    mask_img = None
-    if path_only is False:
-        mask_img = nib.load(mask_fname)
+    if mask_fname is not None:
+        logger.info(f"Loading mask {mask_fname.absolute()}")
+        if path_only is False:
+            mask_img = nib.load(mask_fname)
 
     return mask_img, mask_fname
 

junifer/data/tests/test_masks.py

@@ -5,16 +5,37 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+from typing import Callable, Dict, Union
+
 from pathlib import Path
 
 import pytest
-from numpy.testing import assert_array_almost_equal
+from numpy.testing import (
+    assert_array_almost_equal,
+    assert_array_equal,
+)
+
+from nilearn.image import resample_to_img
+from nilearn.masking import (
+    compute_brain_mask,
+    compute_background_mask,
+    compute_epi_mask,
+)
+from nilearn.datasets import fetch_icbm152_brain_gm_mask
 
 from junifer.data.masks import (
     _load_vickery_patil_mask,
     list_masks,
     load_mask,
     register_mask,
+    get_mask,
+    _available_masks,
+)
+
+from junifer.datareader import DefaultDataReader
+from junifer.testing.datagrabbers import (
+    OasisVBMTestingDatagrabber,
+    SPMAuditoryTestingDatagrabber,
 )
 
 
@@ -151,3 +172,124 @@ def test_vickery_patil() -> None:
 
     with pytest.raises(ValueError, match=r"find a Vickery-Patil mask "):
         _load_vickery_patil_mask("wrong", resolution=2)
+
+
+def test_get_mask() -> None:
+    """Test the get_mask function."""
+    reader = DefaultDataReader()
+    with OasisVBMTestingDatagrabber() as dg:
+        input = dg["sub-01"]
+        input = reader.fit_transform(input)
+        vbm_gm = input["VBM_GM"]
+        vbm_gm_img = vbm_gm["data"]
+        mask = get_mask(mask="GM_prob0.2", 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)
+        res_mask_img = resample_to_img(
+            raw_mask_img,
+            vbm_gm_img,
+            interpolation="nearest",
+            copy=True,
+        )
+        assert_array_equal(mask.get_fdata(), res_mask_img.get_fdata())
+
+
+def test_mask_callable() -> None:
+    """Test using a callable mask."""
+
+    def ident(x):
+        return x
+
+    _available_masks["identity"] = {"family": "Callable", "func": ident}
+    reader = DefaultDataReader()
+    with OasisVBMTestingDatagrabber() as dg:
+        input = dg["sub-01"]
+        input = reader.fit_transform(input)
+        vbm_gm = input["VBM_GM"]
+        vbm_gm_img = vbm_gm["data"]
+        mask = get_mask(mask="identity", target_data=vbm_gm)
+
+        assert_array_equal(mask.get_fdata(), vbm_gm_img.get_fdata())
+
+    del _available_masks["identity"]
+
+
+def test_get_mask_errors() -> None:
+    """Test passing wrong parameters to get_mask."""
+    reader = DefaultDataReader()
+    with OasisVBMTestingDatagrabber() as dg:
+        input = dg["sub-01"]
+        input = reader.fit_transform(input)
+        vbm_gm = input["VBM_GM"]
+        with pytest.raises(ValueError, match=r"only one key"):
+            get_mask(mask={"GM_prob0.2": {}, "Other": {}}, target_data=vbm_gm)
+
+        with pytest.raises(ValueError, match=r"callable params"):
+            get_mask(mask={"GM_prob0.2": {"param": 1}}, target_data=vbm_gm)
+
+
+@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(
+    mask_name: str,
+    function: Callable,
+    params: Union[Dict, None],
+    resample: bool,
+) -> None:
+    """Test using nilearn compute mask functions.
+
+    Parameters
+    ----------
+    mask_name : str
+        Name of the mask.
+    function : callable
+        Function to call.
+    params : dict, optional
+        Parameters to pass to the function.
+    resample : bool
+        Whether to resample the mask to the target data.
+    """
+    reader = DefaultDataReader()
+    with SPMAuditoryTestingDatagrabber() as dg:
+        input = dg["sub001"]
+        input = reader.fit_transform(input)
+        bold = input["BOLD"]
+        bold_img = bold["data"]
+
+        if params is None:
+            params = {}
+            mask_spec = mask_name
+        else:
+            mask_spec = {mask_name: params}
+
+        mask = get_mask(mask=mask_spec, target_data=bold)
+
+        assert_array_equal(mask.affine, bold_img.affine)
+
+        if resample is False:
+            ni_mask = function(bold_img, **params)
+        else:
+            ni_mask = function(**params)
+            # Mask needs resample
+            ni_mask = resample_to_img(
+                ni_mask,
+                bold_img,
+                interpolation="nearest",
+                copy=True,
+            )
+        assert_array_equal(mask.get_fdata(), ni_mask.get_fdata())

junifer/markers/ets_rss.py

@@ -49,7 +49,7 @@ class RSSETSMarker(BaseMarker):
         parcellation: Union[str, List[str]],
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation

junifer/markers/falff/falff_parcels.py

@@ -70,7 +70,7 @@ class AmplitudeLowFrequencyFluctuationParcels(
         lowpass: float = 0.1,
         tr: Optional[float] = None,
         use_afni: Optional[bool] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         method: str = "mean",
         method_params: Optional[Dict] = None,
         name: Optional[str] = None,

junifer/markers/falff/falff_spheres.py

@@ -5,7 +5,7 @@
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, Optional
+from typing import Dict, Optional, Union
 
 from ...api.decorators import register_marker
 from .. import SphereAggregation
@@ -75,7 +75,7 @@ class AmplitudeLowFrequencyFluctuationSpheres(
         lowpass: float = 0.1,
         tr: Optional[float] = None,
         use_afni: Optional[bool] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         method: str = "mean",
         method_params: Optional[Dict] = None,
         name: Optional[str] = None,

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -4,7 +4,7 @@
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Optional, Union
 
 import pandas as pd
 
@@ -47,7 +47,7 @@ class CrossParcellationFC(BaseMarker):
         parcellation_two: str,
         aggregation_method: str = "mean",
         correlation_method: str = "pearson",
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         name: Optional[str] = None,
     ) -> None:
         if parcellation_one == parcellation_two:

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -5,7 +5,7 @@
 
 
 from abc import abstractmethod
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Optional, Union
 
 from nilearn.connectome import ConnectivityMeasure
 from sklearn.covariance import EmpiricalCovariance
@@ -50,7 +50,7 @@ class FunctionalConnectivityBase(BaseMarker):
         agg_method_params: Optional[Dict] = None,
         cor_method: str = "covariance",
         cor_method_params: Optional[Dict] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.agg_method = agg_method

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -51,7 +51,7 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
         agg_method_params: Optional[Dict] = None,
         cor_method: str = "covariance",
         cor_method_params: Optional[Dict] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation

junifer/markers/functional_connectivity/functional_connectivity_spheres.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, Optional
+from typing import Any, Dict, Optional, Union
 
 from ...api.decorators import register_marker
 from ..sphere_aggregation import SphereAggregation
@@ -57,7 +57,7 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
         agg_method_params: Optional[Dict] = None,
         cor_method: str = "covariance",
         cor_method_params: Optional[Dict] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords

junifer/markers/parcel_aggregation.py

@@ -11,7 +11,7 @@ from nilearn.image import math_img, new_img_like, resample_to_img
 from nilearn.maskers import NiftiMasker
 
 from ..api.decorators import register_marker
-from ..data import load_mask, load_parcellation
+from ..data import get_mask, load_parcellation
 from ..stats import get_aggfunc_by_name
 from ..utils import logger
 from .base import BaseMarker
@@ -52,7 +52,7 @@ class ParcelAggregation(BaseMarker):
         parcellation: Union[str, List[str]],
         method: str,
         method_params: Optional[Dict[str, Any]] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         on: Union[List[str], str, None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -126,14 +126,14 @@ class ParcelAggregation(BaseMarker):
             * ``columns`` : the column labels for the computed values as a list
 
         """
-        t_input = input["data"]
+        t_input_img = input["data"]
         logger.debug(f"Parcel aggregation using {self.method}")
         agg_func = get_aggfunc_by_name(
             name=self.method,
             func_params=self.method_params,
         )
         # Get the min of the voxels sizes and use it as the resolution
-        resolution = np.min(t_input.header.get_zooms()[:3])
+        resolution = np.min(t_input_img.header.get_zooms()[:3])
 
         # Load the parcellations
         all_parcelations = []
@@ -146,7 +146,7 @@ class ParcelAggregation(BaseMarker):
             # Resample all of them to the image
             t_parcellation_img_res = resample_to_img(
                 t_parcellation,
-                t_input,
+                t_input_img,
                 interpolation="nearest",
                 copy=True,
             )
@@ -186,13 +186,8 @@ class ParcelAggregation(BaseMarker):
 
         if self.mask is not None:
             logger.debug(f"Masking with {self.mask}")
-            mask_img, _ = load_mask(name=self.mask, resolution=resolution)
-            mask_img = resample_to_img(
-                mask_img,
-                t_input,
-                interpolation="nearest",
-                copy=True,
-            )
+            mask_img = get_mask(mask=self.mask, target_data=input)
+
             parcellation_bin = math_img(
                 "np.logical_and(img, mask)",
                 img=parcellation_bin,
@@ -201,11 +196,11 @@ class ParcelAggregation(BaseMarker):
 
         logger.debug("Masking")
         masker = NiftiMasker(
-            parcellation_bin, target_affine=t_input.affine
+            parcellation_bin, target_affine=t_input_img.affine
         )  # type: ignore
 
         # Mask the input data and the parcellation
-        data = masker.fit_transform(t_input)
+        data = masker.fit_transform(t_input_img)
         parcellation_values = masker.transform(parcellation_img_res)
         parcellation_values = np.squeeze(parcellation_values).astype(int)
 

junifer/markers/reho/reho_parcels.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import Any, Dict, Optional
+from typing import Any, Dict, Optional, Union
 
 import numpy as np
 
@@ -91,7 +91,7 @@ class ReHoParcels(ReHoBase):
         reho_params: Optional[Dict] = None,
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation

junifer/markers/reho/reho_spheres.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import Any, Dict, Optional
+from typing import Any, Dict, Optional, Union
 
 import numpy as np
 
@@ -97,7 +97,7 @@ class ReHoSpheres(ReHoBase):
         reho_params: Optional[Dict] = None,
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords

junifer/markers/sphere_aggregation.py

@@ -7,7 +7,7 @@
 from typing import Any, Dict, List, Optional, Union
 
 from ..api.decorators import register_marker
-from ..data import load_coordinates, load_mask
+from ..data import load_coordinates, get_mask
 from ..external.nilearn import JuniferNiftiSpheresMasker
 from ..stats import get_aggfunc_by_name
 from ..utils import logger
@@ -56,7 +56,7 @@ class SphereAggregation(BaseMarker):
         radius: Optional[float] = None,
         method: str = "mean",
         method_params: Optional[Dict[str, Any]] = None,
-        mask: Optional[str] = None,
+        mask: Union[str, Dict, None] = None,
         on: Union[List[str], str, None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -129,7 +129,7 @@ class SphereAggregation(BaseMarker):
             * ``columns`` : the column labels for the computed values as a list
 
         """
-        t_input = input["data"]
+        t_input_img = input["data"]
         logger.debug(f"Sphere aggregation using {self.method}")
         # Get aggregation function
         agg_func = get_aggfunc_by_name(
@@ -139,7 +139,7 @@ class SphereAggregation(BaseMarker):
         mask_img = None
         if self.mask is not None:
             logger.debug(f"Masking with {self.mask}")
-            mask_img, _ = load_mask(self.mask)
+            mask_img = get_mask(mask=self.mask, target_data=input)
         # Get seeds and labels
         coords, out_labels = load_coordinates(name=self.coords)
         masker = JuniferNiftiSpheresMasker(
@@ -149,7 +149,7 @@ class SphereAggregation(BaseMarker):
             agg_func=agg_func,
         )
         # Fit and transform the marker on the data
-        out_values = masker.fit_transform(t_input)
+        out_values = masker.fit_transform(t_input_img)
         # Format the output
         out = {"data": out_values, "columns": out_labels}
         return out

junifer/markers/tests/test_parcel_aggregation.py

@@ -12,6 +12,7 @@ import pytest
 from nilearn import datasets
 from nilearn.image import concat_imgs, math_img, new_img_like, resample_to_img
 from nilearn.maskers import NiftiLabelsMasker, NiftiMasker
+from nilearn.masking import compute_brain_mask
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 from scipy.stats import trim_mean
 
@@ -240,6 +241,54 @@ def test_ParcelAggregation_3D_mask() -> None:
     assert_array_almost_equal(auto, jun_values3d_mean)
 
 
+def test_ParcelAggregation_3D_mask_computed() -> None:
+    """Test ParcelAggregation object on 3D images with computed masks."""
+
+    # Get the testing parcellation (for nilearn)
+    parcellation = datasets.fetch_atlas_schaefer_2018(n_rois=100)
+
+    # Get the oasis VBM data
+    oasis_dataset = datasets.fetch_oasis_vbm(n_subjects=1)
+    vbm = oasis_dataset.gray_matter_maps[0]
+    img = nib.load(vbm)
+
+    # Get one mask
+    mask_img = compute_brain_mask(img, threshold=0.2)
+
+    # Create NiftiLabelsMasker
+    nifti_masker = NiftiLabelsMasker(
+        labels_img=parcellation.maps, mask_img=mask_img
+    )
+    auto = nifti_masker.fit_transform(img)
+
+    # Get one mask
+    mask_img = compute_brain_mask(img, threshold=0.5)
+
+    # Create NiftiLabelsMasker
+    nifti_masker = NiftiLabelsMasker(
+        labels_img=parcellation.maps, mask_img=mask_img
+    )
+    auto_bad = nifti_masker.fit_transform(img)
+
+    # Use the ParcelAggregation object
+    marker = ParcelAggregation(
+        parcellation="Schaefer100x7",
+        method="mean",
+        mask={"compute_brain_mask": {"threshold": 0.2}},
+        name="gmd_schaefer100x7_mean",
+        on="VBM_GM",
+    )  # Test passing "on" as a keyword argument
+    input = {"VBM_GM": {"data": img, "meta": {}}}
+    jun_values3d_mean = marker.fit_transform(input)["VBM_GM"]["data"]
+
+    assert jun_values3d_mean.ndim == 2
+    assert jun_values3d_mean.shape[0] == 1
+    assert_array_almost_equal(auto, jun_values3d_mean)
+
+    with pytest.raises(AssertionError):
+        assert_array_almost_equal(jun_values3d_mean, auto_bad)
+
+
 def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
     """Test ParcelAggregation with multiple non-overlapping parcellations.