junifer 0.0.2.dev138__py3-none-any.whl → 0.0.2.dev140__py3-none-any.whl

junifer/markers/ets_rss.py

@@ -32,10 +32,10 @@ class RSSETSMarker(BaseMarker):
     agg_method_params : dict, optional
         Parameters to pass to the aggregation function. Check valid options in
         :func:`junifer.stats.get_aggfunc_by_name` (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. If None, will use the class name (default
         None).
@@ -49,13 +49,13 @@ class RSSETSMarker(BaseMarker):
         parcellation: Union[str, List[str]],
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation
         self.agg_method = agg_method
         self.agg_method_params = agg_method_params
-        self.mask = mask
+        self.masks = masks
         super().__init__(name=name)
 
     def get_valid_inputs(self) -> List[str]:
@@ -126,11 +126,11 @@ class RSSETSMarker(BaseMarker):
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
-            mask=self.mask,
+            masks=self.masks,
         )
         # Compute the parcel aggregation
         out = parcel_aggregation.compute(input=input, extra_input=extra_input)
-        edge_ts = _ets(out["data"])
+        edge_ts, _ = _ets(out["data"])
         # Compute the RSS
         out["data"] = np.sum(edge_ts**2, 1) ** 0.5
         # Set correct column label

junifer/markers/falff/falff_parcels.py

@@ -35,10 +35,10 @@ class AmplitudeLowFrequencyFluctuationParcels(
     use_afni : bool, optional
         Whether to use AFNI for computing. If None, will use AFNI only
         if available (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     method : str, optional
         The method to perform aggregation using. Check valid options in
         :func:`junifer.stats.get_aggfunc_by_name` (default "mean").
@@ -70,13 +70,13 @@ class AmplitudeLowFrequencyFluctuationParcels(
         lowpass: float = 0.1,
         tr: Optional[float] = None,
         use_afni: Optional[bool] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         method: str = "mean",
         method_params: Optional[Dict] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation
-        self.mask = mask
+        self.masks = masks
         self.method = method
         self.method_params = method_params
         super().__init__(
@@ -116,7 +116,7 @@ class AmplitudeLowFrequencyFluctuationParcels(
             parcellation=self.parcellation,
             method=self.method,
             method_params=self.method_params,
-            mask=self.mask,
+            masks=self.masks,
             on="fALFF",
         )
 

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, Union
+from typing import Dict, List, Optional, Union
 
 from ...api.decorators import register_marker
 from .. import SphereAggregation
@@ -39,10 +39,10 @@ class AmplitudeLowFrequencyFluctuationSpheres(
     use_afni : bool, optional
         Whether to use AFNI for computing. If None, will use AFNI only
         if available (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     method : str, optional
         The method to perform aggregation using. Check valid options in
         :func:`junifer.stats.get_aggfunc_by_name` (default "mean").
@@ -75,14 +75,14 @@ class AmplitudeLowFrequencyFluctuationSpheres(
         lowpass: float = 0.1,
         tr: Optional[float] = None,
         use_afni: Optional[bool] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         method: str = "mean",
         method_params: Optional[Dict] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords
         self.radius = radius
-        self.mask = mask
+        self.masks = masks
         self.method = method
         self.method_params = method_params
         super().__init__(
@@ -123,7 +123,7 @@ class AmplitudeLowFrequencyFluctuationSpheres(
             radius=self.radius,
             method=self.method,
             method_params=self.method_params,
-            mask=self.mask,
+            masks=self.masks,
             on="fALFF",
         )
 

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -30,10 +30,10 @@ class CrossParcellationFC(BaseMarker):
     correlation_method : str, optional
         Any method that can be passed to
         :any:`pandas.DataFrame.corr` (default "pearson").
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. If None, will use the class name
         (default None).
@@ -47,7 +47,7 @@ class CrossParcellationFC(BaseMarker):
         parcellation_two: str,
         aggregation_method: str = "mean",
         correlation_method: str = "pearson",
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         if parcellation_one == parcellation_two:
@@ -58,7 +58,7 @@ class CrossParcellationFC(BaseMarker):
         self.parcellation_two = parcellation_two
         self.aggregation_method = aggregation_method
         self.correlation_method = correlation_method
-        self.mask = mask
+        self.masks = masks
         super().__init__(on=["BOLD"], name=name)
 
     def get_valid_inputs(self) -> List[str]:
@@ -129,12 +129,12 @@ class CrossParcellationFC(BaseMarker):
         parcellation_one_dict = ParcelAggregation(
             parcellation=self.parcellation_one,
             method=self.aggregation_method,
-            mask=self.mask,
+            masks=self.masks,
         ).compute(input)
         parcellation_two_dict = ParcelAggregation(
             parcellation=self.parcellation_two,
             method=self.aggregation_method,
-            mask=self.mask,
+            masks=self.masks,
         ).compute(input)
 
         parcellated_ts_one = parcellation_one_dict["data"]

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -35,10 +35,10 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
     cor_method_params : dict, optional
         Parameters to pass to the correlation function. Check valid options in
         :class:`nilearn.connectome.ConnectivityMeasure` (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. If None, will use the class name (default
         None).
@@ -59,7 +59,7 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
         agg_method_params: Optional[Dict] = None,
         cor_method: str = "covariance",
         cor_method_params: Optional[Dict] = None,
-        mask: Optional[str] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation
@@ -68,7 +68,7 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
             agg_method_params=agg_method_params,
             cor_method=cor_method,
             cor_method_params=cor_method_params,
-            mask=mask,
+            masks=masks,
             name=name,
         )
 
@@ -78,7 +78,7 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
-            mask=self.mask,
+            masks=self.masks,
             on="BOLD",
         )
 

junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, Optional
+from typing import Any, Dict, List, Optional, Union
 
 from ...api.decorators import register_marker
 from ..sphere_aggregation import SphereAggregation
@@ -37,10 +37,10 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
     cor_method_params : dict, optional
         Parameters to pass to the correlation function. Check valid options in
         :class:`nilearn.connectome.ConnectivityMeasure` (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. By default, it will use
         KIND_EdgeCentricFCSpheres where KIND is the kind of data it
@@ -63,7 +63,7 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
         agg_method_params: Optional[Dict] = None,
         cor_method: str = "covariance",
         cor_method_params: Optional[Dict] = None,
-        mask: Optional[str] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords
@@ -75,7 +75,7 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
             agg_method_params=agg_method_params,
             cor_method=cor_method,
             cor_method_params=cor_method_params,
-            mask=mask,
+            masks=masks,
             name=name,
         )
 
@@ -86,7 +86,7 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
             radius=self.radius,
             method=self.agg_method,
             method_params=self.agg_method_params,
-            mask=self.mask,
+            masks=self.masks,
             on="BOLD",
         )
         bold_aggregated = sphere_aggregation.compute(input)

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -32,10 +32,10 @@ class FunctionalConnectivityBase(BaseMarker):
     cor_method_params : dict, optional
         Parameters to pass to the correlation function. Check valid options in
         :class:`nilearn.connectome.ConnectivityMeasure` (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. If None, will use the class name (default
         None).
@@ -50,7 +50,7 @@ class FunctionalConnectivityBase(BaseMarker):
         agg_method_params: Optional[Dict] = None,
         cor_method: str = "covariance",
         cor_method_params: Optional[Dict] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.agg_method = agg_method
@@ -62,7 +62,7 @@ class FunctionalConnectivityBase(BaseMarker):
         self.cor_method_params["empirical"] = self.cor_method_params.get(
             "empirical", False
         )
-        self.mask = mask
+        self.masks = masks
         super().__init__(on="BOLD", name=name)
 
     @abstractmethod
@@ -134,7 +134,7 @@ class FunctionalConnectivityBase(BaseMarker):
         # Compute correlation
         if self.cor_method_params["empirical"]:
             connectivity = ConnectivityMeasure(
-                cov_estimator=EmpiricalCovariance(),
+                cov_estimator=EmpiricalCovariance(),  # type: ignore
                 kind=self.cor_method,
             )
         else:

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -34,10 +34,10 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
     cor_method_params : dict, optional
         Parameters to pass to the correlation function. Check valid options in
         :class:`nilearn.connectome.ConnectivityMeasure` (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. If None, will use the class name (default
         None).
@@ -51,7 +51,7 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
         agg_method_params: Optional[Dict] = None,
         cor_method: str = "covariance",
         cor_method_params: Optional[Dict] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation
@@ -60,7 +60,7 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
             agg_method_params=agg_method_params,
             cor_method=cor_method,
             cor_method_params=cor_method_params,
-            mask=mask,
+            masks=masks,
             name=name,
         )
 
@@ -70,7 +70,7 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
-            mask=self.mask,
+            masks=self.masks,
             on="BOLD",
         )
         # Return the 2D timeseries after parcel aggregation

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, Union
+from typing import Any, Dict, List, Optional, Union
 
 from ...api.decorators import register_marker
 from ..sphere_aggregation import SphereAggregation
@@ -38,10 +38,10 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
     cor_method_params : dict, optional
         Parameters to pass to the correlation function. Check valid options in
         :class:`nilearn.connectome.ConnectivityMeasure` (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. By default, it will use
         KIND_FunctionalConnectivitySpheres where KIND is the kind of data it
@@ -57,7 +57,7 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
         agg_method_params: Optional[Dict] = None,
         cor_method: str = "covariance",
         cor_method_params: Optional[Dict] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords
@@ -69,7 +69,7 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
             agg_method_params=agg_method_params,
             cor_method=cor_method,
             cor_method_params=cor_method_params,
-            mask=mask,
+            masks=masks,
             name=name,
         )
 
@@ -80,7 +80,7 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
             radius=self.radius,
             method=self.agg_method,
             method_params=self.agg_method_params,
-            mask=self.mask,
+            masks=self.masks,
             on="BOLD",
         )
         # Return the 2D timeseries after sphere aggregation

junifer/markers/functional_connectivity/tests/test_functional_connectivity_base.py

@@ -6,10 +6,12 @@
 import pytest
 
 # done to keep line length 79
-import junifer.markers.functional_connectivity as fc
+from junifer.markers.functional_connectivity import (
+    functional_connectivity_base as fcb,
+)
 
 
 def test_base_functional_connectivity_marker_abstractness() -> None:
     """Test FunctionalConnectivityBase is an abstract base class."""
     with pytest.raises(TypeError, match="abstract"):
-        fc.functional_connectivity_base.FunctionalConnectivityBase()
+        fcb.FunctionalConnectivityBase()  # type: ignore

junifer/markers/parcel_aggregation.py

@@ -32,10 +32,10 @@ class ParcelAggregation(BaseMarker):
     method_params : dict, optional
         Parameters to pass to the aggregation function. Check valid options in
         :func:`junifer.stats.get_aggfunc_by_name`.
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     on : {"T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"} \
          or list of the options, optional
         The data types to apply the marker to. If None, will work on all
@@ -52,7 +52,7 @@ class ParcelAggregation(BaseMarker):
         parcellation: Union[str, List[str]],
         method: str,
         method_params: Optional[Dict[str, Any]] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         on: Union[List[str], str, None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -61,7 +61,7 @@ class ParcelAggregation(BaseMarker):
         self.parcellation = parcellation
         self.method = method
         self.method_params = method_params or {}
-        self.mask = mask
+        self.masks = masks
         super().__init__(on=on, name=name)
 
     def get_valid_inputs(self) -> List[str]:
@@ -184,9 +184,11 @@ class ParcelAggregation(BaseMarker):
             img=parcellation_img_res,
         )
 
-        if self.mask is not None:
-            logger.debug(f"Masking with {self.mask}")
-            mask_img = get_mask(mask=self.mask, target_data=input)
+        if self.masks is not None:
+            logger.debug(f"Masking with {self.masks}")
+            mask_img = get_mask(
+                masks=self.masks, target_data=input, extra_input=extra_input
+            )
 
             parcellation_bin = math_img(
                 "np.logical_and(img, mask)",

junifer/markers/reho/reho_parcels.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import Any, Dict, Optional, Union
+from typing import Any, Dict, List, Optional, Union
 
 import numpy as np
 
@@ -74,10 +74,10 @@ class ReHoParcels(ReHoBase):
     agg_method_params : dict, optional
         Parameters to pass to the aggregation function. Check valid options in
         :func:`junifer.stats.get_aggfunc_by_name` (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. If None, it will use the class name
         (default None).
@@ -91,14 +91,14 @@ class ReHoParcels(ReHoBase):
         reho_params: Optional[Dict] = None,
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.parcellation = parcellation
         self.reho_params = reho_params
         self.agg_method = agg_method
         self.agg_method_params = agg_method_params
-        self.mask = mask
+        self.masks = masks
         super().__init__(use_afni=use_afni, name=name)
 
     def compute(
@@ -136,7 +136,7 @@ class ReHoParcels(ReHoBase):
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
-            mask=self.mask,
+            masks=self.masks,
             on="BOLD",
         )
         # Perform aggregation on reho map

junifer/markers/reho/reho_spheres.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import Any, Dict, Optional, Union
+from typing import Any, Dict, List, Optional, Union
 
 import numpy as np
 
@@ -79,10 +79,10 @@ class ReHoSpheres(ReHoBase):
         (default None).
     agg_method_params : dict, optional
         The parameters to pass to the aggregation method (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     name : str, optional
         The name of the marker. If None, it will use the class name
         (default None).
@@ -97,7 +97,7 @@ class ReHoSpheres(ReHoBase):
         reho_params: Optional[Dict] = None,
         agg_method: str = "mean",
         agg_method_params: Optional[Dict] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         name: Optional[str] = None,
     ) -> None:
         self.coords = coords
@@ -105,7 +105,7 @@ class ReHoSpheres(ReHoBase):
         self.reho_params = reho_params
         self.agg_method = agg_method
         self.agg_method_params = agg_method_params
-        self.mask = mask
+        self.masks = masks
         super().__init__(use_afni=use_afni, name=name)
 
     def compute(
@@ -144,7 +144,7 @@ class ReHoSpheres(ReHoBase):
             radius=self.radius,
             method=self.agg_method,
             method_params=self.agg_method_params,
-            mask=self.mask,
+            masks=self.masks,
             on="BOLD",
         )
         # Perform aggregation on reho map

junifer/markers/sphere_aggregation.py

@@ -34,10 +34,10 @@ class SphereAggregation(BaseMarker):
         (default "mean").
     method_params : dict, optional
         The parameters to pass to the aggregation method (default None).
-    mask : str, optional
-        The name of the mask to apply to regions before extracting signals.
-        Check valid options by calling :func:`junifer.data.masks.list_masks`
-        (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
     on : {"T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"} or \
          list of the options, optional
         The data types to apply the marker to. If None, will work on all
@@ -56,7 +56,7 @@ class SphereAggregation(BaseMarker):
         radius: Optional[float] = None,
         method: str = "mean",
         method_params: Optional[Dict[str, Any]] = None,
-        mask: Union[str, Dict, None] = None,
+        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
         on: Union[List[str], str, None] = None,
         name: Optional[str] = None,
     ) -> None:
@@ -64,7 +64,7 @@ class SphereAggregation(BaseMarker):
         self.radius = radius
         self.method = method
         self.method_params = method_params or {}
-        self.mask = mask
+        self.masks = masks
         super().__init__(on=on, name=name)
 
     def get_valid_inputs(self) -> List[str]:
@@ -137,9 +137,11 @@ class SphereAggregation(BaseMarker):
         )
         # Load mask
         mask_img = None
-        if self.mask is not None:
-            logger.debug(f"Masking with {self.mask}")
-            mask_img = get_mask(mask=self.mask, target_data=input)
+        if self.masks is not None:
+            logger.debug(f"Masking with {self.masks}")
+            mask_img = get_mask(
+                masks=self.masks, target_data=input, extra_input=extra_input
+            )
         # Get seeds and labels
         coords, out_labels = load_coordinates(name=self.coords)
         masker = JuniferNiftiSpheresMasker(