junifer 0.0.6.dev219__tar.gz → 0.0.6.dev248__tar.gz

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev219
+Version: 0.0.6.dev248
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -111,6 +111,7 @@ The documentation is available at [https://juaml.github.io/junifer](https://juam
   * `preprocess`: Preprocessing module.
   * `storage`: Storage module.
   * `testing`: Testing components module.
+  * `typing`: Type hints module.
   * `utils`: Utilities module (e.g. logging).
 
 ## Installation

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/README.md

@@ -39,6 +39,7 @@ The documentation is available at [https://juaml.github.io/junifer](https://juam
   * `preprocess`: Preprocessing module.
   * `storage`: Storage module.
   * `testing`: Testing components module.
+  * `typing`: Type hints module.
   * `utils`: Utilities module (e.g. logging).
 
 ## Installation

junifer-0.0.6.dev248/docs/changes/newsfragments/390.change

@@ -0,0 +1 @@
+:class:`.SpaceWarper`'s ``using`` now supports ``"auto"`` allowing auto tool selection based on DataGrabber specification by `Synchon Mandal`_

junifer-0.0.6.dev248/docs/changes/newsfragments/390.enh

@@ -0,0 +1 @@
+Update ``Warp`` data type to be a list of dictionaries and adapt to allow multiple transforms to be specified by `Synchon Mandal`_

junifer-0.0.6.dev248/docs/changes/newsfragments/392.feature

@@ -0,0 +1 @@
+Introduce ``junifer.typing`` sub-module to organise internal and external type hints by `Synchon Mandal`_

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/docs/extending/dependencies.rst

@@ -28,7 +28,7 @@ component depends on. For example, for :class:`.RSSETSMarker`, we have:
 
 .. code-block:: python
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
 The type annotation is for documentation and static type checking purposes.
 Although not required, we highly recommend you use them, your future self
@@ -39,12 +39,12 @@ and others who use it will thank you.
 Handling external dependencies from toolboxes
 ---------------------------------------------
 
-You can also specify dependencies of external toolboxes like AFIN, FSL and ANTs,
+You can also specify dependencies of external toolboxes like AFNI, FSL and ANTs,
 by having a class attribute like so:
 
 .. code-block:: python
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "afni",
             "commands": ["3dReHo", "3dAFNItoNIFTI"],
@@ -78,7 +78,7 @@ that it shows the problem a bit better and how we solve it:
 
     class SpaceWarper(BasePreprocessor):
         # docstring
-        _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+        _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
             {
                 "using": "fsl",
                 "depends_on": FSLWarper,
@@ -87,6 +87,10 @@ that it shows the problem a bit better and how we solve it:
                 "using": "ants",
                 "depends_on": ANTsWarper,
             },
+            {
+                "using": "auto",
+                "depends_on": [FSLWarper, ANTsWarper],
+            },
         ]
 
         def __init__(
@@ -100,13 +104,20 @@ Here, you see a new class attribute ``_CONDITIONAL_DEPENDENCIES`` which is a
 list of dictionaries with two keys:
 
 * ``using`` (str) : lowercased name of the toolbox
-* ``depends_on`` (object) : a class which implements the particular tool's use
+* ``depends_on`` (object or list of objects) : a class or list of classes which \
+  implements the particular tool's use
 
 It is mandatory to have the ``using`` positional argument in the constructor in
 this case as the validation starts with this and moves further. It is also
 mandatory to only allow the value of ``using`` argument to be one of them
 specified in the ``using`` key of ``_CONDITIONAL_DEPENDENCIES`` entries.
 
+For some cases, like we have here, it might be worth to have ``"auto"`` for
+``"using"`` which eases the choice of a particular tool by the user and
+instead lets ``junifer`` do it automatically. In that case, ``"depends_on"``
+needs to be a list of the tool implementation classes. This also requires the
+user to have all the tools in the ``PATH``.
+
 For brevity, we only show the ``FSLWarper`` here but ``ANTsWarper`` looks very
 similar. ``FSLWarper`` looks like this (only the relevant part is shown here):
 
@@ -115,14 +126,14 @@ similar. ``FSLWarper`` looks like this (only the relevant part is shown here):
     class FSLWarper:
         # docstring
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
             {
                 "name": "fsl",
                 "commands": ["flirt", "applywarp"],
             },
         ]
 
-        _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nibabel"}
 
         def preprocess(
             self,

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/docs/extending/marker.rst

@@ -196,15 +196,16 @@ Finally, we need to register the Marker using the ``@register_marker`` decorator
     from junifer.api.decorators import register_marker
     from junifer.data import get_parcellation
     from junifer.markers import BaseMarker
+    from junifer.typing import Dependencies, MarkerInOutMappings
     from nilearn.maskers import NiftiLabelsMasker
 
 
     @register_marker
     class ParcelMean(BaseMarker):
 
-        _DEPENDENCIES = {"nilearn", "numpy"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "numpy"}
 
-        _MARKER_INOUT_MAPPINGS: ClassVar[dict[str, dict[str, str]]] = {
+        _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
             "BOLD": {
                 "parcel_mean": "timeseries",
             },

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/docs/understanding/preprocess.rst

@@ -146,14 +146,23 @@ Warping to subject's native space
 To warp to subject's native space, the dataset needs to provide ``T1w`` and
 ``Warp`` data types and the DataGrabber needs to at least have
 ``["BOLD", "T1w", "Warp"]`` (if you are warping ``BOLD``) as the ``types``
-parameter's value. The :class:`.SpaceWarper`'s ``reference`` parameter needs
+parameter's value.
+
+The :class:`.SpaceWarper`'s ``reference`` parameter needs
 to be set to ``T1w``, which means that the ``BOLD`` data will be transformed
 using the ``T1w`` as reference (it's resampled internally to match the
-resolution of the ``BOLD``). The ``Warp`` data type is new and it's only purpose
-is to provide the warp or transformation file (can be linear, non-linear or
-linear + non-linear transform) for the purpose. For ``using`` parameter, you can
-pass either ``"fsl"`` or ``"ants"`` depending on the warp or transformation file
-format.
+resolution of the ``BOLD``).
+
+The ``Warp`` data type provides the warp or transformation file (can be linear,
+non-linear or linear + non-linear transform) for the purpose. For ``using``
+parameter, you can pass either ``fsl`` or ``ants`` depending on the warp or
+transformation file format. You can also provide ``auto`` to ``using`` in which
+case either ``FSL`` or ``ANTs`` will be used based on the file format provided
+by the DataGrabber. This also requires that both the tools are in the ``PATH``.
+
+And finally, you would need to set the ``on`` parameter to ``BOLD`` to make it
+clear which data type you intend to warp, as the :class:`.SpaceWarper` is also
+capable of warping ``T1w``.
 
 An example YAML might look like this:
 
@@ -163,6 +172,7 @@ An example YAML might look like this:
          - kind: SpaceWarper
            using: fsl
            reference: T1w
+           on: BOLD
 
 .. _preprocess_warping_template:
 
@@ -174,8 +184,8 @@ data type that you want to work on) in ``MNI152NLin6Asym`` template space but
 you would like to compute features in ``MNI152NLin2009cAsym`` template space,
 you can also use the :class:`.SpaceWarper` by setting the ``reference``
 parameter to the template space's name, in this case,
-``reference="MNI152NLin2009cAsym"``. The ``using`` parameter needs to be set
-to ``"ants"`` as we need it to warp the data.
+``reference: MNI152NLin2009cAsym``. The ``using`` parameter needs to be set
+to ``ants`` as we need it to warp the data.
 
 .. note::
 
@@ -190,3 +200,4 @@ For an YAML example:
          - kind: SpaceWarper
            using: ants
            reference: MNI152NLin2009cAsym
+           on: BOLD

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/__init__.pyi

@@ -13,6 +13,7 @@ __all__ = [
     "external",
     "onthefly",
     "testing",
+    "typing",
     "__version__",
 ]
 
@@ -30,6 +31,7 @@ from . import (
     utils,
     external,
     testing,
+    typing,
     onthefly,
 )
 from ._version import __version__

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev219'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev219')
+__version__ = version = '0.0.6.dev248'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev248')

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/api/decorators.py

@@ -8,6 +8,7 @@
 from typing import Type
 
 from ..pipeline import PipelineComponentRegistry
+from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 
 
 __all__ = [
@@ -19,7 +20,7 @@ __all__ = [
 ]
 
 
-def register_datagrabber(klass: Type) -> Type:
+def register_datagrabber(klass: DataGrabberLike) -> DataGrabberLike:
     """Register DataGrabber.
 
     Registers the DataGrabber so it can be used by name.
@@ -73,7 +74,7 @@ def register_datareader(klass: Type) -> Type:
     return klass
 
 
-def register_preprocessor(klass: Type) -> Type:
+def register_preprocessor(klass: PreprocessorLike) -> PreprocessorLike:
     """Preprocessor registration decorator.
 
     Registers the preprocessor so it can be used by name.
@@ -96,7 +97,7 @@ def register_preprocessor(klass: Type) -> Type:
     return klass
 
 
-def register_marker(klass: Type) -> Type:
+def register_marker(klass: MarkerLike) -> MarkerLike:
     """Marker registration decorator.
 
     Registers the marker so it can be used by name.
@@ -119,7 +120,7 @@ def register_marker(klass: Type) -> Type:
     return klass
 
 
-def register_storage(klass: Type) -> Type:
+def register_storage(klass: StorageLike) -> StorageLike:
     """Storage registration decorator.
 
     Registers the storage so it can be used by name.

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/api/functions.py

@@ -11,22 +11,23 @@ from pathlib import Path
 from typing import Dict, List, Optional, Tuple, Union
 
 from ..api.queue_context import GnuParallelLocalAdapter, HTCondorAdapter
-from ..datagrabber.base import BaseDataGrabber
-from ..markers.base import BaseMarker
+from ..datagrabber import BaseDataGrabber
+from ..markers import BaseMarker
 from ..pipeline import (
     MarkerCollection,
     PipelineComponentRegistry,
     WorkDirManager,
 )
-from ..preprocess.base import BasePreprocessor
-from ..storage.base import BaseFeatureStorage
+from ..preprocess import BasePreprocessor
+from ..storage import BaseFeatureStorage
+from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 from ..utils import logger, raise_error, yaml
 
 
 __all__ = ["run", "collect", "queue", "reset", "list_elements"]
 
 
-def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:
+def _get_datagrabber(datagrabber_config: Dict) -> DataGrabberLike:
     """Get DataGrabber.
 
     Parameters
@@ -48,7 +49,7 @@ def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:
     )
 
 
-def _get_preprocessor(preprocessing_config: Dict) -> BasePreprocessor:
+def _get_preprocessor(preprocessing_config: Dict) -> PreprocessorLike:
     """Get Preprocessor.
 
     Parameters
@@ -70,7 +71,7 @@ def _get_preprocessor(preprocessing_config: Dict) -> BasePreprocessor:
     )
 
 
-def _get_marker(marker_config: Dict) -> BaseMarker:
+def _get_marker(marker_config: Dict) -> MarkerLike:
     """Get Marker.
 
     Parameters
@@ -92,7 +93,7 @@ def _get_marker(marker_config: Dict) -> BaseMarker:
     )
 
 
-def _get_storage(storage_config: Dict) -> BaseFeatureStorage:
+def _get_storage(storage_config: Dict) -> StorageLike:
     """Get Storage.
 
     Parameters

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/data/coordinates/_ants_coordinates_warper.py

@@ -26,7 +26,7 @@ class ANTsCoordinatesWarper:
         self,
         seeds: ArrayLike,
         target_data: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        warp_data: Dict[str, Any],
     ) -> ArrayLike:
         """Warp ``seeds`` to correct space.
 
@@ -37,10 +37,8 @@ class ANTsCoordinatesWarper:
         target_data : dict
             The corresponding item of the data object to which the coordinates
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of coordinates
-            (default None).
+        warp_data : dict or None
+            The warp data item of the data object.
 
         Returns
         -------
@@ -79,7 +77,7 @@ class ANTsCoordinatesWarper:
             "-f 0",
             f"-i {pretransform_coordinates_path.resolve()}",
             f"-o {transformed_coords_path.resolve()}",
-            f"-t {extra_input['Warp']['path'].resolve()};",
+            f"-t {warp_data['path'].resolve()}",
         ]
         # Call antsApplyTransformsToPoints
         run_ext_cmd(

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/data/coordinates/_coordinates.py

@@ -14,6 +14,7 @@ from numpy.typing import ArrayLike
 from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
+from ..utils import get_native_warper
 from ._ants_coordinates_warper import ANTsCoordinatesWarper
 from ._fsl_coordinates_warper import FSLCoordinatesWarper
 
@@ -311,7 +312,8 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         Raises
         ------
         RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
+            If warping specification required for warping using ANTs, is not
+            found.
         ValueError
             If ``extra_input`` is None when ``target_data``'s space is native.
 
@@ -329,27 +331,38 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     f"{target_data['space']} space for further computation."
                 )
 
-            # Check for warp file type to use correct tool
-            warp_file_ext = extra_input["Warp"]["path"].suffix
-            if warp_file_ext == ".mat":
+            # Get native space warper spec
+            warper_spec = get_native_warper(
+                target_data=target_data,
+                other_data=extra_input,
+            )
+            # Conditional for warping tool implementation
+            if warper_spec["warper"] == "fsl":
                 seeds = FSLCoordinatesWarper().warp(
                     seeds=seeds,
                     target_data=target_data,
-                    extra_input=extra_input,
+                    warp_data=warper_spec,
+                )
+            elif warper_spec["warper"] == "ants":
+                # Requires the inverse warp
+                inverse_warper_spec = get_native_warper(
+                    target_data=target_data,
+                    other_data=extra_input,
+                    inverse=True,
                 )
-            elif warp_file_ext == ".h5":
+                # Check warper
+                if inverse_warper_spec["warper"] != "ants":
+                    raise_error(
+                        klass=RuntimeError,
+                        msg=(
+                            "Warping specification mismatch for native space "
+                            "warping of coordinates using ANTs."
+                        ),
+                    )
                 seeds = ANTsCoordinatesWarper().warp(
                     seeds=seeds,
                     target_data=target_data,
-                    extra_input=extra_input,
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "Unknown warp / transformation file extension: "
-                        f"{warp_file_ext}"
-                    ),
-                    klass=RuntimeError,
+                    warp_data=warper_spec,
                 )
 
         return seeds, labels

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -26,7 +26,7 @@ class FSLCoordinatesWarper:
         self,
         seeds: ArrayLike,
         target_data: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        warp_data: Dict[str, Any],
     ) -> ArrayLike:
         """Warp ``seeds`` to correct space.
 
@@ -37,10 +37,8 @@ class FSLCoordinatesWarper:
         target_data : dict
             The corresponding item of the data object to which the coordinates
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of coordinates
-            (default None).
+        warp_data : dict
+            The warp data item of the data object.
 
         Returns
         -------
@@ -72,7 +70,7 @@ class FSLCoordinatesWarper:
             "| img2imgcoord -mm",
             f"-src {target_data['path'].resolve()}",
             f"-dest {target_data['reference_path'].resolve()}",
-            f"-warp {extra_input['Warp']['path'].resolve()}",
+            f"-warp {warp_data['path'].resolve()}",
             f"> {transformed_coords_path.resolve()};",
             f"sed -i 1d {transformed_coords_path.resolve()}",
         ]

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/data/masks/_ants_mask_warper.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any, Dict, Optional
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import logger, raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -34,7 +34,7 @@ class ANTsMaskWarper:
         src: str,
         dst: str,
         target_data: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
+        warp_data: Optional[Dict[str, Any]],
     ) -> "Nifti1Image":
         """Warp ``mask_img`` to correct space.
 
@@ -55,17 +55,20 @@ class ANTsMaskWarper:
         target_data : dict
             The corresponding item of the data object to which the mask
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of mask
-            (default None).
-
+        warp_data : dict or None
+            The warp data item of the data object. The value is unused if
+            ``dst!="T1w"``.
 
         Returns
         -------
         nibabel.nifti1.Nifti1Image
             The transformed mask image.
 
+        Raises
+        ------
+        RuntimeError
+            If ``warp_data`` is None when ``dst="T1w"``.
+
         """
         # Create element-scoped tempdir so that warped mask is
         # available later as nibabel stores file path reference for
@@ -80,7 +83,11 @@ class ANTsMaskWarper:
         )
 
         # Native space warping
-        if dst == "T1w":
+        if dst == "native":
+            # Warp data check
+            if warp_data is None:
+                raise_error("No `warp_data` provided")
+
             logger.debug("Using ANTs for mask transformation")
 
             # Save existing mask image to a tempfile
@@ -98,7 +105,7 @@ class ANTsMaskWarper:
                 f"-i {prewarp_mask_path.resolve()}",
                 # use resampled reference
                 f"-r {target_data['reference_path'].resolve()}",
-                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_mask_path.resolve()}",
             ]
             # Call antsApplyTransforms

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/data/masks/_fsl_mask_warper.py

@@ -31,7 +31,7 @@ class FSLMaskWarper:
         mask_name: str,
         mask_img: "Nifti1Image",
         target_data: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        warp_data: Dict[str, Any],
     ) -> "Nifti1Image":
         """Warp ``mask_img`` to correct space.
 
@@ -44,10 +44,8 @@ class FSLMaskWarper:
         target_data : dict
             The corresponding item of the data object to which the mask
             will be applied.
-        extra_input : dict, optional
-            The other fields in the data object. Useful for accessing other
-            data kinds that needs to be used in the computation of mask
-            (default None).
+        warp_data : dict
+            The warp data item of the data object.
 
         Returns
         -------
@@ -77,7 +75,7 @@ class FSLMaskWarper:
             f"-i {prewarp_mask_path.resolve()}",
             # use resampled reference
             f"-r {target_data['reference_path'].resolve()}",
-            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-w {warp_data['path'].resolve()}",
             f"-o {warped_mask_path.resolve()}",
         ]
         # Call applywarp

{junifer-0.0.6.dev219 → junifer-0.0.6.dev248}/junifer/data/masks/_masks.py

@@ -29,7 +29,7 @@ from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
-from ..utils import closest_resolution
+from ..utils import closest_resolution, get_native_warper
 from ._ants_mask_warper import ANTsMaskWarper
 from ._fsl_mask_warper import FSLMaskWarper
 
@@ -105,14 +105,16 @@ def compute_brain_mask(
                 "data type to infer target template space."
             )
         # Set target standard space to warp file space source
-        target_std_space = extra_input["Warp"]["src"]
+        for entry in extra_input["Warp"]:
+            if entry["dst"] == "native":
+                target_std_space = entry["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",
+        template_type=mask_type,
     )
     # Resample template to target image
     target_img = target_data["data"]
@@ -357,8 +359,6 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         Raises
         ------
-        RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
         ValueError
             If extra key is provided in addition to mask name in ``masks`` or
             if no mask is provided or
@@ -372,8 +372,6 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         """
         # 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
@@ -383,8 +381,16 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     "data types in particular for transformation to "
                     f"{target_data['space']} space for further computation."
                 )
+            # Get native space warper spec
+            warper_spec = get_native_warper(
+                target_data=target_data,
+                other_data=extra_input,
+            )
             # Set target standard space to warp file space source
-            target_std_space = extra_input["Warp"]["src"]
+            target_std_space = warper_spec["src"]
+        else:
+            # Set target standard space to target space
+            target_std_space = target_space
 
         # Get the min of the voxels sizes and use it as the resolution
         target_img = target_data["data"]
@@ -489,7 +495,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                         src=mask_space,
                         dst=target_std_space,
                         target_data=target_data,
-                        extra_input=None,
+                        warp_data=None,
                     )
 
             all_masks.append(mask_img)
@@ -510,32 +516,22 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         # Warp mask if target data is native
         if target_space == "native":
-            # extra_input check done earlier
-            # Check for warp file type to use correct tool
-            warp_file_ext = extra_input["Warp"]["path"].suffix
-            if warp_file_ext == ".mat":
+            # extra_input check done earlier and warper_spec exists
+            if warper_spec["warper"] == "fsl":
                 mask_img = FSLMaskWarper().warp(
                     mask_name="native",
                     mask_img=mask_img,
                     target_data=target_data,
-                    extra_input=extra_input,
+                    warp_data=warper_spec,
                 )
-            elif warp_file_ext == ".h5":
+            elif warper_spec["warper"] == "ants":
                 mask_img = ANTsMaskWarper().warp(
                     mask_name="native",
                     mask_img=mask_img,
                     src="",
-                    dst="T1w",
+                    dst="native",
                     target_data=target_data,
-                    extra_input=extra_input,
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "Unknown warp / transformation file extension: "
-                        f"{warp_file_ext}"
-                    ),
-                    klass=RuntimeError,
+                    warp_data=warper_spec,
                 )
 
         return mask_img