From 1f563f688c71e78db4a4abd25663a8b059ad8b1f Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 13:04:16 +0100
Subject: [PATCH 01/22] update: introduce FSLWarper and ANTsWarper classes

---
 junifer/preprocess/warping/_ants_warper.py | 115 +++++++++++++++++++++
 junifer/preprocess/warping/_fsl_warper.py  | 109 +++++++++++++++++++
 2 files changed, 224 insertions(+)
 create mode 100644 junifer/preprocess/warping/_ants_warper.py
 create mode 100644 junifer/preprocess/warping/_fsl_warper.py

diff --git a/junifer/preprocess/warping/_ants_warper.py b/junifer/preprocess/warping/_ants_warper.py
new file mode 100644
index 000000000..9376ee64a
--- /dev/null
+++ b/junifer/preprocess/warping/_ants_warper.py
@@ -0,0 +1,115 @@
+"""Provide class for space warping via ANTs antsApplyTransforms."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Set,
+    Union,
+)
+
+import nibabel as nib
+import numpy as np
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+class ANTsWarper:
+    """Class for space warping via ANTs antsApplyTransforms.
+
+    This class uses ANTs' ``ResampleImage`` for resampling and
+    ``antsApplyTransforms`` for transformation.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "ants",
+            "commands": ["ResampleImage", "antsApplyTransforms"],
+        },
+    ]
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy"}
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Dict[str, Any],
+    ) -> Dict[str, Any]:
+        """Preprocess using ANTs.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict
+            The other fields in the Junifer Data object. Should have ``T1w``
+            and ``Warp`` data types.
+
+        Returns
+        -------
+        dict
+            The ``input`` dictionary with modified ``data`` and ``space`` key
+            values and new ``reference_path`` key whose value points to the
+            reference file used for warping.
+
+        """
+        logger.debug("Using ANTs for warping")
+
+        # Get the min of the voxel sizes from input and use it as the
+        # resolution
+        resolution = np.min(input["data"].header.get_zooms()[:3])
+
+        # Create element-specific tempdir for storing post-warping assets
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="ants_warper"
+        )
+
+        # Create a tempfile for resampled reference output
+        resample_image_out_path = (
+            element_tempdir / "resampled_reference.nii.gz"
+        )
+        # Set ResampleImage command
+        resample_image_cmd = [
+            "ResampleImage",
+            "3",  # image dimension
+            f"{extra_input['T1w']['path'].resolve()}",
+            f"{resample_image_out_path.resolve()}",
+            f"{resolution}x{resolution}x{resolution}",
+            "0",  # option for spacing and not size
+            "3 3",  # Lanczos windowed sinc
+        ]
+        # Call ResampleImage
+        run_ext_cmd(name="ResampleImage", cmd=resample_image_cmd)
+
+        # Create a tempfile for warped output
+        apply_transforms_out_path = element_tempdir / "output.nii.gz"
+        # Set antsApplyTransforms command
+        apply_transforms_cmd = [
+            "antsApplyTransforms",
+            "-d 3",
+            "-e 3",
+            "-n LanczosWindowedSinc",
+            f"-i {input['path'].resolve()}",
+            # use resampled reference
+            f"-r {resample_image_out_path.resolve()}",
+            f"-t {extra_input['Warp']['path'].resolve()}",
+            f"-o {apply_transforms_out_path.resolve()}",
+        ]
+        # Call antsApplyTransforms
+        run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Load nifti
+        input["data"] = nib.load(apply_transforms_out_path)
+        # Save resampled reference path
+        input["reference_path"] = resample_image_out_path
+
+        # Use reference input's space as warped input's space
+        input["space"] = extra_input["T1w"]["space"]
+
+        return input
diff --git a/junifer/preprocess/warping/_fsl_warper.py b/junifer/preprocess/warping/_fsl_warper.py
new file mode 100644
index 000000000..0586005aa
--- /dev/null
+++ b/junifer/preprocess/warping/_fsl_warper.py
@@ -0,0 +1,109 @@
+"""Provide class for space warping via FSL FLIRT."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Set,
+    Union,
+)
+
+import nibabel as nib
+import numpy as np
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+class FSLWarper:
+    """Class for space warping via FSL FLIRT.
+
+    This class uses FSL FLIRT's ``flirt`` for resampling and ``applywarp`` for
+    transformation.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "fsl",
+            "commands": ["flirt", "applywarp"],
+        },
+    ]
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy"}
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Dict[str, Any],
+    ) -> Dict[str, Any]:
+        """Preprocess using FSL.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict
+            The other fields in the Junifer Data object. Should have ``T1w``
+            and ``Warp`` data types.
+
+        Returns
+        -------
+        dict
+            The ``input`` dictionary with modified ``data`` and ``space`` key
+            values and new ``reference_path`` key whose value points to the
+            reference file used for warping.
+
+        """
+        logger.debug("Using FSL for warping")
+
+        # Get the min of the voxel sizes from input and use it as the
+        # resolution
+        resolution = np.min(input["data"].header.get_zooms()[:3])
+
+        # Create element-specific tempdir for storing post-warping assets
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="fsl_warper"
+        )
+
+        # Create a tempfile for resampled reference output
+        flirt_out_path = element_tempdir / "resampled_reference.nii.gz"
+        # Set flirt command
+        flirt_cmd = [
+            "flirt",
+            "-interp spline",
+            f"-in {extra_input['T1w']['path'].resolve()}",
+            f"-ref {extra_input['T1w']['path'].resolve()}",
+            f"-applyisoxfm {resolution}",
+            f"-out {flirt_out_path.resolve()}",
+        ]
+        # Call flirt
+        run_ext_cmd(name="flirt", cmd=flirt_cmd)
+
+        # Create a tempfile for warped output
+        applywarp_out_path = element_tempdir / "output.nii.gz"
+        # Set applywarp command
+        applywarp_cmd = [
+            "applywarp",
+            "--interp=spline",
+            f"-i {input['path'].resolve()}",
+            f"-r {flirt_out_path.resolve()}",  # use resampled reference
+            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-o {applywarp_out_path.resolve()}",
+        ]
+        # Call applywarp
+        run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
+        # Load nifti
+        input["data"] = nib.load(applywarp_out_path)
+        # Save resampled reference path
+        input["reference_path"] = flirt_out_path
+
+        # Use reference input's space as warped input's space
+        input["space"] = extra_input["T1w"]["space"]
+
+        return input
-- 
2.52.0


From 2d627a0b554425a20f0f6e37e31cd5b3742ed5e0 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 13:05:25 +0100
Subject: [PATCH 02/22] feature: introduce SpaceWarper and add tests

---
 junifer/preprocess/__init__.py                |   1 +
 junifer/preprocess/warping/__init__.py        |   6 +
 junifer/preprocess/warping/space_warper.py    | 258 ++++++++++++++++++
 .../warping/tests/test_space_warper.py        | 153 +++++++++++
 4 files changed, 418 insertions(+)
 create mode 100644 junifer/preprocess/warping/__init__.py
 create mode 100644 junifer/preprocess/warping/space_warper.py
 create mode 100644 junifer/preprocess/warping/tests/test_space_warper.py

diff --git a/junifer/preprocess/__init__.py b/junifer/preprocess/__init__.py
index 804433ecc..15042f0ee 100644
--- a/junifer/preprocess/__init__.py
+++ b/junifer/preprocess/__init__.py
@@ -8,3 +8,4 @@
 from .base import BasePreprocessor
 from .confounds import fMRIPrepConfoundRemover
 from .bold_warper import BOLDWarper
+from .warping import SpaceWarper
diff --git a/junifer/preprocess/warping/__init__.py b/junifer/preprocess/warping/__init__.py
new file mode 100644
index 000000000..1b7a3bc2b
--- /dev/null
+++ b/junifer/preprocess/warping/__init__.py
@@ -0,0 +1,6 @@
+"""Provide imports for warping sub-package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from .space_warper import SpaceWarper
diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
new file mode 100644
index 000000000..70072db8f
--- /dev/null
+++ b/junifer/preprocess/warping/space_warper.py
@@ -0,0 +1,258 @@
+"""Provide class for warping data to other template spaces."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import Any, ClassVar, Dict, List, Optional, Tuple, Type, Union
+
+import nibabel as nib
+from templateflow import api as tflow
+
+from ...api.decorators import register_preprocessor
+from ...data import get_template, get_xfm
+from ...pipeline import WorkDirManager
+from ...utils import logger, raise_error, run_ext_cmd
+from ..base import BasePreprocessor
+from ._ants_warper import ANTsWarper
+from ._fsl_warper import FSLWarper
+
+
+__all__ = ["SpaceWarper"]
+
+
+@register_preprocessor
+class SpaceWarper(BasePreprocessor):
+    """Class for warping data to other template spaces.
+
+    Parameters
+    ----------
+    using : {"fsl", "ants"}
+        Implementation to use for warping:
+
+        * "fsl" : Use FSL's ``applywarp``
+        * "afni" : Use ANTs' ``antsApplyTransforms``
+
+    reference : str
+        The data type to use as reference for warping, can be either a data
+        type like ``"T1w"`` or a template space like ``"MNI152NLin2009cAsym"``.
+    on : {"T1w", "BOLD"} or list of the options
+        The data type to warp.
+
+    Raises
+    ------
+    ValueError
+        If ``using`` is invalid or
+        if ``reference`` is invalid.
+
+    Notes
+    -----
+    If you are setting ``reference`` to a template space like
+    "MNI152NLin2009cAsym", make sure ANTs is available for the
+    transformation else it will fail during runtime. It is tricky to validate
+    this beforehand and difficult to enforce this as a requirement, hence the
+    heads-up.
+
+    """
+
+    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+        {
+            "using": "fsl",
+            "depends_on": FSLWarper,
+        },
+        {
+            "using": "ants",
+            "depends_on": ANTsWarper,
+        },
+    ]
+
+    def __init__(
+        self, using: str, reference: str, on: Union[List[str], str]
+    ) -> None:
+        """Initialize the class."""
+        # Validate `using` parameter
+        valid_using = [dep["using"] for dep in self._CONDITIONAL_DEPENDENCIES]
+        if using not in valid_using:
+            raise_error(
+                f"Invalid value for `using`, should be one of: {valid_using}"
+            )
+        self.using = using
+        self.reference = reference
+        # Set required data types based on reference and
+        # initialize superclass
+        if self.reference == "T1w":
+            required_data_types = [self.reference, "Warp"]
+            # Listify on
+            if not isinstance(on, list):
+                on = [on]
+            # Extend required data types
+            required_data_types.extend(on)
+
+            super().__init__(
+                on=on,
+                required_data_types=required_data_types,
+            )
+        elif self.reference in tflow.templates():
+            super().__init__(on=on)
+        else:
+            raise_error(f"Unknown reference: {self.reference}")
+
+    def get_valid_inputs(self) -> List[str]:
+        """Get valid data types for input.
+
+        Returns
+        -------
+        list of str
+            The list of data types that can be used as input for this
+            preprocessor.
+
+        """
+        return ["T1w", "BOLD"]
+
+    def get_output_type(self, input_type: str) -> str:
+        """Get output type.
+
+        Parameters
+        ----------
+        input_type : str
+            The data type input to the preprocessor.
+
+        Returns
+        -------
+        str
+            The data type output by the preprocessor.
+
+        """
+        # Does not add any new keys
+        return input_type
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Optional[Dict[str, Any]] = None,
+    ) -> Tuple[Dict[str, Any], Optional[Dict[str, Dict[str, Any]]]]:
+        """Preprocess.
+
+        Parameters
+        ----------
+        input : dict
+            The input from the Junifer Data object.
+        extra_input : dict, optional
+            The other fields in the Junifer Data object.
+
+        Returns
+        -------
+        dict
+            The computed result as dictionary.
+        None
+            Extra "helper" data types as dictionary to add to the Junifer Data
+            object.
+
+        Raises
+        ------
+        ValueError
+            If ``extra_input`` is None when transforming to native space
+            i.e., using ``"T1w"`` as reference.
+        RuntimeError
+            If warp / transformation file extension is not ".mat" or ".h5"
+            when transforming to native space or
+            if the data is in the correct space and does not require
+            warping.
+
+        """
+        logger.info(f"Warping to {self.reference} space using SpaceWarper")
+        # Transform to native space
+        if self.reference == "T1w":
+            # Check for extra inputs
+            if extra_input is None:
+                raise_error(
+                    "No extra input provided, requires `Warp` and "
+                    f"`{self.reference}` data types in particular."
+                )
+            # Check for warp file type to use correct tool
+            warp_file_ext = extra_input["Warp"]["path"].suffix
+            if warp_file_ext == ".mat":
+                input = FSLWarper().preprocess(
+                    input=input,
+                    extra_input=extra_input,
+                )
+            elif warp_file_ext == ".h5":
+                input = ANTsWarper().preprocess(
+                    input=input,
+                    extra_input=extra_input,
+                )
+            else:
+                raise_error(
+                    msg=(
+                        "Unknown warp / transformation file extension: "
+                        f"{warp_file_ext}"
+                    ),
+                    klass=RuntimeError,
+                )
+        # Transform to template space
+        else:
+            # Check pre-requirements for space manipulation
+            if self.reference == input["space"]:
+                raise_error(
+                    (
+                        "Skipped warping as the data is in "
+                        f"{self.reference} space which would mean that you "
+                        "can remove the SpaceWarper from the preprocess step."
+                    ),
+                    klass=RuntimeError,
+                )
+            else:
+                # Get xfm file
+                xfm_file_path = get_xfm(src=input["space"], dst=self.reference)
+                # Get template space image
+                template_space_img = get_template(
+                    space=self.reference,
+                    target_data=input,
+                    extra_input=None,
+                )
+
+                # Create component-scoped tempdir
+                tempdir = WorkDirManager().get_tempdir(prefix="space_warper")
+                # Create element-scoped tempdir so that warped data is
+                # available later as nibabel stores file path reference for
+                # loading on computation
+                element_tempdir = WorkDirManager().get_element_tempdir(
+                    prefix="space_warper"
+                )
+
+                # Save template
+                template_space_img_path = (
+                    tempdir / f"{self.reference}_T1w.nii.gz"
+                )
+                nib.save(template_space_img, template_space_img_path)
+
+                # Create a tempfile for warped output
+                warped_output_path = element_tempdir / (
+                    f"data_warped_from_{input['space']}_to_"
+                    f"{self.reference}.nii.gz"
+                )
+
+                logger.debug(
+                    f"Using ANTs to warp data "
+                    f"from {input['space']} to {self.reference}"
+                )
+                # Set antsApplyTransforms command
+                apply_transforms_cmd = [
+                    "antsApplyTransforms",
+                    "-d 3",
+                    "-e 3",
+                    "-n LanczosWindowedSinc",
+                    f"-i {input['path'].resolve()}",
+                    f"-r {template_space_img_path.resolve()}",
+                    f"-t {xfm_file_path.resolve()}",
+                    f"-o {warped_output_path.resolve()}",
+                ]
+                # Call antsApplyTransforms
+                run_ext_cmd(
+                    name="antsApplyTransforms", cmd=apply_transforms_cmd
+                )
+
+                # Modify target data
+                input["data"] = nib.load(warped_output_path)
+                input["space"] = self.reference
+
+        return input, None
diff --git a/junifer/preprocess/warping/tests/test_space_warper.py b/junifer/preprocess/warping/tests/test_space_warper.py
new file mode 100644
index 000000000..b82dfa806
--- /dev/null
+++ b/junifer/preprocess/warping/tests/test_space_warper.py
@@ -0,0 +1,153 @@
+"""Provide tests for SpaceWarper."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import socket
+from typing import TYPE_CHECKING, Tuple
+
+import pytest
+from numpy.testing import assert_array_equal, assert_raises
+
+from junifer.datagrabber import DataladHCP1200, DMCC13Benchmark
+from junifer.datareader import DefaultDataReader
+from junifer.pipeline.utils import _check_ants, _check_fsl
+from junifer.preprocess import SpaceWarper
+
+
+if TYPE_CHECKING:
+    from junifer.datagrabber import BaseDataGrabber
+
+
+@pytest.mark.parametrize(
+    "datagrabber, element, using",
+    [
+        [
+            DMCC13Benchmark(
+                types=["BOLD", "T1w", "Warp"],
+                sessions=["wave1bas"],
+                tasks=["Rest"],
+                phase_encodings=["AP"],
+                runs=["1"],
+                native_t1w=True,
+            ),
+            ("f9057kp", "wave1bas", "Rest", "AP", "1"),
+            "ants",
+        ],
+        [
+            DataladHCP1200(
+                tasks=["REST1"],
+                phase_encodings=["LR"],
+                ica_fix=True,
+            ),
+            ("100206", "REST1", "LR"),
+            "fsl",
+        ],
+    ],
+)
+@pytest.mark.skipif(_check_fsl() is False, reason="requires FSL to be in PATH")
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+@pytest.mark.skipif(
+    socket.gethostname() != "juseless",
+    reason="only for juseless",
+)
+def test_SpaceWarper_native(
+    datagrabber: "BaseDataGrabber", element: Tuple[str, ...], using: str
+) -> None:
+    """Test SpaceWarper for native space warping.
+
+    Parameters
+    ----------
+    datagrabber : DataGrabber-like object
+        The parametrized DataGrabber objects.
+    element : tuple of str
+        The parametrized elements.
+    using : str
+        The parametrized implementation method.
+
+    """
+    with datagrabber as dg:
+        # Read data
+        element_data = DefaultDataReader().fit_transform(dg[element])
+        # Preprocess data
+        output, _ = SpaceWarper(
+            using=using,
+            reference="T1w",
+            on="BOLD",
+        ).preprocess(
+            input=element_data["BOLD"],
+            extra_input=element_data,
+        )
+        # Check
+        assert isinstance(output, dict)
+
+
+@pytest.mark.parametrize(
+    "datagrabber, element, space",
+    [
+        [
+            DMCC13Benchmark(
+                types=["T1w"],
+                sessions=["wave1bas"],
+                tasks=["Rest"],
+                phase_encodings=["AP"],
+                runs=["1"],
+                native_t1w=False,
+            ),
+            ("f9057kp", "wave1bas", "Rest", "AP", "1"),
+            "MNI152NLin2009aAsym",
+        ],
+        [
+            DMCC13Benchmark(
+                types=["T1w"],
+                sessions=["wave1bas"],
+                tasks=["Rest"],
+                phase_encodings=["AP"],
+                runs=["1"],
+                native_t1w=False,
+            ),
+            ("f9057kp", "wave1bas", "Rest", "AP", "1"),
+            "MNI152NLin6Asym",
+        ],
+    ],
+)
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+def test_SpaceWarper_multi_mni(
+    datagrabber: "BaseDataGrabber",
+    element: Tuple[str, ...],
+    space: str,
+) -> None:
+    """Test SpaceWarper for MNI space warping.
+
+    Parameters
+    ----------
+    datagrabber : DataGrabber-like object
+        The parametrized DataGrabber objects.
+    element : tuple of str
+        The parametrized elements.
+    space : str
+        The parametrized template space to transform to.
+
+    """
+    with datagrabber as dg:
+        # Read data
+        element_data = DefaultDataReader().fit_transform(dg[element])
+        pre_xfm_data = element_data["BOLD"]["data"].get_fdata().copy()
+        # Preprocess data
+        output, _ = SpaceWarper(
+            using="ants",
+            reference=space,
+            on=["T1w"],
+        ).preprocess(
+            input=element_data["T1w"],
+            extra_input=element_data,
+        )
+        # Checks
+        assert isinstance(output, dict)
+        assert output["space"] == space
+        with assert_raises(AssertionError):
+            assert_array_equal(pre_xfm_data, output["data"])
-- 
2.52.0


From 8c23cf9cec869413414ec3aefb309f1250121a68 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 13:12:28 +0100
Subject: [PATCH 03/22] chore: add deprecation notice for BOLDWarper

---
 junifer/preprocess/bold_warper.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/junifer/preprocess/bold_warper.py b/junifer/preprocess/bold_warper.py
index 22aeaceb1..304f59bbc 100644
--- a/junifer/preprocess/bold_warper.py
+++ b/junifer/preprocess/bold_warper.py
@@ -30,6 +30,10 @@ from .fsl.apply_warper import _ApplyWarper
 class BOLDWarper(BasePreprocessor):
     """Class for warping BOLD NIfTI images.
 
+    .. deprecated:: 0.0.3
+              `BOLDWarper` will be removed in v0.0.4, it is replaced by
+              `SpaceWarper` because the latter works also with T1w data.
+
     Parameters
     ----------
     using : {"fsl", "ants"}
-- 
2.52.0


From 875dbd9728b7fc862d2fefa75db40e0551f15137 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 13:20:38 +0100
Subject: [PATCH 04/22] chore: add changelogs 301.{feature,removal}

---
 docs/changes/newsfragments/301.feature | 1 +
 docs/changes/newsfragments/301.removal | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 docs/changes/newsfragments/301.feature
 create mode 100644 docs/changes/newsfragments/301.removal

diff --git a/docs/changes/newsfragments/301.feature b/docs/changes/newsfragments/301.feature
new file mode 100644
index 000000000..caf3755d1
--- /dev/null
+++ b/docs/changes/newsfragments/301.feature
@@ -0,0 +1 @@
+Introduce :class:`.SpaceWarper` for warping ``T1w`` and ``BOLD`` data to other spaces by `Synchon Mandal`_
diff --git a/docs/changes/newsfragments/301.removal b/docs/changes/newsfragments/301.removal
new file mode 100644
index 000000000..9b2c343ed
--- /dev/null
+++ b/docs/changes/newsfragments/301.removal
@@ -0,0 +1 @@
+Deprecate :class:`.BOLDWarper` and mark for removal in v0.0.4 by `Synchon Mandal`_
-- 
2.52.0


From 7be9a4293e51a19873ea65db7828c70510d9b307 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 13:47:20 +0100
Subject: [PATCH 05/22] chore: improve dependencies for ANTsWarper an FSLWarper

---
 junifer/preprocess/warping/_ants_warper.py | 2 +-
 junifer/preprocess/warping/_fsl_warper.py  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/junifer/preprocess/warping/_ants_warper.py b/junifer/preprocess/warping/_ants_warper.py
index 9376ee64a..ba658dd78 100644
--- a/junifer/preprocess/warping/_ants_warper.py
+++ b/junifer/preprocess/warping/_ants_warper.py
@@ -34,7 +34,7 @@ class ANTsWarper:
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
 
     def preprocess(
         self,
diff --git a/junifer/preprocess/warping/_fsl_warper.py b/junifer/preprocess/warping/_fsl_warper.py
index 0586005aa..0dbb09649 100644
--- a/junifer/preprocess/warping/_fsl_warper.py
+++ b/junifer/preprocess/warping/_fsl_warper.py
@@ -34,7 +34,7 @@ class FSLWarper:
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
 
     def preprocess(
         self,
-- 
2.52.0


From 55562a5cc7a4cb37596d826e2086e4221dc8d31d Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 13:47:57 +0100
Subject: [PATCH 06/22] update: add _DEPENDENCIES to SpaceWarper

---
 junifer/preprocess/warping/space_warper.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index 70072db8f..d3f6ff6fc 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Tuple, Type, Union
+from typing import Any, ClassVar, Dict, List, Optional, Set, Tuple, Type, Union
 
 import nibabel as nib
 from templateflow import api as tflow
@@ -65,6 +65,8 @@ class SpaceWarper(BasePreprocessor):
         },
     ]
 
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nibabel"}
+
     def __init__(
         self, using: str, reference: str, on: Union[List[str], str]
     ) -> None:
-- 
2.52.0


From d276fef79ad5d4235133c578acd09a68c90b1808 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 13:48:30 +0100
Subject: [PATCH 07/22] refactor: use using parameter for conditional
 preprocessor check in SpaceWarper

---
 junifer/preprocess/warping/space_warper.py | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index d3f6ff6fc..758378ad7 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -155,9 +155,7 @@ class SpaceWarper(BasePreprocessor):
             If ``extra_input`` is None when transforming to native space
             i.e., using ``"T1w"`` as reference.
         RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5"
-            when transforming to native space or
-            if the data is in the correct space and does not require
+            If the data is in the correct space and does not require
             warping.
 
         """
@@ -170,26 +168,17 @@ class SpaceWarper(BasePreprocessor):
                     "No extra input provided, requires `Warp` and "
                     f"`{self.reference}` data types in particular."
                 )
-            # Check for warp file type to use correct tool
-            warp_file_ext = extra_input["Warp"]["path"].suffix
-            if warp_file_ext == ".mat":
+            # Conditional preprocessor
+            if self.using == "fsl":
                 input = FSLWarper().preprocess(
                     input=input,
                     extra_input=extra_input,
                 )
-            elif warp_file_ext == ".h5":
+            elif self.using == "ants":
                 input = ANTsWarper().preprocess(
                     input=input,
                     extra_input=extra_input,
                 )
-            else:
-                raise_error(
-                    msg=(
-                        "Unknown warp / transformation file extension: "
-                        f"{warp_file_ext}"
-                    ),
-                    klass=RuntimeError,
-                )
         # Transform to template space
         else:
             # Check pre-requirements for space manipulation
-- 
2.52.0


From c3128644191a9b84ffc85ff78fff2e53940caac6 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 14:13:30 +0100
Subject: [PATCH 08/22] update: add more supported data types for SpaceWarper

---
 junifer/preprocess/warping/space_warper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index 758378ad7..22cf1ed7c 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -108,7 +108,7 @@ class SpaceWarper(BasePreprocessor):
             preprocessor.
 
         """
-        return ["T1w", "BOLD"]
+        return ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"]
 
     def get_output_type(self, input_type: str) -> str:
         """Get output type.
-- 
2.52.0


From 1e62f125de097e4a97050b4c34a54e9ea5d0c704 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 14:14:56 +0100
Subject: [PATCH 09/22] chore: update 301.feature

---
 docs/changes/newsfragments/301.feature | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/changes/newsfragments/301.feature b/docs/changes/newsfragments/301.feature
index caf3755d1..5ad08b386 100644
--- a/docs/changes/newsfragments/301.feature
+++ b/docs/changes/newsfragments/301.feature
@@ -1 +1 @@
-Introduce :class:`.SpaceWarper` for warping ``T1w`` and ``BOLD`` data to other spaces by `Synchon Mandal`_
+Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``, ``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon Mandal`_
-- 
2.52.0


From d7b8d0504809e934d900a41f3c44681dae272c93 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 14:42:01 +0100
Subject: [PATCH 10/22] update: rename FSLWarper and ANTsWarper to
 FSLNativeWarper and ANTsNativeWarper respectively

---
 ..._ants_warper.py => _ants_native_warper.py} |  8 +++---
 .../{_fsl_warper.py => _fsl_native_warper.py} | 10 ++++----
 junifer/preprocess/warping/space_warper.py    | 25 +++++++++++--------
 3 files changed, 24 insertions(+), 19 deletions(-)
 rename junifer/preprocess/warping/{_ants_warper.py => _ants_native_warper.py} (93%)
 rename junifer/preprocess/warping/{_fsl_warper.py => _fsl_native_warper.py} (92%)

diff --git a/junifer/preprocess/warping/_ants_warper.py b/junifer/preprocess/warping/_ants_native_warper.py
similarity index 93%
rename from junifer/preprocess/warping/_ants_warper.py
rename to junifer/preprocess/warping/_ants_native_warper.py
index ba658dd78..2d4a64364 100644
--- a/junifer/preprocess/warping/_ants_warper.py
+++ b/junifer/preprocess/warping/_ants_native_warper.py
@@ -1,4 +1,4 @@
-"""Provide class for space warping via ANTs antsApplyTransforms."""
+"""Provide class for native space warping via ANTs antsApplyTransforms."""
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
@@ -19,8 +19,8 @@ from ...pipeline import WorkDirManager
 from ...utils import logger, run_ext_cmd
 
 
-class ANTsWarper:
-    """Class for space warping via ANTs antsApplyTransforms.
+class ANTsNativeWarper:
+    """Class for native space warping via ANTs antsApplyTransforms.
 
     This class uses ANTs' ``ResampleImage`` for resampling and
     ``antsApplyTransforms`` for transformation.
@@ -59,7 +59,7 @@ class ANTsWarper:
             reference file used for warping.
 
         """
-        logger.debug("Using ANTs for warping")
+        logger.debug("Using ANTs for native space warping")
 
         # Get the min of the voxel sizes from input and use it as the
         # resolution
diff --git a/junifer/preprocess/warping/_fsl_warper.py b/junifer/preprocess/warping/_fsl_native_warper.py
similarity index 92%
rename from junifer/preprocess/warping/_fsl_warper.py
rename to junifer/preprocess/warping/_fsl_native_warper.py
index 0dbb09649..398fb8f95 100644
--- a/junifer/preprocess/warping/_fsl_warper.py
+++ b/junifer/preprocess/warping/_fsl_native_warper.py
@@ -1,4 +1,4 @@
-"""Provide class for space warping via FSL FLIRT."""
+"""Provide class for native space warping via FSL FLIRT."""
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
@@ -19,8 +19,8 @@ from ...pipeline import WorkDirManager
 from ...utils import logger, run_ext_cmd
 
 
-class FSLWarper:
-    """Class for space warping via FSL FLIRT.
+class FSLNativeWarper:
+    """Class for native space warping via FSL FLIRT.
 
     This class uses FSL FLIRT's ``flirt`` for resampling and ``applywarp`` for
     transformation.
@@ -59,7 +59,7 @@ class FSLWarper:
             reference file used for warping.
 
         """
-        logger.debug("Using FSL for warping")
+        logger.debug("Using FSL for native space warping")
 
         # Get the min of the voxel sizes from input and use it as the
         # resolution
@@ -67,7 +67,7 @@ class FSLWarper:
 
         # Create element-specific tempdir for storing post-warping assets
         element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="fsl_warper"
+            prefix="fsl_native_warper"
         )
 
         # Create a tempfile for resampled reference output
diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index 22cf1ed7c..6df245eec 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -13,8 +13,8 @@ from ...data import get_template, get_xfm
 from ...pipeline import WorkDirManager
 from ...utils import logger, raise_error, run_ext_cmd
 from ..base import BasePreprocessor
-from ._ants_warper import ANTsWarper
-from ._fsl_warper import FSLWarper
+from ._ants_native_warper import ANTsNativeWarper
+from ._fsl_native_warper import FSLNativeWarper
 
 
 __all__ = ["SpaceWarper"]
@@ -29,8 +29,9 @@ class SpaceWarper(BasePreprocessor):
     using : {"fsl", "ants"}
         Implementation to use for warping:
 
-        * "fsl" : Use FSL's ``applywarp``
-        * "afni" : Use ANTs' ``antsApplyTransforms``
+        * "fsl_native" : Use FSL's ``applywarp`` for native space warping
+        * "ants_native" : Use ANTs' ``antsApplyTransforms`` for native space
+                          warping
 
     reference : str
         The data type to use as reference for warping, can be either a data
@@ -56,8 +57,12 @@ class SpaceWarper(BasePreprocessor):
 
     _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
         {
-            "using": "fsl",
-            "depends_on": FSLWarper,
+            "using": "fsl_native",
+            "depends_on": FSLNativeWarper,
+        },
+        {
+            "using": "ants_native",
+            "depends_on": ANTsNativeWarper,
         },
         {
             "using": "ants",
@@ -169,13 +174,13 @@ class SpaceWarper(BasePreprocessor):
                     f"`{self.reference}` data types in particular."
                 )
             # Conditional preprocessor
-            if self.using == "fsl":
-                input = FSLWarper().preprocess(
+            if self.using == "fsl_native":
+                input = FSLNativeWarper().preprocess(
                     input=input,
                     extra_input=extra_input,
                 )
-            elif self.using == "ants":
-                input = ANTsWarper().preprocess(
+            elif self.using == "ants_natice":
+                input = ANTsNativeWarper().preprocess(
                     input=input,
                     extra_input=extra_input,
                 )
-- 
2.52.0


From 4cec3cf3e71840101f5ef0b2aa322a8e00b7155c Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 14:43:16 +0100
Subject: [PATCH 11/22] update: introduce ANTsTemplateWarper

---
 .../warping/_ants_template_warper.py          | 108 ++++++++++++++++++
 junifer/preprocess/warping/space_warper.py    |  84 +++-----------
 2 files changed, 121 insertions(+), 71 deletions(-)
 create mode 100644 junifer/preprocess/warping/_ants_template_warper.py

diff --git a/junifer/preprocess/warping/_ants_template_warper.py b/junifer/preprocess/warping/_ants_template_warper.py
new file mode 100644
index 000000000..e821df859
--- /dev/null
+++ b/junifer/preprocess/warping/_ants_template_warper.py
@@ -0,0 +1,108 @@
+"""Provide class for template space warping via ANTs antsApplyTransforms."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Set,
+    Union,
+)
+
+import nibabel as nib
+
+from ...data import get_template, get_xfm
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+class ANTsTemplateWarper:
+    """Class for template space warping via ANTs antsApplyTransforms.
+
+    This class uses ANTs' ``antsApplyTransforms`` for transformation.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "ants",
+            "commands": ["antsApplyTransforms"],
+        },
+    ]
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nibabel"}
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        dst: str,
+    ) -> Dict[str, Any]:
+        """Preprocess using ANTs.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        dst : str
+            Template space to warp to.
+
+        Returns
+        -------
+        dict
+            The ``input`` dictionary with modified ``data`` and ``space`` key
+            values.
+
+        """
+        logger.debug(
+            f"Using ANTs to warp data " f"from {input['space']} to {dst}"
+        )
+
+        # Get xfm file
+        xfm_file_path = get_xfm(src=input["space"], dst=dst)
+        # Get template space image
+        template_space_img = get_template(
+            space=dst,
+            target_data=input,
+            extra_input=None,
+        )
+
+        # Create component-scoped tempdir
+        tempdir = WorkDirManager().get_tempdir(prefix="ants_template_warper")
+        # Create element-scoped tempdir so that warped data is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="ants_template_warper"
+        )
+
+        # Save template
+        template_space_img_path = tempdir / f"{dst}_T1w.nii.gz"
+        nib.save(template_space_img, template_space_img_path)
+
+        # Create a tempfile for warped output
+        warped_output_path = element_tempdir / (
+            f"data_warped_from_{input['space']}_to_" f"{dst}.nii.gz"
+        )
+
+        # Set antsApplyTransforms command
+        apply_transforms_cmd = [
+            "antsApplyTransforms",
+            "-d 3",
+            "-e 3",
+            "-n LanczosWindowedSinc",
+            f"-i {input['path'].resolve()}",
+            f"-r {template_space_img_path.resolve()}",
+            f"-t {xfm_file_path.resolve()}",
+            f"-o {warped_output_path.resolve()}",
+        ]
+        # Call antsApplyTransforms
+        run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Modify target data
+        input["data"] = nib.load(warped_output_path)
+        input["space"] = dst
+
+        return input
diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index 6df245eec..c366e45e0 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -3,17 +3,15 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Tuple, Type, Union
+from typing import Any, ClassVar, Dict, List, Optional, Tuple, Type, Union
 
-import nibabel as nib
 from templateflow import api as tflow
 
 from ...api.decorators import register_preprocessor
-from ...data import get_template, get_xfm
-from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 from ._ants_native_warper import ANTsNativeWarper
+from ._ants_template_warper import ANTsTemplateWarper
 from ._fsl_native_warper import FSLNativeWarper
 
 
@@ -26,17 +24,20 @@ class SpaceWarper(BasePreprocessor):
 
     Parameters
     ----------
-    using : {"fsl", "ants"}
+    using : {"fsl_native", "ants_native", "ants_template}
         Implementation to use for warping:
 
         * "fsl_native" : Use FSL's ``applywarp`` for native space warping
         * "ants_native" : Use ANTs' ``antsApplyTransforms`` for native space
                           warping
+        * "ants_template" : Use ANTs' ``antsApplyTransforms`` for template
+                            space warping
 
     reference : str
         The data type to use as reference for warping, can be either a data
         type like ``"T1w"`` or a template space like ``"MNI152NLin2009cAsym"``.
-    on : {"T1w", "BOLD"} or list of the options
+        Use ``"T1w"`` for native space warping and named templates for
+        template space warping.
         The data type to warp.
 
     Raises
@@ -45,14 +46,6 @@ class SpaceWarper(BasePreprocessor):
         If ``using`` is invalid or
         if ``reference`` is invalid.
 
-    Notes
-    -----
-    If you are setting ``reference`` to a template space like
-    "MNI152NLin2009cAsym", make sure ANTs is available for the
-    transformation else it will fail during runtime. It is tricky to validate
-    this beforehand and difficult to enforce this as a requirement, hence the
-    heads-up.
-
     """
 
     _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
@@ -65,13 +58,11 @@ class SpaceWarper(BasePreprocessor):
             "depends_on": ANTsNativeWarper,
         },
         {
-            "using": "ants",
-            "depends_on": ANTsWarper,
+            "using": "ants_template",
+            "depends_on": ANTsTemplateWarper,
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nibabel"}
-
     def __init__(
         self, using: str, reference: str, on: Union[List[str], str]
     ) -> None:
@@ -197,58 +188,9 @@ class SpaceWarper(BasePreprocessor):
                     klass=RuntimeError,
                 )
             else:
-                # Get xfm file
-                xfm_file_path = get_xfm(src=input["space"], dst=self.reference)
-                # Get template space image
-                template_space_img = get_template(
-                    space=self.reference,
-                    target_data=input,
-                    extra_input=None,
+                input = ANTsTemplateWarper().preprocess(
+                    input=input,
+                    dst=self.reference,
                 )
 
-                # Create component-scoped tempdir
-                tempdir = WorkDirManager().get_tempdir(prefix="space_warper")
-                # Create element-scoped tempdir so that warped data is
-                # available later as nibabel stores file path reference for
-                # loading on computation
-                element_tempdir = WorkDirManager().get_element_tempdir(
-                    prefix="space_warper"
-                )
-
-                # Save template
-                template_space_img_path = (
-                    tempdir / f"{self.reference}_T1w.nii.gz"
-                )
-                nib.save(template_space_img, template_space_img_path)
-
-                # Create a tempfile for warped output
-                warped_output_path = element_tempdir / (
-                    f"data_warped_from_{input['space']}_to_"
-                    f"{self.reference}.nii.gz"
-                )
-
-                logger.debug(
-                    f"Using ANTs to warp data "
-                    f"from {input['space']} to {self.reference}"
-                )
-                # Set antsApplyTransforms command
-                apply_transforms_cmd = [
-                    "antsApplyTransforms",
-                    "-d 3",
-                    "-e 3",
-                    "-n LanczosWindowedSinc",
-                    f"-i {input['path'].resolve()}",
-                    f"-r {template_space_img_path.resolve()}",
-                    f"-t {xfm_file_path.resolve()}",
-                    f"-o {warped_output_path.resolve()}",
-                ]
-                # Call antsApplyTransforms
-                run_ext_cmd(
-                    name="antsApplyTransforms", cmd=apply_transforms_cmd
-                )
-
-                # Modify target data
-                input["data"] = nib.load(warped_output_path)
-                input["space"] = self.reference
-
         return input, None
-- 
2.52.0


From 5194edc608a43a8cde230ffc7e47b574b8bc7aaa Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 14:43:34 +0100
Subject: [PATCH 12/22] chore: update docstring for SpaceWarper

---
 junifer/preprocess/warping/space_warper.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index c366e45e0..9209f54a1 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -38,6 +38,8 @@ class SpaceWarper(BasePreprocessor):
         type like ``"T1w"`` or a template space like ``"MNI152NLin2009cAsym"``.
         Use ``"T1w"`` for native space warping and named templates for
         template space warping.
+    on : {"T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"} or list \
+         of the options
         The data type to warp.
 
     Raises
-- 
2.52.0


From 5a76512ff18d93d0594b67036d20c4122f34c71a Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 14:48:17 +0100
Subject: [PATCH 13/22] fix: typo in SpaceWarper

---
 junifer/preprocess/warping/space_warper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index 9209f54a1..f71c6c1d0 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -172,7 +172,7 @@ class SpaceWarper(BasePreprocessor):
                     input=input,
                     extra_input=extra_input,
                 )
-            elif self.using == "ants_natice":
+            elif self.using == "ants_native":
                 input = ANTsNativeWarper().preprocess(
                     input=input,
                     extra_input=extra_input,
-- 
2.52.0


From 7ca1565eb3111ba18c7524b0bced11c105297f3b Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 14:49:52 +0100
Subject: [PATCH 14/22] update: delete component tempdir after use in
 ANTsTemplateWarper

---
 junifer/preprocess/warping/_ants_template_warper.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/junifer/preprocess/warping/_ants_template_warper.py b/junifer/preprocess/warping/_ants_template_warper.py
index e821df859..e6fd03417 100644
--- a/junifer/preprocess/warping/_ants_template_warper.py
+++ b/junifer/preprocess/warping/_ants_template_warper.py
@@ -101,6 +101,9 @@ class ANTsTemplateWarper:
         # Call antsApplyTransforms
         run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
 
+        # Delete tempdir
+        WorkDirManager().delete_tempdir(tempdir)
+
         # Modify target data
         input["data"] = nib.load(warped_output_path)
         input["space"] = dst
-- 
2.52.0


From 2d75f448b77b4d7eb16511a26dd4898cb8ad0274 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 15:55:19 +0100
Subject: [PATCH 15/22] chore: fix tests for SpaceWarper

---
 junifer/preprocess/warping/tests/test_space_warper.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/junifer/preprocess/warping/tests/test_space_warper.py b/junifer/preprocess/warping/tests/test_space_warper.py
index b82dfa806..fbd225d41 100644
--- a/junifer/preprocess/warping/tests/test_space_warper.py
+++ b/junifer/preprocess/warping/tests/test_space_warper.py
@@ -32,7 +32,7 @@ if TYPE_CHECKING:
                 native_t1w=True,
             ),
             ("f9057kp", "wave1bas", "Rest", "AP", "1"),
-            "ants",
+            "ants_native",
         ],
         [
             DataladHCP1200(
@@ -41,7 +41,7 @@ if TYPE_CHECKING:
                 ica_fix=True,
             ),
             ("100206", "REST1", "LR"),
-            "fsl",
+            "fsl_native",
         ],
     ],
 )
@@ -139,7 +139,7 @@ def test_SpaceWarper_multi_mni(
         pre_xfm_data = element_data["BOLD"]["data"].get_fdata().copy()
         # Preprocess data
         output, _ = SpaceWarper(
-            using="ants",
+            using="ants_template",
             reference=space,
             on=["T1w"],
         ).preprocess(
-- 
2.52.0


From 7c740a2d54757213ccc6b56e5cbf670cc932ef79 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 15 Mar 2024 17:23:32 +0100
Subject: [PATCH 16/22] chore: correct data key access for SpaceWarper test

---
 junifer/preprocess/warping/tests/test_space_warper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/junifer/preprocess/warping/tests/test_space_warper.py b/junifer/preprocess/warping/tests/test_space_warper.py
index fbd225d41..0950748e7 100644
--- a/junifer/preprocess/warping/tests/test_space_warper.py
+++ b/junifer/preprocess/warping/tests/test_space_warper.py
@@ -136,7 +136,7 @@ def test_SpaceWarper_multi_mni(
     with datagrabber as dg:
         # Read data
         element_data = DefaultDataReader().fit_transform(dg[element])
-        pre_xfm_data = element_data["BOLD"]["data"].get_fdata().copy()
+        pre_xfm_data = element_data["T1w"]["data"].get_fdata().copy()
         # Preprocess data
         output, _ = SpaceWarper(
             using="ants_template",
-- 
2.52.0


From 54493ed3f13ad0f4ab4f6e77cacdc00da029ded9 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 18 Mar 2024 09:06:20 +0100
Subject: [PATCH 17/22] update: improve conditionals for SpaceWarper

---
 junifer/preprocess/warping/space_warper.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index f71c6c1d0..a6743b190 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -159,7 +159,10 @@ class SpaceWarper(BasePreprocessor):
         """
         logger.info(f"Warping to {self.reference} space using SpaceWarper")
         # Transform to native space
-        if self.reference == "T1w":
+        if (
+            self.using in ["fsl_native", "ants_native"]
+            and self.reference == "T1w"
+        ):
             # Check for extra inputs
             if extra_input is None:
                 raise_error(
@@ -178,7 +181,7 @@ class SpaceWarper(BasePreprocessor):
                     extra_input=extra_input,
                 )
         # Transform to template space
-        else:
+        elif self.using == "ants_template" and self.reference != "T1w":
             # Check pre-requirements for space manipulation
             if self.reference == input["space"]:
                 raise_error(
@@ -189,7 +192,7 @@ class SpaceWarper(BasePreprocessor):
                     ),
                     klass=RuntimeError,
                 )
-            else:
+            if self.using == "ants_template":
                 input = ANTsTemplateWarper().preprocess(
                     input=input,
                     dst=self.reference,
-- 
2.52.0


From 7bf50b8cc577f8a8872337631e6be6795ea1abb7 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 18 Mar 2024 14:37:46 +0100
Subject: [PATCH 18/22] update: revert warping helpers to FSLWarper and
 ANTsWarper with improvements

---
 .../preprocess/warping/_ants_native_warper.py | 115 ------------
 .../warping/_ants_template_warper.py          | 111 ------------
 junifer/preprocess/warping/_ants_warper.py    | 167 ++++++++++++++++++
 .../{_fsl_native_warper.py => _fsl_warper.py} |  10 +-
 junifer/preprocess/warping/space_warper.py    |  53 +++---
 5 files changed, 194 insertions(+), 262 deletions(-)
 delete mode 100644 junifer/preprocess/warping/_ants_native_warper.py
 delete mode 100644 junifer/preprocess/warping/_ants_template_warper.py
 create mode 100644 junifer/preprocess/warping/_ants_warper.py
 rename junifer/preprocess/warping/{_fsl_native_warper.py => _fsl_warper.py} (92%)

diff --git a/junifer/preprocess/warping/_ants_native_warper.py b/junifer/preprocess/warping/_ants_native_warper.py
deleted file mode 100644
index 2d4a64364..000000000
--- a/junifer/preprocess/warping/_ants_native_warper.py
+++ /dev/null
@@ -1,115 +0,0 @@
-"""Provide class for native space warping via ANTs antsApplyTransforms."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-from typing import (
-    Any,
-    ClassVar,
-    Dict,
-    List,
-    Set,
-    Union,
-)
-
-import nibabel as nib
-import numpy as np
-
-from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
-
-
-class ANTsNativeWarper:
-    """Class for native space warping via ANTs antsApplyTransforms.
-
-    This class uses ANTs' ``ResampleImage`` for resampling and
-    ``antsApplyTransforms`` for transformation.
-
-    """
-
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
-        {
-            "name": "ants",
-            "commands": ["ResampleImage", "antsApplyTransforms"],
-        },
-    ]
-
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
-
-    def preprocess(
-        self,
-        input: Dict[str, Any],
-        extra_input: Dict[str, Any],
-    ) -> Dict[str, Any]:
-        """Preprocess using ANTs.
-
-        Parameters
-        ----------
-        input : dict
-            A single input from the Junifer Data object in which to preprocess.
-        extra_input : dict
-            The other fields in the Junifer Data object. Should have ``T1w``
-            and ``Warp`` data types.
-
-        Returns
-        -------
-        dict
-            The ``input`` dictionary with modified ``data`` and ``space`` key
-            values and new ``reference_path`` key whose value points to the
-            reference file used for warping.
-
-        """
-        logger.debug("Using ANTs for native space warping")
-
-        # Get the min of the voxel sizes from input and use it as the
-        # resolution
-        resolution = np.min(input["data"].header.get_zooms()[:3])
-
-        # Create element-specific tempdir for storing post-warping assets
-        element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="ants_warper"
-        )
-
-        # Create a tempfile for resampled reference output
-        resample_image_out_path = (
-            element_tempdir / "resampled_reference.nii.gz"
-        )
-        # Set ResampleImage command
-        resample_image_cmd = [
-            "ResampleImage",
-            "3",  # image dimension
-            f"{extra_input['T1w']['path'].resolve()}",
-            f"{resample_image_out_path.resolve()}",
-            f"{resolution}x{resolution}x{resolution}",
-            "0",  # option for spacing and not size
-            "3 3",  # Lanczos windowed sinc
-        ]
-        # Call ResampleImage
-        run_ext_cmd(name="ResampleImage", cmd=resample_image_cmd)
-
-        # Create a tempfile for warped output
-        apply_transforms_out_path = element_tempdir / "output.nii.gz"
-        # Set antsApplyTransforms command
-        apply_transforms_cmd = [
-            "antsApplyTransforms",
-            "-d 3",
-            "-e 3",
-            "-n LanczosWindowedSinc",
-            f"-i {input['path'].resolve()}",
-            # use resampled reference
-            f"-r {resample_image_out_path.resolve()}",
-            f"-t {extra_input['Warp']['path'].resolve()}",
-            f"-o {apply_transforms_out_path.resolve()}",
-        ]
-        # Call antsApplyTransforms
-        run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
-
-        # Load nifti
-        input["data"] = nib.load(apply_transforms_out_path)
-        # Save resampled reference path
-        input["reference_path"] = resample_image_out_path
-
-        # Use reference input's space as warped input's space
-        input["space"] = extra_input["T1w"]["space"]
-
-        return input
diff --git a/junifer/preprocess/warping/_ants_template_warper.py b/junifer/preprocess/warping/_ants_template_warper.py
deleted file mode 100644
index e6fd03417..000000000
--- a/junifer/preprocess/warping/_ants_template_warper.py
+++ /dev/null
@@ -1,111 +0,0 @@
-"""Provide class for template space warping via ANTs antsApplyTransforms."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-from typing import (
-    Any,
-    ClassVar,
-    Dict,
-    List,
-    Set,
-    Union,
-)
-
-import nibabel as nib
-
-from ...data import get_template, get_xfm
-from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
-
-
-class ANTsTemplateWarper:
-    """Class for template space warping via ANTs antsApplyTransforms.
-
-    This class uses ANTs' ``antsApplyTransforms`` for transformation.
-
-    """
-
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
-        {
-            "name": "ants",
-            "commands": ["antsApplyTransforms"],
-        },
-    ]
-
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nibabel"}
-
-    def preprocess(
-        self,
-        input: Dict[str, Any],
-        dst: str,
-    ) -> Dict[str, Any]:
-        """Preprocess using ANTs.
-
-        Parameters
-        ----------
-        input : dict
-            A single input from the Junifer Data object in which to preprocess.
-        dst : str
-            Template space to warp to.
-
-        Returns
-        -------
-        dict
-            The ``input`` dictionary with modified ``data`` and ``space`` key
-            values.
-
-        """
-        logger.debug(
-            f"Using ANTs to warp data " f"from {input['space']} to {dst}"
-        )
-
-        # Get xfm file
-        xfm_file_path = get_xfm(src=input["space"], dst=dst)
-        # Get template space image
-        template_space_img = get_template(
-            space=dst,
-            target_data=input,
-            extra_input=None,
-        )
-
-        # Create component-scoped tempdir
-        tempdir = WorkDirManager().get_tempdir(prefix="ants_template_warper")
-        # Create element-scoped tempdir so that warped data is
-        # available later as nibabel stores file path reference for
-        # loading on computation
-        element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="ants_template_warper"
-        )
-
-        # Save template
-        template_space_img_path = tempdir / f"{dst}_T1w.nii.gz"
-        nib.save(template_space_img, template_space_img_path)
-
-        # Create a tempfile for warped output
-        warped_output_path = element_tempdir / (
-            f"data_warped_from_{input['space']}_to_" f"{dst}.nii.gz"
-        )
-
-        # Set antsApplyTransforms command
-        apply_transforms_cmd = [
-            "antsApplyTransforms",
-            "-d 3",
-            "-e 3",
-            "-n LanczosWindowedSinc",
-            f"-i {input['path'].resolve()}",
-            f"-r {template_space_img_path.resolve()}",
-            f"-t {xfm_file_path.resolve()}",
-            f"-o {warped_output_path.resolve()}",
-        ]
-        # Call antsApplyTransforms
-        run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
-
-        # Delete tempdir
-        WorkDirManager().delete_tempdir(tempdir)
-
-        # Modify target data
-        input["data"] = nib.load(warped_output_path)
-        input["space"] = dst
-
-        return input
diff --git a/junifer/preprocess/warping/_ants_warper.py b/junifer/preprocess/warping/_ants_warper.py
new file mode 100644
index 000000000..a78d67702
--- /dev/null
+++ b/junifer/preprocess/warping/_ants_warper.py
@@ -0,0 +1,167 @@
+"""Provide class for space warping via ANTs antsApplyTransforms."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Set,
+    Union,
+)
+
+import nibabel as nib
+import numpy as np
+
+from ...data import get_template, get_xfm
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+class ANTsWarper:
+    """Class for space warping via ANTs antsApplyTransforms.
+
+    This class uses ANTs' ``ResampleImage`` for resampling (if required) and
+    ``antsApplyTransforms`` for transformation.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "ants",
+            "commands": ["ResampleImage", "antsApplyTransforms"],
+        },
+    ]
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Dict[str, Any],
+        reference: str,
+    ) -> Dict[str, Any]:
+        """Preprocess using ANTs.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict
+            The other fields in the Junifer Data object. Should have ``T1w``
+            and ``Warp`` data types.
+        reference : str
+            The data type or template space to use as reference for warping.
+
+        Returns
+        -------
+        dict
+            The ``input`` dictionary with modified ``data`` and ``space`` key
+            values and new ``reference_path`` key whose value points to the
+            reference file used for warping.
+
+        """
+        # Create element-specific tempdir for storing post-warping assets
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="ants_warper"
+        )
+
+        # Native space warping
+        if reference == "T1w":
+            logger.debug("Using ANTs for space warping")
+
+            # Get the min of the voxel sizes from input and use it as the
+            # resolution
+            resolution = np.min(input["data"].header.get_zooms()[:3])
+
+            # Create a tempfile for resampled reference output
+            resample_image_out_path = (
+                element_tempdir / "resampled_reference.nii.gz"
+            )
+            # Set ResampleImage command
+            resample_image_cmd = [
+                "ResampleImage",
+                "3",  # image dimension
+                f"{extra_input['T1w']['path'].resolve()}",
+                f"{resample_image_out_path.resolve()}",
+                f"{resolution}x{resolution}x{resolution}",
+                "0",  # option for spacing and not size
+                "3 3",  # Lanczos windowed sinc
+            ]
+            # Call ResampleImage
+            run_ext_cmd(name="ResampleImage", cmd=resample_image_cmd)
+
+            # Create a tempfile for warped output
+            apply_transforms_out_path = element_tempdir / "output.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {input['path'].resolve()}",
+                # use resampled reference
+                f"-r {resample_image_out_path.resolve()}",
+                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-o {apply_transforms_out_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+            # Load nifti
+            input["data"] = nib.load(apply_transforms_out_path)
+            # Save resampled reference path
+            input["reference_path"] = resample_image_out_path
+            # Use reference input's space as warped input's space
+            input["space"] = extra_input["T1w"]["space"]
+
+        # Template space warping
+        else:
+            logger.debug(
+                f"Using ANTs to warp data from {input['space']} to {reference}"
+            )
+
+            # Get xfm file
+            xfm_file_path = get_xfm(src=input["space"], dst=reference)
+            # Get template space image
+            template_space_img = get_template(
+                space=reference,
+                target_data=input,
+                extra_input=None,
+            )
+
+            # Create component-scoped tempdir
+            tempdir = WorkDirManager().get_tempdir(prefix="ants_warper")
+            # Save template
+            template_space_img_path = tempdir / f"{reference}_T1w.nii.gz"
+            nib.save(template_space_img, template_space_img_path)
+
+            # Create a tempfile for warped output
+            warped_output_path = element_tempdir / (
+                f"data_warped_from_{input['space']}_to_" f"{reference}.nii.gz"
+            )
+
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {input['path'].resolve()}",
+                f"-r {template_space_img_path.resolve()}",
+                f"-t {xfm_file_path.resolve()}",
+                f"-o {warped_output_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+            # Delete tempdir
+            WorkDirManager().delete_tempdir(tempdir)
+
+            # Modify target data
+            input["data"] = nib.load(warped_output_path)
+            input["space"] = reference
+
+        return input
diff --git a/junifer/preprocess/warping/_fsl_native_warper.py b/junifer/preprocess/warping/_fsl_warper.py
similarity index 92%
rename from junifer/preprocess/warping/_fsl_native_warper.py
rename to junifer/preprocess/warping/_fsl_warper.py
index 398fb8f95..32ded0e60 100644
--- a/junifer/preprocess/warping/_fsl_native_warper.py
+++ b/junifer/preprocess/warping/_fsl_warper.py
@@ -1,4 +1,4 @@
-"""Provide class for native space warping via FSL FLIRT."""
+"""Provide class for space warping via FSL FLIRT."""
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
@@ -19,8 +19,8 @@ from ...pipeline import WorkDirManager
 from ...utils import logger, run_ext_cmd
 
 
-class FSLNativeWarper:
-    """Class for native space warping via FSL FLIRT.
+class FSLWarper:
+    """Class for space warping via FSL FLIRT.
 
     This class uses FSL FLIRT's ``flirt`` for resampling and ``applywarp`` for
     transformation.
@@ -59,7 +59,7 @@ class FSLNativeWarper:
             reference file used for warping.
 
         """
-        logger.debug("Using FSL for native space warping")
+        logger.debug("Using FSL for space warping")
 
         # Get the min of the voxel sizes from input and use it as the
         # resolution
@@ -67,7 +67,7 @@ class FSLNativeWarper:
 
         # Create element-specific tempdir for storing post-warping assets
         element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="fsl_native_warper"
+            prefix="fsl_warper"
         )
 
         # Create a tempfile for resampled reference output
diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index a6743b190..84cbb9c1d 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -10,9 +10,8 @@ from templateflow import api as tflow
 from ...api.decorators import register_preprocessor
 from ...utils import logger, raise_error
 from ..base import BasePreprocessor
-from ._ants_native_warper import ANTsNativeWarper
-from ._ants_template_warper import ANTsTemplateWarper
-from ._fsl_native_warper import FSLNativeWarper
+from ._ants_warper import ANTsWarper
+from ._fsl_warper import FSLWarper
 
 
 __all__ = ["SpaceWarper"]
@@ -24,14 +23,11 @@ class SpaceWarper(BasePreprocessor):
 
     Parameters
     ----------
-    using : {"fsl_native", "ants_native", "ants_template}
+    using : {"fsl", "ants"}
         Implementation to use for warping:
 
-        * "fsl_native" : Use FSL's ``applywarp`` for native space warping
-        * "ants_native" : Use ANTs' ``antsApplyTransforms`` for native space
-                          warping
-        * "ants_template" : Use ANTs' ``antsApplyTransforms`` for template
-                            space warping
+        * "fsl" : Use FSL's ``applywarp``
+        * "ants" : Use ANTs' ``antsApplyTransforms``
 
     reference : str
         The data type to use as reference for warping, can be either a data
@@ -52,16 +48,12 @@ class SpaceWarper(BasePreprocessor):
 
     _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
         {
-            "using": "fsl_native",
-            "depends_on": FSLNativeWarper,
+            "using": "fsl",
+            "depends_on": FSLWarper,
         },
         {
-            "using": "ants_native",
-            "depends_on": ANTsNativeWarper,
-        },
-        {
-            "using": "ants_template",
-            "depends_on": ANTsTemplateWarper,
+            "using": "ants",
+            "depends_on": ANTsWarper,
         },
     ]
 
@@ -159,10 +151,7 @@ class SpaceWarper(BasePreprocessor):
         """
         logger.info(f"Warping to {self.reference} space using SpaceWarper")
         # Transform to native space
-        if (
-            self.using in ["fsl_native", "ants_native"]
-            and self.reference == "T1w"
-        ):
+        if self.using in ["fsl", "ants"] and self.reference == "T1w":
             # Check for extra inputs
             if extra_input is None:
                 raise_error(
@@ -170,18 +159,19 @@ class SpaceWarper(BasePreprocessor):
                     f"`{self.reference}` data types in particular."
                 )
             # Conditional preprocessor
-            if self.using == "fsl_native":
-                input = FSLNativeWarper().preprocess(
+            if self.using == "fsl":
+                input = FSLWarper().preprocess(
                     input=input,
                     extra_input=extra_input,
                 )
-            elif self.using == "ants_native":
-                input = ANTsNativeWarper().preprocess(
+            elif self.using == "ants":
+                input = ANTsWarper().preprocess(
                     input=input,
                     extra_input=extra_input,
+                    reference=self.reference,
                 )
         # Transform to template space
-        elif self.using == "ants_template" and self.reference != "T1w":
+        elif self.using == "ants" and self.reference != "T1w":
             # Check pre-requirements for space manipulation
             if self.reference == input["space"]:
                 raise_error(
@@ -192,10 +182,11 @@ class SpaceWarper(BasePreprocessor):
                     ),
                     klass=RuntimeError,
                 )
-            if self.using == "ants_template":
-                input = ANTsTemplateWarper().preprocess(
-                    input=input,
-                    dst=self.reference,
-                )
+
+            input = ANTsWarper().preprocess(
+                input=input,
+                extra_input={},
+                reference=self.reference,
+            )
 
         return input, None
-- 
2.52.0


From cc3c35acc7ef553a2e6d790da833a323a0b07575 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 18 Mar 2024 14:38:19 +0100
Subject: [PATCH 19/22] update: correct test parameters for SpaceWarper

---
 junifer/preprocess/warping/tests/test_space_warper.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/junifer/preprocess/warping/tests/test_space_warper.py b/junifer/preprocess/warping/tests/test_space_warper.py
index 0950748e7..0c03d1fb4 100644
--- a/junifer/preprocess/warping/tests/test_space_warper.py
+++ b/junifer/preprocess/warping/tests/test_space_warper.py
@@ -32,7 +32,7 @@ if TYPE_CHECKING:
                 native_t1w=True,
             ),
             ("f9057kp", "wave1bas", "Rest", "AP", "1"),
-            "ants_native",
+            "ants",
         ],
         [
             DataladHCP1200(
@@ -41,7 +41,7 @@ if TYPE_CHECKING:
                 ica_fix=True,
             ),
             ("100206", "REST1", "LR"),
-            "fsl_native",
+            "fsl",
         ],
     ],
 )
@@ -139,7 +139,7 @@ def test_SpaceWarper_multi_mni(
         pre_xfm_data = element_data["T1w"]["data"].get_fdata().copy()
         # Preprocess data
         output, _ = SpaceWarper(
-            using="ants_template",
+            using="ants",
             reference=space,
             on=["T1w"],
         ).preprocess(
-- 
2.52.0


From 2734615f332b7ce1818aad201af3c5a854535043 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 22 Mar 2024 11:26:54 +0100
Subject: [PATCH 20/22] update: handle use of FSL without T1w as reference for
 SpaceWarper

---
 junifer/preprocess/warping/space_warper.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index 84cbb9c1d..77b5e1e21 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -146,7 +146,8 @@ class SpaceWarper(BasePreprocessor):
             i.e., using ``"T1w"`` as reference.
         RuntimeError
             If the data is in the correct space and does not require
-            warping.
+            warping or
+            if FSL is used for template space warping.
 
         """
         logger.info(f"Warping to {self.reference} space using SpaceWarper")
@@ -170,7 +171,7 @@ class SpaceWarper(BasePreprocessor):
                     extra_input=extra_input,
                     reference=self.reference,
                 )
-        # Transform to template space
+        # Transform to template space with ANTs possible
         elif self.using == "ants" and self.reference != "T1w":
             # Check pre-requirements for space manipulation
             if self.reference == input["space"]:
@@ -188,5 +189,14 @@ class SpaceWarper(BasePreprocessor):
                 extra_input={},
                 reference=self.reference,
             )
+        # Transform to template space with FSL not possible
+        elif self.using == "fsl" and self.reference != "T1w":
+            raise_error(
+                (
+                    f"Warping to {self.reference} space not possible with "
+                    "FSL, use ANTs instead."
+                ),
+                klass=RuntimeError,
+            )
 
         return input, None
-- 
2.52.0


From 555e856bcc142af957802f7abf1269694aee17bb Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 22 Mar 2024 11:27:27 +0100
Subject: [PATCH 21/22] update: improve error message when SpaceWarper
 shouldn't be used in the pipeline

---
 junifer/preprocess/warping/space_warper.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/junifer/preprocess/warping/space_warper.py b/junifer/preprocess/warping/space_warper.py
index 77b5e1e21..18b9e9cca 100644
--- a/junifer/preprocess/warping/space_warper.py
+++ b/junifer/preprocess/warping/space_warper.py
@@ -177,9 +177,10 @@ class SpaceWarper(BasePreprocessor):
             if self.reference == input["space"]:
                 raise_error(
                     (
-                        "Skipped warping as the data is in "
-                        f"{self.reference} space which would mean that you "
-                        "can remove the SpaceWarper from the preprocess step."
+                        f"The target data is in {self.reference} space "
+                        "and thus warping will not be performed, hence you "
+                        "should remove the SpaceWarper from the preprocess "
+                        "step."
                     ),
                     klass=RuntimeError,
                 )
-- 
2.52.0


From 8a5bc77c642ec578657b1fad6b8d40d23e202c63 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 22 Mar 2024 11:28:05 +0100
Subject: [PATCH 22/22] update: add tests for SpaceWarper errors

---
 .../warping/tests/test_space_warper.py        | 47 ++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/junifer/preprocess/warping/tests/test_space_warper.py b/junifer/preprocess/warping/tests/test_space_warper.py
index 0c03d1fb4..1d21d9fae 100644
--- a/junifer/preprocess/warping/tests/test_space_warper.py
+++ b/junifer/preprocess/warping/tests/test_space_warper.py
@@ -4,7 +4,7 @@
 # License: AGPL
 
 import socket
-from typing import TYPE_CHECKING, Tuple
+from typing import TYPE_CHECKING, Tuple, Type
 
 import pytest
 from numpy.testing import assert_array_equal, assert_raises
@@ -13,12 +13,57 @@ from junifer.datagrabber import DataladHCP1200, DMCC13Benchmark
 from junifer.datareader import DefaultDataReader
 from junifer.pipeline.utils import _check_ants, _check_fsl
 from junifer.preprocess import SpaceWarper
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
 if TYPE_CHECKING:
     from junifer.datagrabber import BaseDataGrabber
 
 
+@pytest.mark.parametrize(
+    "using, reference, error_type, error_msg",
+    [
+        ("jam", "T1w", ValueError, "`using`"),
+        ("ants", "juice", ValueError, "reference"),
+        ("ants", "MNI152NLin2009cAsym", RuntimeError, "remove"),
+        ("fsl", "MNI152NLin2009cAsym", RuntimeError, "ANTs"),
+    ],
+)
+def test_SpaceWarper_errors(
+    using: str,
+    reference: str,
+    error_type: Type[Exception],
+    error_msg: str,
+) -> None:
+    """Test SpaceWarper errors.
+
+    Parameters
+    ----------
+    using : str
+        The parametrized implementation method.
+    reference : str
+        The parametrized reference to use.
+    error_type : Exception-like object
+        The parametrized exception to check.
+    error_msg : str
+        The parametrized exception message to check.
+
+    """
+    with PartlyCloudyTestingDataGrabber() as dg:
+        # Read data
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Preprocess data
+        with pytest.raises(error_type, match=error_msg):
+            SpaceWarper(
+                using=using,
+                reference=reference,
+                on="BOLD",
+            ).preprocess(
+                input=element_data["BOLD"],
+                extra_input=element_data,
+            )
+
+
 @pytest.mark.parametrize(
     "datagrabber, element, using",
     [
-- 
2.52.0