niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrtransform.py

@@ -0,0 +1,1372 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRTRANSFORM_METADATA = Metadata(
+    id="3eb2d0d1d0da497152ef0293f2b94667de8b3275.boutiques",
+    name="mrtransform",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_MrtransformFslgradParamsDictNoTag = typing.TypedDict('_MrtransformFslgradParamsDictNoTag', {
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+MrtransformFslgradParamsDictTagged = typing.TypedDict('MrtransformFslgradParamsDictTagged', {
+    "@type": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+MrtransformFslgradParamsDict = _MrtransformFslgradParamsDictNoTag | MrtransformFslgradParamsDictTagged
+
+
+_MrtransformExportGradFslParamsDictNoTag = typing.TypedDict('_MrtransformExportGradFslParamsDictNoTag', {
+    "bvecs_path": str,
+    "bvals_path": str,
+})
+MrtransformExportGradFslParamsDictTagged = typing.TypedDict('MrtransformExportGradFslParamsDictTagged', {
+    "@type": typing.Literal["export_grad_fsl"],
+    "bvecs_path": str,
+    "bvals_path": str,
+})
+MrtransformExportGradFslParamsDict = _MrtransformExportGradFslParamsDictNoTag | MrtransformExportGradFslParamsDictTagged
+
+
+_MrtransformVariousStringParamsDictNoTag = typing.TypedDict('_MrtransformVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+MrtransformVariousStringParamsDictTagged = typing.TypedDict('MrtransformVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+MrtransformVariousStringParamsDict = _MrtransformVariousStringParamsDictNoTag | MrtransformVariousStringParamsDictTagged
+
+
+_MrtransformVariousFileParamsDictNoTag = typing.TypedDict('_MrtransformVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+MrtransformVariousFileParamsDictTagged = typing.TypedDict('MrtransformVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+MrtransformVariousFileParamsDict = _MrtransformVariousFileParamsDictNoTag | MrtransformVariousFileParamsDictTagged
+
+
+_MrtransformConfigParamsDictNoTag = typing.TypedDict('_MrtransformConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+MrtransformConfigParamsDictTagged = typing.TypedDict('MrtransformConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+MrtransformConfigParamsDict = _MrtransformConfigParamsDictNoTag | MrtransformConfigParamsDictTagged
+
+
+_MrtransformParamsDictNoTag = typing.TypedDict('_MrtransformParamsDictNoTag', {
+    "linear": typing.NotRequired[InputPathType | None],
+    "flip": typing.NotRequired[list[int] | None],
+    "inverse": bool,
+    "half": bool,
+    "replace": typing.NotRequired[InputPathType | None],
+    "identity": bool,
+    "template": typing.NotRequired[InputPathType | None],
+    "midway_space": bool,
+    "interp": typing.NotRequired[str | None],
+    "oversample": typing.NotRequired[list[int] | None],
+    "warp": typing.NotRequired[InputPathType | None],
+    "warp_full": typing.NotRequired[InputPathType | None],
+    "from": typing.NotRequired[int | None],
+    "modulate": typing.NotRequired[str | None],
+    "directions": typing.NotRequired[InputPathType | None],
+    "reorient_fod": typing.NotRequired[str | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[MrtransformFslgradParamsDict | None],
+    "export_grad_mrtrix": typing.NotRequired[str | None],
+    "export_grad_fsl": typing.NotRequired[MrtransformExportGradFslParamsDict | None],
+    "datatype": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[MrtransformVariousStringParamsDictTagged, MrtransformVariousFileParamsDictTagged] | None],
+    "nan": bool,
+    "no_reorientation": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrtransformConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+MrtransformParamsDictTagged = typing.TypedDict('MrtransformParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/mrtransform"],
+    "linear": typing.NotRequired[InputPathType | None],
+    "flip": typing.NotRequired[list[int] | None],
+    "inverse": bool,
+    "half": bool,
+    "replace": typing.NotRequired[InputPathType | None],
+    "identity": bool,
+    "template": typing.NotRequired[InputPathType | None],
+    "midway_space": bool,
+    "interp": typing.NotRequired[str | None],
+    "oversample": typing.NotRequired[list[int] | None],
+    "warp": typing.NotRequired[InputPathType | None],
+    "warp_full": typing.NotRequired[InputPathType | None],
+    "from": typing.NotRequired[int | None],
+    "modulate": typing.NotRequired[str | None],
+    "directions": typing.NotRequired[InputPathType | None],
+    "reorient_fod": typing.NotRequired[str | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[MrtransformFslgradParamsDict | None],
+    "export_grad_mrtrix": typing.NotRequired[str | None],
+    "export_grad_fsl": typing.NotRequired[MrtransformExportGradFslParamsDict | None],
+    "datatype": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[MrtransformVariousStringParamsDictTagged, MrtransformVariousFileParamsDictTagged] | None],
+    "nan": bool,
+    "no_reorientation": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrtransformConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+MrtransformParamsDict = _MrtransformParamsDictNoTag | MrtransformParamsDictTagged
+
+
+def mrtransform_strides_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString": mrtransform_various_string_cargs,
+        "VariousFile": mrtransform_various_file_cargs,
+    }.get(t)
+
+
+def mrtransform_strides_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString": mrtransform_various_string_validate,
+        "VariousFile": mrtransform_various_file_validate,
+    }.get(t)
+
+
+def mrtransform_fslgrad(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> MrtransformFslgradParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        bvals: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "fslgrad",
+        "bvecs": bvecs,
+        "bvals": bvals,
+    }
+    return params
+
+
+def mrtransform_fslgrad_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrtransformFslgradParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("bvecs", None) is None:
+        raise StyxValidationError("`bvecs` must not be None")
+    if not isinstance(params["bvecs"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`bvecs` has the wrong type: Received `{type(params.get("bvecs", None))}` expected `InputPathType`')
+    if params.get("bvals", None) is None:
+        raise StyxValidationError("`bvals` must not be None")
+    if not isinstance(params["bvals"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`bvals` has the wrong type: Received `{type(params.get("bvals", None))}` expected `InputPathType`')
+
+
+def mrtransform_fslgrad_cargs(
+    params: MrtransformFslgradParamsDict,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("-fslgrad")
+    cargs.append(execution.input_file(params.get("bvecs", None)))
+    cargs.append(execution.input_file(params.get("bvals", None)))
+    return cargs
+
+
+class MrtransformExportGradFslOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrtransformExportGradFslParamsDict | None(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    bvecs_path: OutputPathType
+    """export the diffusion-weighted gradient table to files in FSL (bvecs /
+    bvals) format"""
+    bvals_path: OutputPathType
+    """export the diffusion-weighted gradient table to files in FSL (bvecs /
+    bvals) format"""
+
+
+def mrtransform_export_grad_fsl(
+    bvecs_path: str,
+    bvals_path: str,
+) -> MrtransformExportGradFslParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs_path: export the diffusion-weighted gradient table to files in\
+            FSL (bvecs / bvals) format.
+        bvals_path: export the diffusion-weighted gradient table to files in\
+            FSL (bvecs / bvals) format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "export_grad_fsl",
+        "bvecs_path": bvecs_path,
+        "bvals_path": bvals_path,
+    }
+    return params
+
+
+def mrtransform_export_grad_fsl_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrtransformExportGradFslParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("bvecs_path", None) is None:
+        raise StyxValidationError("`bvecs_path` must not be None")
+    if not isinstance(params["bvecs_path"], str):
+        raise StyxValidationError(f'`bvecs_path` has the wrong type: Received `{type(params.get("bvecs_path", None))}` expected `str`')
+    if params.get("bvals_path", None) is None:
+        raise StyxValidationError("`bvals_path` must not be None")
+    if not isinstance(params["bvals_path"], str):
+        raise StyxValidationError(f'`bvals_path` has the wrong type: Received `{type(params.get("bvals_path", None))}` expected `str`')
+
+
+def mrtransform_export_grad_fsl_cargs(
+    params: MrtransformExportGradFslParamsDict,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("-export_grad_fsl")
+    cargs.append(params.get("bvecs_path", None))
+    cargs.append(params.get("bvals_path", None))
+    return cargs
+
+
+def mrtransform_export_grad_fsl_outputs(
+    params: MrtransformExportGradFslParamsDict,
+    execution: Execution,
+) -> MrtransformExportGradFslOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MrtransformExportGradFslOutputs(
+        root=execution.output_file("."),
+        bvecs_path=execution.output_file(params.get("bvecs_path", None)),
+        bvals_path=execution.output_file(params.get("bvals_path", None)),
+    )
+    return ret
+
+
+def mrtransform_various_string(
+    obj: str,
+) -> MrtransformVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def mrtransform_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrtransformVariousStringParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], str):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `str`')
+
+
+def mrtransform_various_string_cargs(
+    params: MrtransformVariousStringParamsDict,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append(params.get("obj", None))
+    return cargs
+
+
+def mrtransform_various_file(
+    obj: InputPathType,
+) -> MrtransformVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def mrtransform_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrtransformVariousFileParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `InputPathType`')
+
+
+def mrtransform_various_file_cargs(
+    params: MrtransformVariousFileParamsDict,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append(execution.input_file(params.get("obj", None)))
+    return cargs
+
+
+def mrtransform_config(
+    key: str,
+    value: str,
+) -> MrtransformConfigParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def mrtransform_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrtransformConfigParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("key", None) is None:
+        raise StyxValidationError("`key` must not be None")
+    if not isinstance(params["key"], str):
+        raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
+    if params.get("value", None) is None:
+        raise StyxValidationError("`value` must not be None")
+    if not isinstance(params["value"], str):
+        raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
+
+
+def mrtransform_config_cargs(
+    params: MrtransformConfigParamsDict,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("-config")
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
+    return cargs
+
+
+class MrtransformOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrtransformParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image."""
+    export_grad_mrtrix: OutputPathType | None
+    """export the diffusion-weighted gradient table to file in MRtrix format """
+    export_grad_fsl: MrtransformExportGradFslOutputs | None
+    """Outputs from `mrtransform_export_grad_fsl_outputs`."""
+
+
+def mrtransform_params(
+    input_: InputPathType,
+    output: str,
+    linear: InputPathType | None = None,
+    flip: list[int] | None = None,
+    inverse: bool = False,
+    half: bool = False,
+    replace: InputPathType | None = None,
+    identity: bool = False,
+    template: InputPathType | None = None,
+    midway_space: bool = False,
+    interp: str | None = None,
+    oversample: list[int] | None = None,
+    warp: InputPathType | None = None,
+    warp_full: InputPathType | None = None,
+    from_: int | None = None,
+    modulate: str | None = None,
+    directions: InputPathType | None = None,
+    reorient_fod: str | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: MrtransformFslgradParamsDict | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: MrtransformExportGradFslParamsDict | None = None,
+    datatype: str | None = None,
+    strides: typing.Union[MrtransformVariousStringParamsDictTagged, MrtransformVariousFileParamsDictTagged] | None = None,
+    nan: bool = False,
+    no_reorientation: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrtransformConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrtransformParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: input image to be transformed.
+        output: the output image.
+        linear: specify a linear transform to apply, in the form of a 3x4 or\
+            4x4 ascii file. Note the standard 'reverse' convention is used, where\
+            the transform maps points in the template image to the moving image.\
+            Note that the reverse convention is still assumed even if no -template\
+            image is supplied.
+        flip: flip the specified axes, provided as a comma-separated list of\
+            indices (0:x, 1:y, 2:z).
+        inverse: apply the inverse transformation.
+        half: apply the matrix square root of the transformation. This can be\
+            combined with the inverse option.
+        replace: replace the linear transform of the original image by that\
+            specified, rather than applying it to the original image. The specified\
+            transform can be either a template image, or a 3x4 or 4x4 ascii file.
+        identity: set the header transform of the image to the identity matrix.
+        template: reslice the input image to match the specified template image\
+            grid.
+        midway_space: reslice the input image to the midway space. Requires\
+            either the -template or -warp option. If used with -template and\
+            -linear option the input image will be resliced onto the grid halfway\
+            between the input and template. If used with the -warp option the input\
+            will be warped to the midway space defined by the grid of the input\
+            warp (i.e. half way between image1 and image2).
+        interp: set the interpolation method to use when reslicing (choices:\
+            nearest, linear, cubic, sinc. Default: cubic).
+        oversample: set the amount of over-sampling (in the target space) to\
+            perform when regridding. This is particularly relevant when downsamping\
+            a high-resolution image to a low-resolution image, to avoid aliasing\
+            artefacts. This can consist of a single integer, or a comma-separated\
+            list of 3 integers if different oversampling factors are desired along\
+            the different axes. Default is determined from ratio of voxel\
+            dimensions (disabled for nearest-neighbour interpolation).
+        warp: apply a non-linear 4D deformation field to warp the input image.\
+            Each voxel in the deformation field must define the scanner space\
+            position that will be used to interpolate the input image during\
+            warping (i.e. pull-back/reverse warp convention). If the -template\
+            image is also supplied the deformation field will be resliced first to\
+            the template image grid. If no -template option is supplied then the\
+            output image will have the same image grid as the deformation field.\
+            This option can be used in combination with the -affine option, in\
+            which case the affine will be applied first).
+        warp_full: warp the input image using a 5D warp file output from\
+            mrregister. Any linear transforms in the warp image header will also be\
+            applied. The -warp_full option must be used in combination with either\
+            the -template option or the -midway_space option. If a -template image\
+            is supplied then the full warp will be used. By default the\
+            image1->image2 transform will be applied, however the -from 2 option\
+            can be used to apply the image2->image1 transform. Use the\
+            -midway_space option to warp the input image to the midway space. The\
+            -from option can also be used to define which warp to use when\
+            transforming to midway space.
+        from_: used to define which space the input image is when using the\
+            -warp_mid option. Use -from 1 to warp from image1 or -from 2 to warp\
+            from image2.
+        modulate: Valid choices are: fod and jac.\
+            fod: modulate FODs during reorientation to preserve the apparent\
+            fibre density across fibre bundle widths before and after the\
+            transformation.\
+            jac: modulate the image intensity with the determinant of the\
+            Jacobian of the warp of linear transformation to preserve the total\
+            intensity before and after the transformation.
+        directions: directions defining the number and orientation of the\
+            apodised point spread functions used in FOD reorientation (Default: 300\
+            directions).
+        reorient_fod: specify whether to perform FOD reorientation. This is\
+            required if the number of volumes in the 4th dimension corresponds to\
+            the number of coefficients in an antipodally symmetric spherical\
+            harmonic series with lmax >= 2 (i.e. 6, 15, 28, 45, 66 volumes).
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        export_grad_mrtrix: export the diffusion-weighted gradient table to\
+            file in MRtrix format.
+        export_grad_fsl: export the diffusion-weighted gradient table to files\
+            in FSL (bvecs / bvals) format.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        nan: Use NaN as the out of bounds value (Default: 0.0).
+        no_reorientation: deprecated, use -reorient_fod instead.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "mrtrix/mrtransform",
+        "inverse": inverse,
+        "half": half,
+        "identity": identity,
+        "midway_space": midway_space,
+        "nan": nan,
+        "no_reorientation": no_reorientation,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if linear is not None:
+        params["linear"] = linear
+    if flip is not None:
+        params["flip"] = flip
+    if replace is not None:
+        params["replace"] = replace
+    if template is not None:
+        params["template"] = template
+    if interp is not None:
+        params["interp"] = interp
+    if oversample is not None:
+        params["oversample"] = oversample
+    if warp is not None:
+        params["warp"] = warp
+    if warp_full is not None:
+        params["warp_full"] = warp_full
+    if from_ is not None:
+        params["from"] = from_
+    if modulate is not None:
+        params["modulate"] = modulate
+    if directions is not None:
+        params["directions"] = directions
+    if reorient_fod is not None:
+        params["reorient_fod"] = reorient_fod
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if export_grad_mrtrix is not None:
+        params["export_grad_mrtrix"] = export_grad_mrtrix
+    if export_grad_fsl is not None:
+        params["export_grad_fsl"] = export_grad_fsl
+    if datatype is not None:
+        params["datatype"] = datatype
+    if strides is not None:
+        params["strides"] = strides
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrtransform_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrtransformParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("linear", None) is not None:
+        if not isinstance(params["linear"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`linear` has the wrong type: Received `{type(params.get("linear", None))}` expected `InputPathType | None`')
+    if params.get("flip", None) is not None:
+        if not isinstance(params["flip"], list):
+            raise StyxValidationError(f'`flip` has the wrong type: Received `{type(params.get("flip", None))}` expected `list[int] | None`')
+        for e in params["flip"]:
+            if not isinstance(e, int):
+                raise StyxValidationError(f'`flip` has the wrong type: Received `{type(params.get("flip", None))}` expected `list[int] | None`')
+    if params.get("inverse", False) is None:
+        raise StyxValidationError("`inverse` must not be None")
+    if not isinstance(params["inverse"], bool):
+        raise StyxValidationError(f'`inverse` has the wrong type: Received `{type(params.get("inverse", False))}` expected `bool`')
+    if params.get("half", False) is None:
+        raise StyxValidationError("`half` must not be None")
+    if not isinstance(params["half"], bool):
+        raise StyxValidationError(f'`half` has the wrong type: Received `{type(params.get("half", False))}` expected `bool`')
+    if params.get("replace", None) is not None:
+        if not isinstance(params["replace"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`replace` has the wrong type: Received `{type(params.get("replace", None))}` expected `InputPathType | None`')
+    if params.get("identity", False) is None:
+        raise StyxValidationError("`identity` must not be None")
+    if not isinstance(params["identity"], bool):
+        raise StyxValidationError(f'`identity` has the wrong type: Received `{type(params.get("identity", False))}` expected `bool`')
+    if params.get("template", None) is not None:
+        if not isinstance(params["template"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`template` has the wrong type: Received `{type(params.get("template", None))}` expected `InputPathType | None`')
+    if params.get("midway_space", False) is None:
+        raise StyxValidationError("`midway_space` must not be None")
+    if not isinstance(params["midway_space"], bool):
+        raise StyxValidationError(f'`midway_space` has the wrong type: Received `{type(params.get("midway_space", False))}` expected `bool`')
+    if params.get("interp", None) is not None:
+        if not isinstance(params["interp"], str):
+            raise StyxValidationError(f'`interp` has the wrong type: Received `{type(params.get("interp", None))}` expected `str | None`')
+    if params.get("oversample", None) is not None:
+        if not isinstance(params["oversample"], list):
+            raise StyxValidationError(f'`oversample` has the wrong type: Received `{type(params.get("oversample", None))}` expected `list[int] | None`')
+        for e in params["oversample"]:
+            if not isinstance(e, int):
+                raise StyxValidationError(f'`oversample` has the wrong type: Received `{type(params.get("oversample", None))}` expected `list[int] | None`')
+    if params.get("warp", None) is not None:
+        if not isinstance(params["warp"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`warp` has the wrong type: Received `{type(params.get("warp", None))}` expected `InputPathType | None`')
+    if params.get("warp_full", None) is not None:
+        if not isinstance(params["warp_full"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`warp_full` has the wrong type: Received `{type(params.get("warp_full", None))}` expected `InputPathType | None`')
+    if params.get("from", None) is not None:
+        if not isinstance(params["from"], int):
+            raise StyxValidationError(f'`from` has the wrong type: Received `{type(params.get("from", None))}` expected `int | None`')
+    if params.get("modulate", None) is not None:
+        if not isinstance(params["modulate"], str):
+            raise StyxValidationError(f'`modulate` has the wrong type: Received `{type(params.get("modulate", None))}` expected `str | None`')
+    if params.get("directions", None) is not None:
+        if not isinstance(params["directions"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`directions` has the wrong type: Received `{type(params.get("directions", None))}` expected `InputPathType | None`')
+    if params.get("reorient_fod", None) is not None:
+        if not isinstance(params["reorient_fod"], str):
+            raise StyxValidationError(f'`reorient_fod` has the wrong type: Received `{type(params.get("reorient_fod", None))}` expected `str | None`')
+    if params.get("grad", None) is not None:
+        if not isinstance(params["grad"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`grad` has the wrong type: Received `{type(params.get("grad", None))}` expected `InputPathType | None`')
+    if params.get("fslgrad", None) is not None:
+        mrtransform_fslgrad_validate(params["fslgrad"])
+    if params.get("export_grad_mrtrix", None) is not None:
+        if not isinstance(params["export_grad_mrtrix"], str):
+            raise StyxValidationError(f'`export_grad_mrtrix` has the wrong type: Received `{type(params.get("export_grad_mrtrix", None))}` expected `str | None`')
+    if params.get("export_grad_fsl", None) is not None:
+        mrtransform_export_grad_fsl_validate(params["export_grad_fsl"])
+    if params.get("datatype", None) is not None:
+        if not isinstance(params["datatype"], str):
+            raise StyxValidationError(f'`datatype` has the wrong type: Received `{type(params.get("datatype", None))}` expected `str | None`')
+    if params.get("strides", None) is not None:
+        if not isinstance(params["strides"], dict):
+            raise StyxValidationError(f'Params object has the wrong type \'{type(params["strides"])}\'')
+        if "@type" not in params["strides"]:
+            raise StyxValidationError("Params object is missing `@type`")
+        if params["strides"]["@type"] not in ["VariousString", "VariousFile"]:
+            raise StyxValidationError("Parameter `strides`s `@type` must be one of [\"VariousString\", \"VariousFile\"]")
+        mrtransform_strides_validate_dyn_fn(params["strides"]["@type"])(params["strides"])
+    if params.get("nan", False) is None:
+        raise StyxValidationError("`nan` must not be None")
+    if not isinstance(params["nan"], bool):
+        raise StyxValidationError(f'`nan` has the wrong type: Received `{type(params.get("nan", False))}` expected `bool`')
+    if params.get("no_reorientation", False) is None:
+        raise StyxValidationError("`no_reorientation` must not be None")
+    if not isinstance(params["no_reorientation"], bool):
+        raise StyxValidationError(f'`no_reorientation` has the wrong type: Received `{type(params.get("no_reorientation", False))}` expected `bool`')
+    if params.get("info", False) is None:
+        raise StyxValidationError("`info` must not be None")
+    if not isinstance(params["info"], bool):
+        raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
+    if params.get("quiet", False) is None:
+        raise StyxValidationError("`quiet` must not be None")
+    if not isinstance(params["quiet"], bool):
+        raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
+    if params.get("debug", False) is None:
+        raise StyxValidationError("`debug` must not be None")
+    if not isinstance(params["debug"], bool):
+        raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
+    if params.get("force", False) is None:
+        raise StyxValidationError("`force` must not be None")
+    if not isinstance(params["force"], bool):
+        raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
+    if params.get("nthreads", None) is not None:
+        if not isinstance(params["nthreads"], int):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
+    if params.get("config", None) is not None:
+        if not isinstance(params["config"], list):
+            raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[MrtransformConfigParamsDict] | None`')
+        for e in params["config"]:
+            mrtransform_config_validate(e)
+    if params.get("help", False) is None:
+        raise StyxValidationError("`help` must not be None")
+    if not isinstance(params["help"], bool):
+        raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
+    if params.get("version", False) is None:
+        raise StyxValidationError("`version` must not be None")
+    if not isinstance(params["version"], bool):
+        raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
+    if params.get("input", None) is None:
+        raise StyxValidationError("`input` must not be None")
+    if not isinstance(params["input"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `InputPathType`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], str):
+        raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str`')
+
+
+def mrtransform_cargs(
+    params: MrtransformParamsDict,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("mrtransform")
+    if params.get("linear", None) is not None:
+        cargs.extend([
+            "-linear",
+            execution.input_file(params.get("linear", None))
+        ])
+    if params.get("flip", None) is not None:
+        cargs.extend([
+            "-flip",
+            ",".join(map(str, params.get("flip", None)))
+        ])
+    if params.get("inverse", False):
+        cargs.append("-inverse")
+    if params.get("half", False):
+        cargs.append("-half")
+    if params.get("replace", None) is not None:
+        cargs.extend([
+            "-replace",
+            execution.input_file(params.get("replace", None))
+        ])
+    if params.get("identity", False):
+        cargs.append("-identity")
+    if params.get("template", None) is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template", None))
+        ])
+    if params.get("midway_space", False):
+        cargs.append("-midway_space")
+    if params.get("interp", None) is not None:
+        cargs.extend([
+            "-interp",
+            params.get("interp", None)
+        ])
+    if params.get("oversample", None) is not None:
+        cargs.extend([
+            "-oversample",
+            ",".join(map(str, params.get("oversample", None)))
+        ])
+    if params.get("warp", None) is not None:
+        cargs.extend([
+            "-warp",
+            execution.input_file(params.get("warp", None))
+        ])
+    if params.get("warp_full", None) is not None:
+        cargs.extend([
+            "-warp_full",
+            execution.input_file(params.get("warp_full", None))
+        ])
+    if params.get("from", None) is not None:
+        cargs.extend([
+            "-from",
+            str(params.get("from", None))
+        ])
+    if params.get("modulate", None) is not None:
+        cargs.extend([
+            "-modulate",
+            params.get("modulate", None)
+        ])
+    if params.get("directions", None) is not None:
+        cargs.extend([
+            "-directions",
+            execution.input_file(params.get("directions", None))
+        ])
+    if params.get("reorient_fod", None) is not None:
+        cargs.extend([
+            "-reorient_fod",
+            params.get("reorient_fod", None)
+        ])
+    if params.get("grad", None) is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad", None))
+        ])
+    if params.get("fslgrad", None) is not None:
+        cargs.extend(mrtransform_fslgrad_cargs(params.get("fslgrad", None), execution))
+    if params.get("export_grad_mrtrix", None) is not None:
+        cargs.extend([
+            "-export_grad_mrtrix",
+            params.get("export_grad_mrtrix", None)
+        ])
+    if params.get("export_grad_fsl", None) is not None:
+        cargs.extend(mrtransform_export_grad_fsl_cargs(params.get("export_grad_fsl", None), execution))
+    if params.get("datatype", None) is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype", None)
+        ])
+    if params.get("strides", None) is not None:
+        cargs.extend([
+            "-strides",
+            *mrtransform_strides_cargs_dyn_fn(params.get("strides", None)["@type"])(params.get("strides", None), execution)
+        ])
+    if params.get("nan", False):
+        cargs.append("-nan")
+    if params.get("no_reorientation", False):
+        cargs.append("-no_reorientation")
+    if params.get("info", False):
+        cargs.append("-info")
+    if params.get("quiet", False):
+        cargs.append("-quiet")
+    if params.get("debug", False):
+        cargs.append("-debug")
+    if params.get("force", False):
+        cargs.append("-force")
+    if params.get("nthreads", None) is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads", None))
+        ])
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [mrtransform_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def mrtransform_outputs(
+    params: MrtransformParamsDict,
+    execution: Execution,
+) -> MrtransformOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MrtransformOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+        export_grad_mrtrix=execution.output_file(params.get("export_grad_mrtrix", None)) if (params.get("export_grad_mrtrix") is not None) else None,
+        export_grad_fsl=mrtransform_export_grad_fsl_outputs(params.get("export_grad_fsl"), execution) if params.get("export_grad_fsl") else None,
+    )
+    return ret
+
+
+def mrtransform_execute(
+    params: MrtransformParamsDict,
+    runner: Runner | None = None,
+) -> MrtransformOutputs:
+    """
+    mrtransform
+    
+    Apply spatial transformations to an image.
+    
+    If a linear transform is applied without a template image the command will
+    modify the image header transform matrix
+    
+    FOD reorientation (with apodised point spread functions) can be performed if
+    the number of volumes in the 4th dimension equals the number of coefficients
+    in an antipodally symmetric spherical harmonic series (e.g. 6, 15, 28 etc).
+    For such data, the -reorient_fod yes/no option must be used to specify if
+    reorientation is required.
+    
+    The output image intensity can be modulated using the (local or global)
+    volume change if a linear or nonlinear transformation is applied. 'FOD'
+    modulation preserves the apparent fibre density across the fibre bundle
+    width and can only be applied if FOD reorientation is used. Alternatively,
+    non-directional scaling by the Jacobian determinant can be applied to any
+    image type.
+    
+    If a DW scheme is contained in the header (or specified separately), and the
+    number of directions matches the number of volumes in the images, any
+    transformation applied using the -linear option will also be applied to the
+    directions.
+    
+    When the -template option is used to specify the target image grid, the
+    image provided via this option will not influence the axis data strides of
+    the output image; these are determined based on the input image, or the
+    input to the -strides option.
+    
+    References:
+    
+    * If FOD reorientation is being performed:
+    Raffelt, D.; Tournier, J.-D.; Crozier, S.; Connelly, A. & Salvado, O.
+    Reorientation of fiber orientation distributions using apodized point spread
+    functions. Magnetic Resonance in Medicine, 2012, 67, 844-855
+    
+    * If FOD modulation is being performed:
+    Raffelt, D.; Tournier, J.-D.; Rose, S.; Ridgway, G.R.; Henderson, R.;
+    Crozier, S.; Salvado, O.; Connelly, A.; Apparent Fibre Density: a novel
+    measure for the analysis of diffusion-weighted magnetic resonance images.
+    NeuroImage, 2012, 15;59(4), 3976-94.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrtransformOutputs`).
+    """
+    mrtransform_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRTRANSFORM_METADATA)
+    params = execution.params(params)
+    cargs = mrtransform_cargs(params, execution)
+    ret = mrtransform_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrtransform(
+    input_: InputPathType,
+    output: str,
+    linear: InputPathType | None = None,
+    flip: list[int] | None = None,
+    inverse: bool = False,
+    half: bool = False,
+    replace: InputPathType | None = None,
+    identity: bool = False,
+    template: InputPathType | None = None,
+    midway_space: bool = False,
+    interp: str | None = None,
+    oversample: list[int] | None = None,
+    warp: InputPathType | None = None,
+    warp_full: InputPathType | None = None,
+    from_: int | None = None,
+    modulate: str | None = None,
+    directions: InputPathType | None = None,
+    reorient_fod: str | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: MrtransformFslgradParamsDict | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: MrtransformExportGradFslParamsDict | None = None,
+    datatype: str | None = None,
+    strides: typing.Union[MrtransformVariousStringParamsDictTagged, MrtransformVariousFileParamsDictTagged] | None = None,
+    nan: bool = False,
+    no_reorientation: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrtransformConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrtransformOutputs:
+    """
+    mrtransform
+    
+    Apply spatial transformations to an image.
+    
+    If a linear transform is applied without a template image the command will
+    modify the image header transform matrix
+    
+    FOD reorientation (with apodised point spread functions) can be performed if
+    the number of volumes in the 4th dimension equals the number of coefficients
+    in an antipodally symmetric spherical harmonic series (e.g. 6, 15, 28 etc).
+    For such data, the -reorient_fod yes/no option must be used to specify if
+    reorientation is required.
+    
+    The output image intensity can be modulated using the (local or global)
+    volume change if a linear or nonlinear transformation is applied. 'FOD'
+    modulation preserves the apparent fibre density across the fibre bundle
+    width and can only be applied if FOD reorientation is used. Alternatively,
+    non-directional scaling by the Jacobian determinant can be applied to any
+    image type.
+    
+    If a DW scheme is contained in the header (or specified separately), and the
+    number of directions matches the number of volumes in the images, any
+    transformation applied using the -linear option will also be applied to the
+    directions.
+    
+    When the -template option is used to specify the target image grid, the
+    image provided via this option will not influence the axis data strides of
+    the output image; these are determined based on the input image, or the
+    input to the -strides option.
+    
+    References:
+    
+    * If FOD reorientation is being performed:
+    Raffelt, D.; Tournier, J.-D.; Crozier, S.; Connelly, A. & Salvado, O.
+    Reorientation of fiber orientation distributions using apodized point spread
+    functions. Magnetic Resonance in Medicine, 2012, 67, 844-855
+    
+    * If FOD modulation is being performed:
+    Raffelt, D.; Tournier, J.-D.; Rose, S.; Ridgway, G.R.; Henderson, R.;
+    Crozier, S.; Salvado, O.; Connelly, A.; Apparent Fibre Density: a novel
+    measure for the analysis of diffusion-weighted magnetic resonance images.
+    NeuroImage, 2012, 15;59(4), 3976-94.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: input image to be transformed.
+        output: the output image.
+        linear: specify a linear transform to apply, in the form of a 3x4 or\
+            4x4 ascii file. Note the standard 'reverse' convention is used, where\
+            the transform maps points in the template image to the moving image.\
+            Note that the reverse convention is still assumed even if no -template\
+            image is supplied.
+        flip: flip the specified axes, provided as a comma-separated list of\
+            indices (0:x, 1:y, 2:z).
+        inverse: apply the inverse transformation.
+        half: apply the matrix square root of the transformation. This can be\
+            combined with the inverse option.
+        replace: replace the linear transform of the original image by that\
+            specified, rather than applying it to the original image. The specified\
+            transform can be either a template image, or a 3x4 or 4x4 ascii file.
+        identity: set the header transform of the image to the identity matrix.
+        template: reslice the input image to match the specified template image\
+            grid.
+        midway_space: reslice the input image to the midway space. Requires\
+            either the -template or -warp option. If used with -template and\
+            -linear option the input image will be resliced onto the grid halfway\
+            between the input and template. If used with the -warp option the input\
+            will be warped to the midway space defined by the grid of the input\
+            warp (i.e. half way between image1 and image2).
+        interp: set the interpolation method to use when reslicing (choices:\
+            nearest, linear, cubic, sinc. Default: cubic).
+        oversample: set the amount of over-sampling (in the target space) to\
+            perform when regridding. This is particularly relevant when downsamping\
+            a high-resolution image to a low-resolution image, to avoid aliasing\
+            artefacts. This can consist of a single integer, or a comma-separated\
+            list of 3 integers if different oversampling factors are desired along\
+            the different axes. Default is determined from ratio of voxel\
+            dimensions (disabled for nearest-neighbour interpolation).
+        warp: apply a non-linear 4D deformation field to warp the input image.\
+            Each voxel in the deformation field must define the scanner space\
+            position that will be used to interpolate the input image during\
+            warping (i.e. pull-back/reverse warp convention). If the -template\
+            image is also supplied the deformation field will be resliced first to\
+            the template image grid. If no -template option is supplied then the\
+            output image will have the same image grid as the deformation field.\
+            This option can be used in combination with the -affine option, in\
+            which case the affine will be applied first).
+        warp_full: warp the input image using a 5D warp file output from\
+            mrregister. Any linear transforms in the warp image header will also be\
+            applied. The -warp_full option must be used in combination with either\
+            the -template option or the -midway_space option. If a -template image\
+            is supplied then the full warp will be used. By default the\
+            image1->image2 transform will be applied, however the -from 2 option\
+            can be used to apply the image2->image1 transform. Use the\
+            -midway_space option to warp the input image to the midway space. The\
+            -from option can also be used to define which warp to use when\
+            transforming to midway space.
+        from_: used to define which space the input image is when using the\
+            -warp_mid option. Use -from 1 to warp from image1 or -from 2 to warp\
+            from image2.
+        modulate: Valid choices are: fod and jac.\
+            fod: modulate FODs during reorientation to preserve the apparent\
+            fibre density across fibre bundle widths before and after the\
+            transformation.\
+            jac: modulate the image intensity with the determinant of the\
+            Jacobian of the warp of linear transformation to preserve the total\
+            intensity before and after the transformation.
+        directions: directions defining the number and orientation of the\
+            apodised point spread functions used in FOD reorientation (Default: 300\
+            directions).
+        reorient_fod: specify whether to perform FOD reorientation. This is\
+            required if the number of volumes in the 4th dimension corresponds to\
+            the number of coefficients in an antipodally symmetric spherical\
+            harmonic series with lmax >= 2 (i.e. 6, 15, 28, 45, 66 volumes).
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        export_grad_mrtrix: export the diffusion-weighted gradient table to\
+            file in MRtrix format.
+        export_grad_fsl: export the diffusion-weighted gradient table to files\
+            in FSL (bvecs / bvals) format.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        nan: Use NaN as the out of bounds value (Default: 0.0).
+        no_reorientation: deprecated, use -reorient_fod instead.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrtransformOutputs`).
+    """
+    params = mrtransform_params(
+        linear=linear,
+        flip=flip,
+        inverse=inverse,
+        half=half,
+        replace=replace,
+        identity=identity,
+        template=template,
+        midway_space=midway_space,
+        interp=interp,
+        oversample=oversample,
+        warp=warp,
+        warp_full=warp_full,
+        from_=from_,
+        modulate=modulate,
+        directions=directions,
+        reorient_fod=reorient_fod,
+        grad=grad,
+        fslgrad=fslgrad,
+        export_grad_mrtrix=export_grad_mrtrix,
+        export_grad_fsl=export_grad_fsl,
+        datatype=datatype,
+        strides=strides,
+        nan=nan,
+        no_reorientation=no_reorientation,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return mrtransform_execute(params, runner)
+
+
+__all__ = [
+    "MRTRANSFORM_METADATA",
+    "MrtransformConfigParamsDict",
+    "MrtransformConfigParamsDictTagged",
+    "MrtransformExportGradFslOutputs",
+    "MrtransformExportGradFslParamsDict",
+    "MrtransformExportGradFslParamsDictTagged",
+    "MrtransformFslgradParamsDict",
+    "MrtransformFslgradParamsDictTagged",
+    "MrtransformOutputs",
+    "MrtransformParamsDict",
+    "MrtransformParamsDictTagged",
+    "MrtransformVariousFileParamsDict",
+    "MrtransformVariousFileParamsDictTagged",
+    "MrtransformVariousStringParamsDict",
+    "MrtransformVariousStringParamsDictTagged",
+    "mrtransform",
+    "mrtransform_config",
+    "mrtransform_execute",
+    "mrtransform_export_grad_fsl",
+    "mrtransform_fslgrad",
+    "mrtransform_params",
+    "mrtransform_various_file",
+    "mrtransform_various_string",
+]