niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrtransform.py

@@ -0,0 +1,1061 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRTRANSFORM_METADATA = Metadata(
+    id="faaa07c120c0bcc84911ab27778920e0d881a5ea.boutiques",
+    name="mrtransform",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrtransformFslgradParameters = typing.TypedDict('MrtransformFslgradParameters', {
+    "__STYX_TYPE__": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+
+
+MrtransformExportGradFslParameters = typing.TypedDict('MrtransformExportGradFslParameters', {
+    "__STYX_TYPE__": typing.Literal["export_grad_fsl"],
+    "bvecs_path": str,
+    "bvals_path": str,
+})
+
+
+MrtransformVariousStringParameters = typing.TypedDict('MrtransformVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+MrtransformVariousFileParameters = typing.TypedDict('MrtransformVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+MrtransformConfigParameters = typing.TypedDict('MrtransformConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrtransformParameters = typing.TypedDict('MrtransformParameters', {
+    "__STYX_TYPE__": typing.Literal["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[MrtransformFslgradParameters | None],
+    "export_grad_mrtrix": typing.NotRequired[str | None],
+    "export_grad_fsl": typing.NotRequired[MrtransformExportGradFslParameters | None],
+    "datatype": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[MrtransformVariousStringParameters, MrtransformVariousFileParameters] | None],
+    "nan": bool,
+    "no_reorientation": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrtransformConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrtransform": mrtransform_cargs,
+        "fslgrad": mrtransform_fslgrad_cargs,
+        "export_grad_fsl": mrtransform_export_grad_fsl_cargs,
+        "VariousString": mrtransform_various_string_cargs,
+        "VariousFile": mrtransform_various_file_cargs,
+        "config": mrtransform_config_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "mrtransform": mrtransform_outputs,
+        "export_grad_fsl": mrtransform_export_grad_fsl_outputs,
+    }.get(t)
+
+
+def mrtransform_fslgrad_params(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> MrtransformFslgradParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "fslgrad",
+        "bvecs": bvecs,
+        "bvals": bvals,
+    }
+    return params
+
+
+def mrtransform_fslgrad_cargs(
+    params: MrtransformFslgradParameters,
+    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")))
+    cargs.append(execution.input_file(params.get("bvals")))
+    return cargs
+
+
+class MrtransformExportGradFslOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrtransformExportGradFslParameters | 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_params(
+    bvecs_path: str,
+    bvals_path: str,
+) -> MrtransformExportGradFslParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "export_grad_fsl",
+        "bvecs_path": bvecs_path,
+        "bvals_path": bvals_path,
+    }
+    return params
+
+
+def mrtransform_export_grad_fsl_cargs(
+    params: MrtransformExportGradFslParameters,
+    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"))
+    cargs.append(params.get("bvals_path"))
+    return cargs
+
+
+def mrtransform_export_grad_fsl_outputs(
+    params: MrtransformExportGradFslParameters,
+    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")),
+        bvals_path=execution.output_file(params.get("bvals_path")),
+    )
+    return ret
+
+
+def mrtransform_various_string_params(
+    obj: str,
+) -> MrtransformVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def mrtransform_various_string_cargs(
+    params: MrtransformVariousStringParameters,
+    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"))
+    return cargs
+
+
+def mrtransform_various_file_params(
+    obj: InputPathType,
+) -> MrtransformVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def mrtransform_various_file_cargs(
+    params: MrtransformVariousFileParameters,
+    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")))
+    return cargs
+
+
+def mrtransform_config_params(
+    key: str,
+    value: str,
+) -> MrtransformConfigParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def mrtransform_config_cargs(
+    params: MrtransformConfigParameters,
+    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"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class MrtransformOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrtransform(...)`.
+    """
+    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: MrtransformFslgradParameters | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: MrtransformExportGradFslParameters | None = None,
+    datatype: str | None = None,
+    strides: typing.Union[MrtransformVariousStringParameters, MrtransformVariousFileParameters] | 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[MrtransformConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrtransformParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: MrtransformParameters,
+    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") is not None:
+        cargs.extend([
+            "-linear",
+            execution.input_file(params.get("linear"))
+        ])
+    if params.get("flip") is not None:
+        cargs.extend([
+            "-flip",
+            ",".join(map(str, params.get("flip")))
+        ])
+    if params.get("inverse"):
+        cargs.append("-inverse")
+    if params.get("half"):
+        cargs.append("-half")
+    if params.get("replace") is not None:
+        cargs.extend([
+            "-replace",
+            execution.input_file(params.get("replace"))
+        ])
+    if params.get("identity"):
+        cargs.append("-identity")
+    if params.get("template") is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template"))
+        ])
+    if params.get("midway_space"):
+        cargs.append("-midway_space")
+    if params.get("interp") is not None:
+        cargs.extend([
+            "-interp",
+            params.get("interp")
+        ])
+    if params.get("oversample") is not None:
+        cargs.extend([
+            "-oversample",
+            ",".join(map(str, params.get("oversample")))
+        ])
+    if params.get("warp") is not None:
+        cargs.extend([
+            "-warp",
+            execution.input_file(params.get("warp"))
+        ])
+    if params.get("warp_full") is not None:
+        cargs.extend([
+            "-warp_full",
+            execution.input_file(params.get("warp_full"))
+        ])
+    if params.get("from") is not None:
+        cargs.extend([
+            "-from",
+            str(params.get("from"))
+        ])
+    if params.get("modulate") is not None:
+        cargs.extend([
+            "-modulate",
+            params.get("modulate")
+        ])
+    if params.get("directions") is not None:
+        cargs.extend([
+            "-directions",
+            execution.input_file(params.get("directions"))
+        ])
+    if params.get("reorient_fod") is not None:
+        cargs.extend([
+            "-reorient_fod",
+            params.get("reorient_fod")
+        ])
+    if params.get("grad") is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad"))
+        ])
+    if params.get("fslgrad") is not None:
+        cargs.extend(dyn_cargs(params.get("fslgrad")["__STYXTYPE__"])(params.get("fslgrad"), execution))
+    if params.get("export_grad_mrtrix") is not None:
+        cargs.extend([
+            "-export_grad_mrtrix",
+            params.get("export_grad_mrtrix")
+        ])
+    if params.get("export_grad_fsl") is not None:
+        cargs.extend(dyn_cargs(params.get("export_grad_fsl")["__STYXTYPE__"])(params.get("export_grad_fsl"), execution))
+    if params.get("datatype") is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype")
+        ])
+    if params.get("strides") is not None:
+        cargs.extend([
+            "-strides",
+            *dyn_cargs(params.get("strides")["__STYXTYPE__"])(params.get("strides"), execution)
+        ])
+    if params.get("nan"):
+        cargs.append("-nan")
+    if params.get("no_reorientation"):
+        cargs.append("-no_reorientation")
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("input")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def mrtransform_outputs(
+    params: MrtransformParameters,
+    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")),
+        export_grad_mrtrix=execution.output_file(params.get("export_grad_mrtrix")) if (params.get("export_grad_mrtrix") is not None) else None,
+        export_grad_fsl=dyn_outputs(params.get("export_grad_fsl")["__STYXTYPE__"])(params.get("export_grad_fsl"), execution) if params.get("export_grad_fsl") else None,
+    )
+    return ret
+
+
+def mrtransform_execute(
+    params: MrtransformParameters,
+    execution: Execution,
+) -> MrtransformOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrtransformOutputs`).
+    """
+    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: MrtransformFslgradParameters | None = None,
+    export_grad_mrtrix: str | None = None,
+    export_grad_fsl: MrtransformExportGradFslParameters | None = None,
+    datatype: str | None = None,
+    strides: typing.Union[MrtransformVariousStringParameters, MrtransformVariousFileParameters] | 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[MrtransformConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrtransformOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRTRANSFORM_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "MRTRANSFORM_METADATA",
+    "MrtransformConfigParameters",
+    "MrtransformExportGradFslOutputs",
+    "MrtransformExportGradFslParameters",
+    "MrtransformFslgradParameters",
+    "MrtransformOutputs",
+    "MrtransformParameters",
+    "MrtransformVariousFileParameters",
+    "MrtransformVariousStringParameters",
+    "mrtransform",
+    "mrtransform_config_params",
+    "mrtransform_export_grad_fsl_params",
+    "mrtransform_fslgrad_params",
+    "mrtransform_params",
+    "mrtransform_various_file_params",
+    "mrtransform_various_string_params",
+]