niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/v_5ttgen.py

@@ -0,0 +1,1107 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_5TTGEN_METADATA = Metadata(
+    id="213c8cb30d8d1a68c488abbf08a42cf6809dc622.boutiques",
+    name="5ttgen",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_V5ttgenFreesurferParamsDictNoTag = typing.TypedDict('_V5ttgenFreesurferParamsDictNoTag', {
+    "input": InputPathType,
+    "output": str,
+    "lut": typing.NotRequired[InputPathType | None],
+})
+V5ttgenFreesurferParamsDictTagged = typing.TypedDict('V5ttgenFreesurferParamsDictTagged', {
+    "@type": typing.Literal["freesurfer"],
+    "input": InputPathType,
+    "output": str,
+    "lut": typing.NotRequired[InputPathType | None],
+})
+V5ttgenFreesurferParamsDict = _V5ttgenFreesurferParamsDictNoTag | V5ttgenFreesurferParamsDictTagged
+
+
+_V5ttgenFslParamsDictNoTag = typing.TypedDict('_V5ttgenFslParamsDictNoTag', {
+    "input": InputPathType,
+    "output": str,
+    "t2": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "premasked": bool,
+})
+V5ttgenFslParamsDictTagged = typing.TypedDict('V5ttgenFslParamsDictTagged', {
+    "@type": typing.Literal["fsl"],
+    "input": InputPathType,
+    "output": str,
+    "t2": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "premasked": bool,
+})
+V5ttgenFslParamsDict = _V5ttgenFslParamsDictNoTag | V5ttgenFslParamsDictTagged
+
+
+_V5ttgenGifParamsDictNoTag = typing.TypedDict('_V5ttgenGifParamsDictNoTag', {
+    "input": InputPathType,
+    "output": str,
+})
+V5ttgenGifParamsDictTagged = typing.TypedDict('V5ttgenGifParamsDictTagged', {
+    "@type": typing.Literal["gif"],
+    "input": InputPathType,
+    "output": str,
+})
+V5ttgenGifParamsDict = _V5ttgenGifParamsDictNoTag | V5ttgenGifParamsDictTagged
+
+
+_V5ttgenHsvsParamsDictNoTag = typing.TypedDict('_V5ttgenHsvsParamsDictNoTag', {
+    "input": InputPathType,
+    "output": str,
+    "template": typing.NotRequired[InputPathType | None],
+    "hippocampi": typing.NotRequired[typing.Literal["subfields", "first", "aseg"] | None],
+    "thalami": typing.NotRequired[typing.Literal["nuclei", "first", "aseg"] | None],
+    "white_stem": bool,
+})
+V5ttgenHsvsParamsDictTagged = typing.TypedDict('V5ttgenHsvsParamsDictTagged', {
+    "@type": typing.Literal["hsvs"],
+    "input": InputPathType,
+    "output": str,
+    "template": typing.NotRequired[InputPathType | None],
+    "hippocampi": typing.NotRequired[typing.Literal["subfields", "first", "aseg"] | None],
+    "thalami": typing.NotRequired[typing.Literal["nuclei", "first", "aseg"] | None],
+    "white_stem": bool,
+})
+V5ttgenHsvsParamsDict = _V5ttgenHsvsParamsDictNoTag | V5ttgenHsvsParamsDictTagged
+
+
+_V5ttgenConfigParamsDictNoTag = typing.TypedDict('_V5ttgenConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+V5ttgenConfigParamsDictTagged = typing.TypedDict('V5ttgenConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+V5ttgenConfigParamsDict = _V5ttgenConfigParamsDictNoTag | V5ttgenConfigParamsDictTagged
+
+
+_V5ttgenParamsDictNoTag = typing.TypedDict('_V5ttgenParamsDictNoTag', {
+    "algorithm": typing.Union[V5ttgenFreesurferParamsDictTagged, V5ttgenFslParamsDictTagged, V5ttgenGifParamsDictTagged, V5ttgenHsvsParamsDictTagged],
+    "nocrop": bool,
+    "sgm_amyg_hipp": bool,
+    "nocleanup": bool,
+    "scratch": typing.NotRequired[str | None],
+    "continue": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[V5ttgenConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+})
+V5ttgenParamsDictTagged = typing.TypedDict('V5ttgenParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/5ttgen"],
+    "algorithm": typing.Union[V5ttgenFreesurferParamsDictTagged, V5ttgenFslParamsDictTagged, V5ttgenGifParamsDictTagged, V5ttgenHsvsParamsDictTagged],
+    "nocrop": bool,
+    "sgm_amyg_hipp": bool,
+    "nocleanup": bool,
+    "scratch": typing.NotRequired[str | None],
+    "continue": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[V5ttgenConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+})
+V5ttgenParamsDict = _V5ttgenParamsDictNoTag | V5ttgenParamsDictTagged
+
+
+def v_5ttgen_algorithm_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "freesurfer": v_5ttgen_freesurfer_cargs,
+        "fsl": v_5ttgen_fsl_cargs,
+        "gif": v_5ttgen_gif_cargs,
+        "hsvs": v_5ttgen_hsvs_cargs,
+    }.get(t)
+
+
+def v_5ttgen_algorithm_outputs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "freesurfer": v_5ttgen_freesurfer_outputs,
+        "fsl": v_5ttgen_fsl_outputs,
+        "gif": v_5ttgen_gif_outputs,
+        "hsvs": v_5ttgen_hsvs_outputs,
+    }.get(t)
+
+
+def v_5ttgen_algorithm_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "freesurfer": v_5ttgen_freesurfer_validate,
+        "fsl": v_5ttgen_fsl_validate,
+        "gif": v_5ttgen_gif_validate,
+        "hsvs": v_5ttgen_hsvs_validate,
+    }.get(t)
+
+
+class V5ttgenFreesurferOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `V5ttgenFreesurferParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """The output 5TT image"""
+
+
+def v_5ttgen_freesurfer(
+    input_: InputPathType,
+    output: str,
+    lut: InputPathType | None = None,
+) -> V5ttgenFreesurferParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: The input FreeSurfer parcellation image (any image containing\
+            'aseg' in its name).
+        output: The output 5TT image.
+        lut: Manually provide path to the lookup table on which the input\
+            parcellation image is based (e.g. FreeSurferColorLUT.txt).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "freesurfer",
+        "input": input_,
+        "output": output,
+    }
+    if lut is not None:
+        params["lut"] = lut
+    return params
+
+
+def v_5ttgen_freesurfer_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `V5ttgenFreesurferParamsDict` 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("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`')
+    if params.get("lut", None) is not None:
+        if not isinstance(params["lut"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`lut` has the wrong type: Received `{type(params.get("lut", None))}` expected `InputPathType | None`')
+
+
+def v_5ttgen_freesurfer_cargs(
+    params: V5ttgenFreesurferParamsDict,
+    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("freesurfer")
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("output", None))
+    if params.get("lut", None) is not None:
+        cargs.extend([
+            "-lut",
+            execution.input_file(params.get("lut", None))
+        ])
+    return cargs
+
+
+def v_5ttgen_freesurfer_outputs(
+    params: V5ttgenFreesurferParamsDict,
+    execution: Execution,
+) -> V5ttgenFreesurferOutputs:
+    """
+    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 = V5ttgenFreesurferOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+class V5ttgenFslOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `V5ttgenFslParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """The output 5TT image"""
+
+
+def v_5ttgen_fsl(
+    input_: InputPathType,
+    output: str,
+    t2: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    premasked: bool = False,
+) -> V5ttgenFslParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: The input T1-weighted image.
+        output: The output 5TT image.
+        t2: Provide a T2-weighted image in addition to the default T1-weighted\
+            image; this will be used as a second input to FSL FAST.
+        mask: Manually provide a brain mask, rather than deriving one in the\
+            script.
+        premasked: Indicate that brain masking has already been applied to the\
+            input image.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "fsl",
+        "input": input_,
+        "output": output,
+        "premasked": premasked,
+    }
+    if t2 is not None:
+        params["t2"] = t2
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_5ttgen_fsl_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `V5ttgenFslParamsDict` 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("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`')
+    if params.get("t2", None) is not None:
+        if not isinstance(params["t2"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`t2` has the wrong type: Received `{type(params.get("t2", None))}` expected `InputPathType | None`')
+    if params.get("mask", None) is not None:
+        if not isinstance(params["mask"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask` has the wrong type: Received `{type(params.get("mask", None))}` expected `InputPathType | None`')
+    if params.get("premasked", False) is None:
+        raise StyxValidationError("`premasked` must not be None")
+    if not isinstance(params["premasked"], bool):
+        raise StyxValidationError(f'`premasked` has the wrong type: Received `{type(params.get("premasked", False))}` expected `bool`')
+
+
+def v_5ttgen_fsl_cargs(
+    params: V5ttgenFslParamsDict,
+    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("fsl")
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("output", None))
+    if params.get("t2", None) is not None:
+        cargs.extend([
+            "-t2",
+            execution.input_file(params.get("t2", None))
+        ])
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", None))
+        ])
+    if params.get("premasked", False):
+        cargs.append("-premasked")
+    return cargs
+
+
+def v_5ttgen_fsl_outputs(
+    params: V5ttgenFslParamsDict,
+    execution: Execution,
+) -> V5ttgenFslOutputs:
+    """
+    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 = V5ttgenFslOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+class V5ttgenGifOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `V5ttgenGifParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """The output 5TT image"""
+
+
+def v_5ttgen_gif(
+    input_: InputPathType,
+    output: str,
+) -> V5ttgenGifParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: The input Geodesic Information Flow (GIF) segmentation image.
+        output: The output 5TT image.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "gif",
+        "input": input_,
+        "output": output,
+    }
+    return params
+
+
+def v_5ttgen_gif_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `V5ttgenGifParamsDict` 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("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 v_5ttgen_gif_cargs(
+    params: V5ttgenGifParamsDict,
+    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("gif")
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def v_5ttgen_gif_outputs(
+    params: V5ttgenGifParamsDict,
+    execution: Execution,
+) -> V5ttgenGifOutputs:
+    """
+    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 = V5ttgenGifOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+class V5ttgenHsvsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `V5ttgenHsvsParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """The output 5TT image"""
+
+
+def v_5ttgen_hsvs(
+    input_: InputPathType,
+    output: str,
+    template: InputPathType | None = None,
+    hippocampi: typing.Literal["subfields", "first", "aseg"] | None = None,
+    thalami: typing.Literal["nuclei", "first", "aseg"] | None = None,
+    white_stem: bool = False,
+) -> V5ttgenHsvsParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: The input FreeSurfer subject directory.
+        output: The output 5TT image.
+        template: Provide an image that will form the template for the\
+            generated 5TT image.
+        hippocampi: Select method to be used for hippocampi (& amygdalae)\
+            segmentation; options are: subfields,first,aseg.
+        thalami: Select method to be used for thalamic segmentation; options\
+            are: nuclei,first,aseg.
+        white_stem: Classify the brainstem as white matter.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "hsvs",
+        "input": input_,
+        "output": output,
+        "white_stem": white_stem,
+    }
+    if template is not None:
+        params["template"] = template
+    if hippocampi is not None:
+        params["hippocampi"] = hippocampi
+    if thalami is not None:
+        params["thalami"] = thalami
+    return params
+
+
+def v_5ttgen_hsvs_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `V5ttgenHsvsParamsDict` 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("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`')
+    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("hippocampi", None) is not None:
+        if not isinstance(params["hippocampi"], str):
+            raise StyxValidationError(f'`hippocampi` has the wrong type: Received `{type(params.get("hippocampi", None))}` expected `typing.Literal["subfields", "first", "aseg"] | None`')
+        if params["hippocampi"] not in ["subfields", "first", "aseg"]:
+            raise StyxValidationError("Parameter `hippocampi` must be one of [\"subfields\", \"first\", \"aseg\"]")
+    if params.get("thalami", None) is not None:
+        if not isinstance(params["thalami"], str):
+            raise StyxValidationError(f'`thalami` has the wrong type: Received `{type(params.get("thalami", None))}` expected `typing.Literal["nuclei", "first", "aseg"] | None`')
+        if params["thalami"] not in ["nuclei", "first", "aseg"]:
+            raise StyxValidationError("Parameter `thalami` must be one of [\"nuclei\", \"first\", \"aseg\"]")
+    if params.get("white_stem", False) is None:
+        raise StyxValidationError("`white_stem` must not be None")
+    if not isinstance(params["white_stem"], bool):
+        raise StyxValidationError(f'`white_stem` has the wrong type: Received `{type(params.get("white_stem", False))}` expected `bool`')
+
+
+def v_5ttgen_hsvs_cargs(
+    params: V5ttgenHsvsParamsDict,
+    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("hsvs")
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("output", None))
+    if params.get("template", None) is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template", None))
+        ])
+    if params.get("hippocampi", None) is not None:
+        cargs.extend([
+            "-hippocampi",
+            params.get("hippocampi", None)
+        ])
+    if params.get("thalami", None) is not None:
+        cargs.extend([
+            "-thalami",
+            params.get("thalami", None)
+        ])
+    if params.get("white_stem", False):
+        cargs.append("-white_stem")
+    return cargs
+
+
+def v_5ttgen_hsvs_outputs(
+    params: V5ttgenHsvsParamsDict,
+    execution: Execution,
+) -> V5ttgenHsvsOutputs:
+    """
+    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 = V5ttgenHsvsOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def v_5ttgen_config(
+    key: str,
+    value: str,
+) -> V5ttgenConfigParamsDictTagged:
+    """
+    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 v_5ttgen_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `V5ttgenConfigParamsDict` 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 v_5ttgen_config_cargs(
+    params: V5ttgenConfigParamsDict,
+    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 V5ttgenOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `V5ttgenParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    algorithm: typing.Union[V5ttgenFreesurferOutputs, V5ttgenFslOutputs, V5ttgenGifOutputs, V5ttgenHsvsOutputs]
+    """Outputs from `V5ttgenFreesurferParamsDict` or `V5ttgenFslParamsDict` or
+    `V5ttgenGifParamsDict` or `V5ttgenHsvsParamsDict`."""
+
+
+def v_5ttgen_params(
+    algorithm: typing.Union[V5ttgenFreesurferParamsDictTagged, V5ttgenFslParamsDictTagged, V5ttgenGifParamsDictTagged, V5ttgenHsvsParamsDictTagged],
+    nocrop: bool = False,
+    sgm_amyg_hipp: bool = False,
+    nocleanup: bool = False,
+    scratch: str | None = None,
+    continue_: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[V5ttgenConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> V5ttgenParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        algorithm: Select the algorithm to be used to complete the script\
+            operation; additional details and options become available once an\
+            algorithm is nominated. Options are: freesurfer, fsl, gif, hsvs.
+        nocrop: Do NOT crop the resulting 5TT image to reduce its size (keep\
+            the same dimensions as the input image).
+        sgm_amyg_hipp: Represent the amygdalae and hippocampi as sub-cortical\
+            grey matter in the 5TT image.
+        nocleanup: do not delete intermediate files during script execution,\
+            and do not delete scratch directory at script completion.
+        scratch: manually specify the path in which to generate the scratch\
+            directory.
+        continue_: continue the script from a previous execution; must provide\
+            the scratch directory path, and the name of the last\
+            successfully-generated file.
+        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/5ttgen",
+        "algorithm": algorithm,
+        "nocrop": nocrop,
+        "sgm_amyg_hipp": sgm_amyg_hipp,
+        "nocleanup": nocleanup,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+    }
+    if scratch is not None:
+        params["scratch"] = scratch
+    if continue_ is not None:
+        params["continue"] = continue_
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def v_5ttgen_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `V5ttgenParamsDict` 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("algorithm", None) is None:
+        raise StyxValidationError("`algorithm` must not be None")
+    if not isinstance(params["algorithm"], dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params["algorithm"])}\'')
+    if "@type" not in params["algorithm"]:
+        raise StyxValidationError("Params object is missing `@type`")
+    if params["algorithm"]["@type"] not in ["freesurfer", "fsl", "gif", "hsvs"]:
+        raise StyxValidationError("Parameter `algorithm`s `@type` must be one of [\"freesurfer\", \"fsl\", \"gif\", \"hsvs\"]")
+    v_5ttgen_algorithm_validate_dyn_fn(params["algorithm"]["@type"])(params["algorithm"])
+    if params.get("nocrop", False) is None:
+        raise StyxValidationError("`nocrop` must not be None")
+    if not isinstance(params["nocrop"], bool):
+        raise StyxValidationError(f'`nocrop` has the wrong type: Received `{type(params.get("nocrop", False))}` expected `bool`')
+    if params.get("sgm_amyg_hipp", False) is None:
+        raise StyxValidationError("`sgm_amyg_hipp` must not be None")
+    if not isinstance(params["sgm_amyg_hipp"], bool):
+        raise StyxValidationError(f'`sgm_amyg_hipp` has the wrong type: Received `{type(params.get("sgm_amyg_hipp", False))}` expected `bool`')
+    if params.get("nocleanup", False) is None:
+        raise StyxValidationError("`nocleanup` must not be None")
+    if not isinstance(params["nocleanup"], bool):
+        raise StyxValidationError(f'`nocleanup` has the wrong type: Received `{type(params.get("nocleanup", False))}` expected `bool`')
+    if params.get("scratch", None) is not None:
+        if not isinstance(params["scratch"], str):
+            raise StyxValidationError(f'`scratch` has the wrong type: Received `{type(params.get("scratch", None))}` expected `str | None`')
+    if params.get("continue", None) is not None:
+        if not isinstance(params["continue"], str):
+            raise StyxValidationError(f'`continue` has the wrong type: Received `{type(params.get("continue", None))}` expected `str | None`')
+    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[V5ttgenConfigParamsDict] | None`')
+        for e in params["config"]:
+            v_5ttgen_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`')
+
+
+def v_5ttgen_cargs(
+    params: V5ttgenParamsDict,
+    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("5ttgen")
+    cargs.extend(v_5ttgen_algorithm_cargs_dyn_fn(params.get("algorithm", None)["@type"])(params.get("algorithm", None), execution))
+    if params.get("nocrop", False):
+        cargs.append("-nocrop")
+    if params.get("sgm_amyg_hipp", False):
+        cargs.append("-sgm_amyg_hipp")
+    if params.get("nocleanup", False):
+        cargs.append("-nocleanup")
+    if params.get("scratch", None) is not None:
+        cargs.extend([
+            "-scratch",
+            params.get("scratch", None)
+        ])
+    if params.get("continue", None) is not None:
+        cargs.extend([
+            "-continue",
+            params.get("continue", None)
+        ])
+    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 [v_5ttgen_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")
+    return cargs
+
+
+def v_5ttgen_outputs(
+    params: V5ttgenParamsDict,
+    execution: Execution,
+) -> V5ttgenOutputs:
+    """
+    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 = V5ttgenOutputs(
+        root=execution.output_file("."),
+        algorithm=v_5ttgen_algorithm_outputs_dyn_fn(params.get("algorithm")["@type"])(params.get("algorithm"), execution),
+    )
+    return ret
+
+
+def v_5ttgen_execute(
+    params: V5ttgenParamsDict,
+    runner: Runner | None = None,
+) -> V5ttgenOutputs:
+    """
+    5ttgen
+    
+    Generate a 5TT image suitable for ACT.
+    
+    5ttgen acts as a 'master' script for generating a five-tissue-type (5TT)
+    segmented tissue image suitable for use in Anatomically-Constrained
+    Tractography (ACT). A range of different algorithms are available for
+    completing this task. When using this script, the name of the algorithm to
+    be used must appear as the first argument on the command-line after
+    '5ttgen'. The subsequent compulsory arguments and options available depend
+    on the particular algorithm being invoked.
+    Each algorithm available also has its own help page, including necessary
+    references; e.g. to see the help page of the 'fsl' algorithm, type '5ttgen
+    fsl'.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V5ttgenOutputs`).
+    """
+    v_5ttgen_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_5TTGEN_METADATA)
+    params = execution.params(params)
+    cargs = v_5ttgen_cargs(params, execution)
+    ret = v_5ttgen_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_5ttgen(
+    algorithm: typing.Union[V5ttgenFreesurferParamsDictTagged, V5ttgenFslParamsDictTagged, V5ttgenGifParamsDictTagged, V5ttgenHsvsParamsDictTagged],
+    nocrop: bool = False,
+    sgm_amyg_hipp: bool = False,
+    nocleanup: bool = False,
+    scratch: str | None = None,
+    continue_: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[V5ttgenConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> V5ttgenOutputs:
+    """
+    5ttgen
+    
+    Generate a 5TT image suitable for ACT.
+    
+    5ttgen acts as a 'master' script for generating a five-tissue-type (5TT)
+    segmented tissue image suitable for use in Anatomically-Constrained
+    Tractography (ACT). A range of different algorithms are available for
+    completing this task. When using this script, the name of the algorithm to
+    be used must appear as the first argument on the command-line after
+    '5ttgen'. The subsequent compulsory arguments and options available depend
+    on the particular algorithm being invoked.
+    Each algorithm available also has its own help page, including necessary
+    references; e.g. to see the help page of the 'fsl' algorithm, type '5ttgen
+    fsl'.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        algorithm: Select the algorithm to be used to complete the script\
+            operation; additional details and options become available once an\
+            algorithm is nominated. Options are: freesurfer, fsl, gif, hsvs.
+        nocrop: Do NOT crop the resulting 5TT image to reduce its size (keep\
+            the same dimensions as the input image).
+        sgm_amyg_hipp: Represent the amygdalae and hippocampi as sub-cortical\
+            grey matter in the 5TT image.
+        nocleanup: do not delete intermediate files during script execution,\
+            and do not delete scratch directory at script completion.
+        scratch: manually specify the path in which to generate the scratch\
+            directory.
+        continue_: continue the script from a previous execution; must provide\
+            the scratch directory path, and the name of the last\
+            successfully-generated file.
+        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 `V5ttgenOutputs`).
+    """
+    params = v_5ttgen_params(
+        algorithm=algorithm,
+        nocrop=nocrop,
+        sgm_amyg_hipp=sgm_amyg_hipp,
+        nocleanup=nocleanup,
+        scratch=scratch,
+        continue_=continue_,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+    )
+    return v_5ttgen_execute(params, runner)
+
+
+__all__ = [
+    "V5ttgenConfigParamsDict",
+    "V5ttgenConfigParamsDictTagged",
+    "V5ttgenFreesurferOutputs",
+    "V5ttgenFreesurferParamsDict",
+    "V5ttgenFreesurferParamsDictTagged",
+    "V5ttgenFslOutputs",
+    "V5ttgenFslParamsDict",
+    "V5ttgenFslParamsDictTagged",
+    "V5ttgenGifOutputs",
+    "V5ttgenGifParamsDict",
+    "V5ttgenGifParamsDictTagged",
+    "V5ttgenHsvsOutputs",
+    "V5ttgenHsvsParamsDict",
+    "V5ttgenHsvsParamsDictTagged",
+    "V5ttgenOutputs",
+    "V5ttgenParamsDict",
+    "V5ttgenParamsDictTagged",
+    "V_5TTGEN_METADATA",
+    "v_5ttgen",
+    "v_5ttgen_config",
+    "v_5ttgen_execute",
+    "v_5ttgen_freesurfer",
+    "v_5ttgen_fsl",
+    "v_5ttgen_gif",
+    "v_5ttgen_hsvs",
+    "v_5ttgen_params",
+]