niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dwi2fod.py

@@ -0,0 +1,1156 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DWI2FOD_METADATA = Metadata(
+    id="6d16386fcfa6e4701ad68f4333de7173683fda45.boutiques",
+    name="dwi2fod",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Dwi2fodFslgradParamsDictNoTag = typing.TypedDict('_Dwi2fodFslgradParamsDictNoTag', {
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Dwi2fodFslgradParamsDictTagged = typing.TypedDict('Dwi2fodFslgradParamsDictTagged', {
+    "@type": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Dwi2fodFslgradParamsDict = _Dwi2fodFslgradParamsDictNoTag | Dwi2fodFslgradParamsDictTagged
+
+
+_Dwi2fodVariousStringParamsDictNoTag = typing.TypedDict('_Dwi2fodVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+Dwi2fodVariousStringParamsDictTagged = typing.TypedDict('Dwi2fodVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+Dwi2fodVariousStringParamsDict = _Dwi2fodVariousStringParamsDictNoTag | Dwi2fodVariousStringParamsDictTagged
+
+
+_Dwi2fodVariousFileParamsDictNoTag = typing.TypedDict('_Dwi2fodVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+Dwi2fodVariousFileParamsDictTagged = typing.TypedDict('Dwi2fodVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+Dwi2fodVariousFileParamsDict = _Dwi2fodVariousFileParamsDictNoTag | Dwi2fodVariousFileParamsDictTagged
+
+
+_Dwi2fodConfigParamsDictNoTag = typing.TypedDict('_Dwi2fodConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Dwi2fodConfigParamsDictTagged = typing.TypedDict('Dwi2fodConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Dwi2fodConfigParamsDict = _Dwi2fodConfigParamsDictNoTag | Dwi2fodConfigParamsDictTagged
+
+
+_Dwi2fodResponseOdfParamsDictNoTag = typing.TypedDict('_Dwi2fodResponseOdfParamsDictNoTag', {
+    "response": InputPathType,
+    "odf": str,
+})
+Dwi2fodResponseOdfParamsDictTagged = typing.TypedDict('Dwi2fodResponseOdfParamsDictTagged', {
+    "@type": typing.Literal["response_odf"],
+    "response": InputPathType,
+    "odf": str,
+})
+Dwi2fodResponseOdfParamsDict = _Dwi2fodResponseOdfParamsDictNoTag | Dwi2fodResponseOdfParamsDictTagged
+
+
+_Dwi2fodParamsDictNoTag = typing.TypedDict('_Dwi2fodParamsDictNoTag', {
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Dwi2fodFslgradParamsDict | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "directions": typing.NotRequired[InputPathType | None],
+    "lmax": typing.NotRequired[list[int] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "filter": typing.NotRequired[InputPathType | None],
+    "neg_lambda": typing.NotRequired[float | None],
+    "norm_lambda": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[int | None],
+    "norm_lambda_1": typing.NotRequired[float | None],
+    "neg_lambda_1": typing.NotRequired[float | None],
+    "predicted_signal": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[Dwi2fodVariousStringParamsDictTagged, Dwi2fodVariousFileParamsDictTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Dwi2fodConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "algorithm": str,
+    "dwi": InputPathType,
+    "response_odf": list[Dwi2fodResponseOdfParamsDict],
+})
+Dwi2fodParamsDictTagged = typing.TypedDict('Dwi2fodParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/dwi2fod"],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Dwi2fodFslgradParamsDict | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "directions": typing.NotRequired[InputPathType | None],
+    "lmax": typing.NotRequired[list[int] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "filter": typing.NotRequired[InputPathType | None],
+    "neg_lambda": typing.NotRequired[float | None],
+    "norm_lambda": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[int | None],
+    "norm_lambda_1": typing.NotRequired[float | None],
+    "neg_lambda_1": typing.NotRequired[float | None],
+    "predicted_signal": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[Dwi2fodVariousStringParamsDictTagged, Dwi2fodVariousFileParamsDictTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Dwi2fodConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "algorithm": str,
+    "dwi": InputPathType,
+    "response_odf": list[Dwi2fodResponseOdfParamsDict],
+})
+Dwi2fodParamsDict = _Dwi2fodParamsDictNoTag | Dwi2fodParamsDictTagged
+
+
+def dwi2fod_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": dwi2fod_various_string_cargs,
+        "VariousFile": dwi2fod_various_file_cargs,
+    }.get(t)
+
+
+def dwi2fod_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": dwi2fod_various_string_validate,
+        "VariousFile": dwi2fod_various_file_validate,
+    }.get(t)
+
+
+def dwi2fod_fslgrad(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> Dwi2fodFslgradParamsDictTagged:
+    """
+    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 dwi2fod_fslgrad_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2fodFslgradParamsDict` 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 dwi2fod_fslgrad_cargs(
+    params: Dwi2fodFslgradParamsDict,
+    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
+
+
+def dwi2fod_various_string(
+    obj: str,
+) -> Dwi2fodVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def dwi2fod_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2fodVariousStringParamsDict` 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 dwi2fod_various_string_cargs(
+    params: Dwi2fodVariousStringParamsDict,
+    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 dwi2fod_various_file(
+    obj: InputPathType,
+) -> Dwi2fodVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def dwi2fod_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2fodVariousFileParamsDict` 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 dwi2fod_various_file_cargs(
+    params: Dwi2fodVariousFileParamsDict,
+    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 dwi2fod_config(
+    key: str,
+    value: str,
+) -> Dwi2fodConfigParamsDictTagged:
+    """
+    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 dwi2fod_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2fodConfigParamsDict` 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 dwi2fod_config_cargs(
+    params: Dwi2fodConfigParamsDict,
+    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 Dwi2fodResponseOdfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `list[Dwi2fodResponseOdfParamsDict](...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    odf: OutputPathType
+    """output ODF image"""
+
+
+def dwi2fod_response_odf(
+    response: InputPathType,
+    odf: str,
+) -> Dwi2fodResponseOdfParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        response: input tissue response.
+        odf: output ODF image.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "response_odf",
+        "response": response,
+        "odf": odf,
+    }
+    return params
+
+
+def dwi2fod_response_odf_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2fodResponseOdfParamsDict` 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("response", None) is None:
+        raise StyxValidationError("`response` must not be None")
+    if not isinstance(params["response"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`response` has the wrong type: Received `{type(params.get("response", None))}` expected `InputPathType`')
+    if params.get("odf", None) is None:
+        raise StyxValidationError("`odf` must not be None")
+    if not isinstance(params["odf"], str):
+        raise StyxValidationError(f'`odf` has the wrong type: Received `{type(params.get("odf", None))}` expected `str`')
+
+
+def dwi2fod_response_odf_cargs(
+    params: Dwi2fodResponseOdfParamsDict,
+    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("response", None)))
+    cargs.append(params.get("odf", None))
+    return cargs
+
+
+def dwi2fod_response_odf_outputs(
+    params: Dwi2fodResponseOdfParamsDict,
+    execution: Execution,
+) -> Dwi2fodResponseOdfOutputs:
+    """
+    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 = Dwi2fodResponseOdfOutputs(
+        root=execution.output_file("."),
+        odf=execution.output_file(params.get("odf", None)),
+    )
+    return ret
+
+
+class Dwi2fodOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Dwi2fodParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    predicted_signal: OutputPathType | None
+    """output the predicted dwi image. """
+    response_odf: list[Dwi2fodResponseOdfOutputs]
+    """Outputs from `dwi2fod_response_odf_outputs`.This is a list of outputs
+    with the same length and order as the inputs."""
+
+
+def dwi2fod_params(
+    algorithm: str,
+    dwi: InputPathType,
+    response_odf: list[Dwi2fodResponseOdfParamsDict],
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2fodFslgradParamsDict | None = None,
+    shells: list[float] | None = None,
+    directions: InputPathType | None = None,
+    lmax: list[int] | None = None,
+    mask: InputPathType | None = None,
+    filter_: InputPathType | None = None,
+    neg_lambda: float | None = None,
+    norm_lambda: float | None = None,
+    threshold: float | None = None,
+    niter: int | None = None,
+    norm_lambda_1: float | None = None,
+    neg_lambda_1: float | None = None,
+    predicted_signal: str | None = None,
+    strides: typing.Union[Dwi2fodVariousStringParamsDictTagged, Dwi2fodVariousFileParamsDictTagged] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2fodConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Dwi2fodParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        algorithm: the algorithm to use for FOD estimation. (options are:\
+            csd,msmt_csd).
+        dwi: the input diffusion-weighted image.
+        response_odf: pairs of input tissue response and output ODF images.
+        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.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        directions: specify the directions over which to apply the\
+            non-negativity constraint (by default, the built-in 300 direction set\
+            is used). These should be supplied as a text file containing [ az el ]\
+            pairs for the directions.
+        lmax: the maximum spherical harmonic order for the output FOD(s).For\
+            algorithms with multiple outputs, this should be provided as a\
+            comma-separated list of integers, one for each output image; for\
+            single-output algorithms, only a single integer should be provided. If\
+            omitted, the command will use the lmax of the corresponding response\
+            function (i.e based on its number of coefficients), up to a maximum of\
+            8.
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        filter_: the linear frequency filtering parameters used for the initial\
+            linear spherical deconvolution step (default = [ 1 1 1 0 0 ]). These\
+            should be supplied as a text file containing the filtering coefficients\
+            for each even harmonic order.
+        neg_lambda: the regularisation parameter lambda that controls the\
+            strength of the non-negativity constraint (default = 1).
+        norm_lambda: the regularisation parameter lambda that controls the\
+            strength of the constraint on the norm of the solution (default = 1).
+        threshold: the threshold below which the amplitude of the FOD is\
+            assumed to be zero, expressed as an absolute amplitude (default = 0).
+        niter: the maximum number of iterations to perform for each voxel\
+            (default = 50). Use '-niter 0' for a linear unconstrained spherical\
+            deconvolution.
+        norm_lambda_1: the regularisation parameter lambda that controls the\
+            strength of the constraint on the norm of the solution (default =\
+            1e-10).
+        neg_lambda_1: the regularisation parameter lambda that controls the\
+            strength of the non-negativity constraint (default = 1e-10).
+        predicted_signal: output the predicted dwi image.
+        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.
+        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/dwi2fod",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "algorithm": algorithm,
+        "dwi": dwi,
+        "response_odf": response_odf,
+    }
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if shells is not None:
+        params["shells"] = shells
+    if directions is not None:
+        params["directions"] = directions
+    if lmax is not None:
+        params["lmax"] = lmax
+    if mask is not None:
+        params["mask"] = mask
+    if filter_ is not None:
+        params["filter"] = filter_
+    if neg_lambda is not None:
+        params["neg_lambda"] = neg_lambda
+    if norm_lambda is not None:
+        params["norm_lambda"] = norm_lambda
+    if threshold is not None:
+        params["threshold"] = threshold
+    if niter is not None:
+        params["niter"] = niter
+    if norm_lambda_1 is not None:
+        params["norm_lambda_1"] = norm_lambda_1
+    if neg_lambda_1 is not None:
+        params["neg_lambda_1"] = neg_lambda_1
+    if predicted_signal is not None:
+        params["predicted_signal"] = predicted_signal
+    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 dwi2fod_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2fodParamsDict` 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("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:
+        dwi2fod_fslgrad_validate(params["fslgrad"])
+    if params.get("shells", None) is not None:
+        if not isinstance(params["shells"], list):
+            raise StyxValidationError(f'`shells` has the wrong type: Received `{type(params.get("shells", None))}` expected `list[float] | None`')
+        for e in params["shells"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`shells` has the wrong type: Received `{type(params.get("shells", None))}` expected `list[float] | 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("lmax", None) is not None:
+        if not isinstance(params["lmax"], list):
+            raise StyxValidationError(f'`lmax` has the wrong type: Received `{type(params.get("lmax", None))}` expected `list[int] | None`')
+        for e in params["lmax"]:
+            if not isinstance(e, int):
+                raise StyxValidationError(f'`lmax` has the wrong type: Received `{type(params.get("lmax", None))}` expected `list[int] | 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("filter", None) is not None:
+        if not isinstance(params["filter"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`filter` has the wrong type: Received `{type(params.get("filter", None))}` expected `InputPathType | None`')
+    if params.get("neg_lambda", None) is not None:
+        if not isinstance(params["neg_lambda"], (float, int)):
+            raise StyxValidationError(f'`neg_lambda` has the wrong type: Received `{type(params.get("neg_lambda", None))}` expected `float | None`')
+    if params.get("norm_lambda", None) is not None:
+        if not isinstance(params["norm_lambda"], (float, int)):
+            raise StyxValidationError(f'`norm_lambda` has the wrong type: Received `{type(params.get("norm_lambda", None))}` expected `float | None`')
+    if params.get("threshold", None) is not None:
+        if not isinstance(params["threshold"], (float, int)):
+            raise StyxValidationError(f'`threshold` has the wrong type: Received `{type(params.get("threshold", None))}` expected `float | None`')
+    if params.get("niter", None) is not None:
+        if not isinstance(params["niter"], int):
+            raise StyxValidationError(f'`niter` has the wrong type: Received `{type(params.get("niter", None))}` expected `int | None`')
+    if params.get("norm_lambda_1", None) is not None:
+        if not isinstance(params["norm_lambda_1"], (float, int)):
+            raise StyxValidationError(f'`norm_lambda_1` has the wrong type: Received `{type(params.get("norm_lambda_1", None))}` expected `float | None`')
+    if params.get("neg_lambda_1", None) is not None:
+        if not isinstance(params["neg_lambda_1"], (float, int)):
+            raise StyxValidationError(f'`neg_lambda_1` has the wrong type: Received `{type(params.get("neg_lambda_1", None))}` expected `float | None`')
+    if params.get("predicted_signal", None) is not None:
+        if not isinstance(params["predicted_signal"], str):
+            raise StyxValidationError(f'`predicted_signal` has the wrong type: Received `{type(params.get("predicted_signal", 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\"]")
+        dwi2fod_strides_validate_dyn_fn(params["strides"]["@type"])(params["strides"])
+    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[Dwi2fodConfigParamsDict] | None`')
+        for e in params["config"]:
+            dwi2fod_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("algorithm", None) is None:
+        raise StyxValidationError("`algorithm` must not be None")
+    if not isinstance(params["algorithm"], str):
+        raise StyxValidationError(f'`algorithm` has the wrong type: Received `{type(params.get("algorithm", None))}` expected `str`')
+    if params.get("dwi", None) is None:
+        raise StyxValidationError("`dwi` must not be None")
+    if not isinstance(params["dwi"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`dwi` has the wrong type: Received `{type(params.get("dwi", None))}` expected `InputPathType`')
+    if params.get("response_odf", None) is None:
+        raise StyxValidationError("`response_odf` must not be None")
+    if not isinstance(params["response_odf"], list):
+        raise StyxValidationError(f'`response_odf` has the wrong type: Received `{type(params.get("response_odf", None))}` expected `list[Dwi2fodResponseOdfParamsDict]`')
+    for e in params["response_odf"]:
+        dwi2fod_response_odf_validate(e)
+
+
+def dwi2fod_cargs(
+    params: Dwi2fodParamsDict,
+    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("dwi2fod")
+    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(dwi2fod_fslgrad_cargs(params.get("fslgrad", None), execution))
+    if params.get("shells", None) is not None:
+        cargs.extend([
+            "-shells",
+            ",".join(map(str, params.get("shells", None)))
+        ])
+    if params.get("directions", None) is not None:
+        cargs.extend([
+            "-directions",
+            execution.input_file(params.get("directions", None))
+        ])
+    if params.get("lmax", None) is not None:
+        cargs.extend([
+            "-lmax",
+            ",".join(map(str, params.get("lmax", None)))
+        ])
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", None))
+        ])
+    if params.get("filter", None) is not None:
+        cargs.extend([
+            "-filter",
+            execution.input_file(params.get("filter", None))
+        ])
+    if params.get("neg_lambda", None) is not None:
+        cargs.extend([
+            "-neg_lambda",
+            str(params.get("neg_lambda", None))
+        ])
+    if params.get("norm_lambda", None) is not None:
+        cargs.extend([
+            "-norm_lambda",
+            str(params.get("norm_lambda", None))
+        ])
+    if params.get("threshold", None) is not None:
+        cargs.extend([
+            "-threshold",
+            str(params.get("threshold", None))
+        ])
+    if params.get("niter", None) is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("niter", None))
+        ])
+    if params.get("norm_lambda_1", None) is not None:
+        cargs.extend([
+            "-norm_lambda",
+            str(params.get("norm_lambda_1", None))
+        ])
+    if params.get("neg_lambda_1", None) is not None:
+        cargs.extend([
+            "-neg_lambda",
+            str(params.get("neg_lambda_1", None))
+        ])
+    if params.get("predicted_signal", None) is not None:
+        cargs.extend([
+            "-predicted_signal",
+            params.get("predicted_signal", None)
+        ])
+    if params.get("strides", None) is not None:
+        cargs.extend([
+            "-strides",
+            *dwi2fod_strides_cargs_dyn_fn(params.get("strides", None)["@type"])(params.get("strides", None), execution)
+        ])
+    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 [dwi2fod_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(params.get("algorithm", None))
+    cargs.append(execution.input_file(params.get("dwi", None)))
+    cargs.extend([a for c in [dwi2fod_response_odf_cargs(s, execution) for s in params.get("response_odf", None)] for a in c])
+    return cargs
+
+
+def dwi2fod_outputs(
+    params: Dwi2fodParamsDict,
+    execution: Execution,
+) -> Dwi2fodOutputs:
+    """
+    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 = Dwi2fodOutputs(
+        root=execution.output_file("."),
+        predicted_signal=execution.output_file(params.get("predicted_signal", None)) if (params.get("predicted_signal") is not None) else None,
+        response_odf=[dwi2fod_response_odf_outputs(i, execution) if dwi2fod_response_odf_outputs else None for i in params.get("response_odf")],
+    )
+    return ret
+
+
+def dwi2fod_execute(
+    params: Dwi2fodParamsDict,
+    runner: Runner | None = None,
+) -> Dwi2fodOutputs:
+    """
+    dwi2fod
+    
+    Estimate fibre orientation distributions from diffusion data using spherical
+    deconvolution.
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    * If using csd algorithm:
+    Tournier, J.-D.; Calamante, F. & Connelly, A. Robust determination of the
+    fibre orientation distribution in diffusion MRI: Non-negativity constrained
+    super-resolved spherical deconvolution. NeuroImage, 2007, 35, 1459-1472
+    
+    * If using msmt_csd algorithm:
+    Jeurissen, B; Tournier, J-D; Dhollander, T; Connelly, A & Sijbers, J.
+    Multi-tissue constrained spherical deconvolution for improved analysis of
+    multi-shell diffusion MRI data. NeuroImage, 2014, 103, 411-426
+    
+    Tournier, J.-D.; Calamante, F., Gadian, D.G. & Connelly, A. Direct
+    estimation of the fiber orientation density function from diffusion-weighted
+    MRI data using spherical deconvolution. NeuroImage, 2004, 23, 1176-1185.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Dwi2fodOutputs`).
+    """
+    dwi2fod_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DWI2FOD_METADATA)
+    params = execution.params(params)
+    cargs = dwi2fod_cargs(params, execution)
+    ret = dwi2fod_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dwi2fod(
+    algorithm: str,
+    dwi: InputPathType,
+    response_odf: list[Dwi2fodResponseOdfParamsDict],
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2fodFslgradParamsDict | None = None,
+    shells: list[float] | None = None,
+    directions: InputPathType | None = None,
+    lmax: list[int] | None = None,
+    mask: InputPathType | None = None,
+    filter_: InputPathType | None = None,
+    neg_lambda: float | None = None,
+    norm_lambda: float | None = None,
+    threshold: float | None = None,
+    niter: int | None = None,
+    norm_lambda_1: float | None = None,
+    neg_lambda_1: float | None = None,
+    predicted_signal: str | None = None,
+    strides: typing.Union[Dwi2fodVariousStringParamsDictTagged, Dwi2fodVariousFileParamsDictTagged] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2fodConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Dwi2fodOutputs:
+    """
+    dwi2fod
+    
+    Estimate fibre orientation distributions from diffusion data using spherical
+    deconvolution.
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    * If using csd algorithm:
+    Tournier, J.-D.; Calamante, F. & Connelly, A. Robust determination of the
+    fibre orientation distribution in diffusion MRI: Non-negativity constrained
+    super-resolved spherical deconvolution. NeuroImage, 2007, 35, 1459-1472
+    
+    * If using msmt_csd algorithm:
+    Jeurissen, B; Tournier, J-D; Dhollander, T; Connelly, A & Sijbers, J.
+    Multi-tissue constrained spherical deconvolution for improved analysis of
+    multi-shell diffusion MRI data. NeuroImage, 2014, 103, 411-426
+    
+    Tournier, J.-D.; Calamante, F., Gadian, D.G. & Connelly, A. Direct
+    estimation of the fiber orientation density function from diffusion-weighted
+    MRI data using spherical deconvolution. NeuroImage, 2004, 23, 1176-1185.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        algorithm: the algorithm to use for FOD estimation. (options are:\
+            csd,msmt_csd).
+        dwi: the input diffusion-weighted image.
+        response_odf: pairs of input tissue response and output ODF images.
+        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.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        directions: specify the directions over which to apply the\
+            non-negativity constraint (by default, the built-in 300 direction set\
+            is used). These should be supplied as a text file containing [ az el ]\
+            pairs for the directions.
+        lmax: the maximum spherical harmonic order for the output FOD(s).For\
+            algorithms with multiple outputs, this should be provided as a\
+            comma-separated list of integers, one for each output image; for\
+            single-output algorithms, only a single integer should be provided. If\
+            omitted, the command will use the lmax of the corresponding response\
+            function (i.e based on its number of coefficients), up to a maximum of\
+            8.
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        filter_: the linear frequency filtering parameters used for the initial\
+            linear spherical deconvolution step (default = [ 1 1 1 0 0 ]). These\
+            should be supplied as a text file containing the filtering coefficients\
+            for each even harmonic order.
+        neg_lambda: the regularisation parameter lambda that controls the\
+            strength of the non-negativity constraint (default = 1).
+        norm_lambda: the regularisation parameter lambda that controls the\
+            strength of the constraint on the norm of the solution (default = 1).
+        threshold: the threshold below which the amplitude of the FOD is\
+            assumed to be zero, expressed as an absolute amplitude (default = 0).
+        niter: the maximum number of iterations to perform for each voxel\
+            (default = 50). Use '-niter 0' for a linear unconstrained spherical\
+            deconvolution.
+        norm_lambda_1: the regularisation parameter lambda that controls the\
+            strength of the constraint on the norm of the solution (default =\
+            1e-10).
+        neg_lambda_1: the regularisation parameter lambda that controls the\
+            strength of the non-negativity constraint (default = 1e-10).
+        predicted_signal: output the predicted dwi image.
+        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.
+        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 `Dwi2fodOutputs`).
+    """
+    params = dwi2fod_params(
+        grad=grad,
+        fslgrad=fslgrad,
+        shells=shells,
+        directions=directions,
+        lmax=lmax,
+        mask=mask,
+        filter_=filter_,
+        neg_lambda=neg_lambda,
+        norm_lambda=norm_lambda,
+        threshold=threshold,
+        niter=niter,
+        norm_lambda_1=norm_lambda_1,
+        neg_lambda_1=neg_lambda_1,
+        predicted_signal=predicted_signal,
+        strides=strides,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        algorithm=algorithm,
+        dwi=dwi,
+        response_odf=response_odf,
+    )
+    return dwi2fod_execute(params, runner)
+
+
+__all__ = [
+    "DWI2FOD_METADATA",
+    "Dwi2fodConfigParamsDict",
+    "Dwi2fodConfigParamsDictTagged",
+    "Dwi2fodFslgradParamsDict",
+    "Dwi2fodFslgradParamsDictTagged",
+    "Dwi2fodOutputs",
+    "Dwi2fodParamsDict",
+    "Dwi2fodParamsDictTagged",
+    "Dwi2fodResponseOdfOutputs",
+    "Dwi2fodResponseOdfParamsDict",
+    "Dwi2fodResponseOdfParamsDictTagged",
+    "Dwi2fodVariousFileParamsDict",
+    "Dwi2fodVariousFileParamsDictTagged",
+    "Dwi2fodVariousStringParamsDict",
+    "Dwi2fodVariousStringParamsDictTagged",
+    "dwi2fod",
+    "dwi2fod_config",
+    "dwi2fod_execute",
+    "dwi2fod_fslgrad",
+    "dwi2fod_params",
+    "dwi2fod_response_odf",
+    "dwi2fod_various_file",
+    "dwi2fod_various_string",
+]