niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dwi2fod.py

@@ -0,0 +1,879 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DWI2FOD_METADATA = Metadata(
+    id="9a7e655a0db0138d987e71f2ed64a274b8c286e0.boutiques",
+    name="dwi2fod",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Dwi2fodFslgradParameters = typing.TypedDict('Dwi2fodFslgradParameters', {
+    "__STYX_TYPE__": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+
+
+Dwi2fodVariousStringParameters = typing.TypedDict('Dwi2fodVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+Dwi2fodVariousFileParameters = typing.TypedDict('Dwi2fodVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+Dwi2fodConfigParameters = typing.TypedDict('Dwi2fodConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Dwi2fodResponseOdfParameters = typing.TypedDict('Dwi2fodResponseOdfParameters', {
+    "__STYX_TYPE__": typing.Literal["response_odf"],
+    "response": InputPathType,
+    "odf": str,
+})
+
+
+Dwi2fodParameters = typing.TypedDict('Dwi2fodParameters', {
+    "__STYX_TYPE__": typing.Literal["dwi2fod"],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Dwi2fodFslgradParameters | 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[Dwi2fodVariousStringParameters, Dwi2fodVariousFileParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Dwi2fodConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "algorithm": str,
+    "dwi": InputPathType,
+    "response_odf": list[Dwi2fodResponseOdfParameters],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dwi2fod": dwi2fod_cargs,
+        "fslgrad": dwi2fod_fslgrad_cargs,
+        "VariousString": dwi2fod_various_string_cargs,
+        "VariousFile": dwi2fod_various_file_cargs,
+        "config": dwi2fod_config_cargs,
+        "response_odf": dwi2fod_response_odf_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 {
+        "dwi2fod": dwi2fod_outputs,
+        "response_odf": dwi2fod_response_odf_outputs,
+    }.get(t)
+
+
+def dwi2fod_fslgrad_params(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> Dwi2fodFslgradParameters:
+    """
+    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 dwi2fod_fslgrad_cargs(
+    params: Dwi2fodFslgradParameters,
+    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
+
+
+def dwi2fod_various_string_params(
+    obj: str,
+) -> Dwi2fodVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def dwi2fod_various_string_cargs(
+    params: Dwi2fodVariousStringParameters,
+    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 dwi2fod_various_file_params(
+    obj: InputPathType,
+) -> Dwi2fodVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def dwi2fod_various_file_cargs(
+    params: Dwi2fodVariousFileParameters,
+    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 dwi2fod_config_params(
+    key: str,
+    value: str,
+) -> Dwi2fodConfigParameters:
+    """
+    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 dwi2fod_config_cargs(
+    params: Dwi2fodConfigParameters,
+    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 Dwi2fodResponseOdfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `list[Dwi2fodResponseOdfParameters](...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    odf: OutputPathType
+    """output ODF image"""
+
+
+def dwi2fod_response_odf_params(
+    response: InputPathType,
+    odf: str,
+) -> Dwi2fodResponseOdfParameters:
+    """
+    Build parameters.
+    
+    Args:
+        response: input tissue response.
+        odf: output ODF image.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "response_odf",
+        "response": response,
+        "odf": odf,
+    }
+    return params
+
+
+def dwi2fod_response_odf_cargs(
+    params: Dwi2fodResponseOdfParameters,
+    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")))
+    cargs.append(params.get("odf"))
+    return cargs
+
+
+def dwi2fod_response_odf_outputs(
+    params: Dwi2fodResponseOdfParameters,
+    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")),
+    )
+    return ret
+
+
+class Dwi2fodOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dwi2fod(...)`.
+    """
+    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[Dwi2fodResponseOdfParameters],
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2fodFslgradParameters | 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[Dwi2fodVariousStringParameters, Dwi2fodVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2fodConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Dwi2fodParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: Dwi2fodParameters,
+    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") 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("shells") is not None:
+        cargs.extend([
+            "-shells",
+            ",".join(map(str, params.get("shells")))
+        ])
+    if params.get("directions") is not None:
+        cargs.extend([
+            "-directions",
+            execution.input_file(params.get("directions"))
+        ])
+    if params.get("lmax") is not None:
+        cargs.extend([
+            "-lmax",
+            ",".join(map(str, params.get("lmax")))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("filter") is not None:
+        cargs.extend([
+            "-filter",
+            execution.input_file(params.get("filter"))
+        ])
+    if params.get("neg_lambda") is not None:
+        cargs.extend([
+            "-neg_lambda",
+            str(params.get("neg_lambda"))
+        ])
+    if params.get("norm_lambda") is not None:
+        cargs.extend([
+            "-norm_lambda",
+            str(params.get("norm_lambda"))
+        ])
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-threshold",
+            str(params.get("threshold"))
+        ])
+    if params.get("niter") is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("niter"))
+        ])
+    if params.get("norm_lambda_1") is not None:
+        cargs.extend([
+            "-norm_lambda",
+            str(params.get("norm_lambda_1"))
+        ])
+    if params.get("neg_lambda_1") is not None:
+        cargs.extend([
+            "-neg_lambda",
+            str(params.get("neg_lambda_1"))
+        ])
+    if params.get("predicted_signal") is not None:
+        cargs.extend([
+            "-predicted_signal",
+            params.get("predicted_signal")
+        ])
+    if params.get("strides") is not None:
+        cargs.extend([
+            "-strides",
+            *dyn_cargs(params.get("strides")["__STYXTYPE__"])(params.get("strides"), execution)
+        ])
+    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(params.get("algorithm"))
+    cargs.append(execution.input_file(params.get("dwi")))
+    cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("response_odf")] for a in c])
+    return cargs
+
+
+def dwi2fod_outputs(
+    params: Dwi2fodParameters,
+    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")) if (params.get("predicted_signal") is not None) else None,
+        response_odf=[dyn_outputs(i["__STYXTYPE__"])(i, execution) if dyn_outputs(i["__STYXTYPE__"]) else None for i in params.get("response_odf")],
+    )
+    return ret
+
+
+def dwi2fod_execute(
+    params: Dwi2fodParameters,
+    execution: Execution,
+) -> Dwi2fodOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Dwi2fodOutputs`).
+    """
+    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[Dwi2fodResponseOdfParameters],
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2fodFslgradParameters | 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[Dwi2fodVariousStringParameters, Dwi2fodVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2fodConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Dwi2fodOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DWI2FOD_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "DWI2FOD_METADATA",
+    "Dwi2fodConfigParameters",
+    "Dwi2fodFslgradParameters",
+    "Dwi2fodOutputs",
+    "Dwi2fodParameters",
+    "Dwi2fodResponseOdfOutputs",
+    "Dwi2fodResponseOdfParameters",
+    "Dwi2fodVariousFileParameters",
+    "Dwi2fodVariousStringParameters",
+    "dwi2fod",
+    "dwi2fod_config_params",
+    "dwi2fod_fslgrad_params",
+    "dwi2fod_params",
+    "dwi2fod_response_odf_params",
+    "dwi2fod_various_file_params",
+    "dwi2fod_various_string_params",
+]