niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dwi2tensor.py

@@ -0,0 +1,715 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DWI2TENSOR_METADATA = Metadata(
+    id="700cecd2ddde8992557eb31468df42097fa6e2b1.boutiques",
+    name="dwi2tensor",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Dwi2tensorFslgradParamsDictNoTag = typing.TypedDict('_Dwi2tensorFslgradParamsDictNoTag', {
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Dwi2tensorFslgradParamsDictTagged = typing.TypedDict('Dwi2tensorFslgradParamsDictTagged', {
+    "@type": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Dwi2tensorFslgradParamsDict = _Dwi2tensorFslgradParamsDictNoTag | Dwi2tensorFslgradParamsDictTagged
+
+
+_Dwi2tensorConfigParamsDictNoTag = typing.TypedDict('_Dwi2tensorConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Dwi2tensorConfigParamsDictTagged = typing.TypedDict('Dwi2tensorConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Dwi2tensorConfigParamsDict = _Dwi2tensorConfigParamsDictNoTag | Dwi2tensorConfigParamsDictTagged
+
+
+_Dwi2tensorParamsDictNoTag = typing.TypedDict('_Dwi2tensorParamsDictNoTag', {
+    "ols": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "b0": typing.NotRequired[str | None],
+    "dkt": typing.NotRequired[str | None],
+    "iter": typing.NotRequired[int | None],
+    "predicted_signal": typing.NotRequired[str | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Dwi2tensorFslgradParamsDict | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Dwi2tensorConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "dwi": InputPathType,
+    "dt": str,
+})
+Dwi2tensorParamsDictTagged = typing.TypedDict('Dwi2tensorParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/dwi2tensor"],
+    "ols": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "b0": typing.NotRequired[str | None],
+    "dkt": typing.NotRequired[str | None],
+    "iter": typing.NotRequired[int | None],
+    "predicted_signal": typing.NotRequired[str | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Dwi2tensorFslgradParamsDict | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Dwi2tensorConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "dwi": InputPathType,
+    "dt": str,
+})
+Dwi2tensorParamsDict = _Dwi2tensorParamsDictNoTag | Dwi2tensorParamsDictTagged
+
+
+def dwi2tensor_fslgrad(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> Dwi2tensorFslgradParamsDictTagged:
+    """
+    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 dwi2tensor_fslgrad_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2tensorFslgradParamsDict` 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 dwi2tensor_fslgrad_cargs(
+    params: Dwi2tensorFslgradParamsDict,
+    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 dwi2tensor_config(
+    key: str,
+    value: str,
+) -> Dwi2tensorConfigParamsDictTagged:
+    """
+    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 dwi2tensor_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2tensorConfigParamsDict` 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 dwi2tensor_config_cargs(
+    params: Dwi2tensorConfigParamsDict,
+    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 Dwi2tensorOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Dwi2tensorParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    dt: OutputPathType
+    """the output dt image."""
+    b0: OutputPathType | None
+    """the output b0 image. """
+    dkt: OutputPathType | None
+    """the output dkt image. """
+    predicted_signal: OutputPathType | None
+    """the predicted dwi image. """
+
+
+def dwi2tensor_params(
+    dwi: InputPathType,
+    dt: str,
+    ols: bool = False,
+    mask: InputPathType | None = None,
+    b0: str | None = None,
+    dkt: str | None = None,
+    iter_: int | None = None,
+    predicted_signal: str | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2tensorFslgradParamsDict | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2tensorConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Dwi2tensorParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        dwi: the input dwi image.
+        dt: the output dt image.
+        ols: perform initial fit using an ordinary least-squares (OLS) fit (see\
+            Description).
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        b0: the output b0 image.
+        dkt: the output dkt image.
+        iter_: number of iterative reweightings for IWLS algorithm (default: 2)\
+            (see Description).
+        predicted_signal: the predicted dwi image.
+        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.
+        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/dwi2tensor",
+        "ols": ols,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "dwi": dwi,
+        "dt": dt,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if b0 is not None:
+        params["b0"] = b0
+    if dkt is not None:
+        params["dkt"] = dkt
+    if iter_ is not None:
+        params["iter"] = iter_
+    if predicted_signal is not None:
+        params["predicted_signal"] = predicted_signal
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dwi2tensor_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Dwi2tensorParamsDict` 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("ols", False) is None:
+        raise StyxValidationError("`ols` must not be None")
+    if not isinstance(params["ols"], bool):
+        raise StyxValidationError(f'`ols` has the wrong type: Received `{type(params.get("ols", False))}` expected `bool`')
+    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("b0", None) is not None:
+        if not isinstance(params["b0"], str):
+            raise StyxValidationError(f'`b0` has the wrong type: Received `{type(params.get("b0", None))}` expected `str | None`')
+    if params.get("dkt", None) is not None:
+        if not isinstance(params["dkt"], str):
+            raise StyxValidationError(f'`dkt` has the wrong type: Received `{type(params.get("dkt", None))}` expected `str | None`')
+    if params.get("iter", None) is not None:
+        if not isinstance(params["iter"], int):
+            raise StyxValidationError(f'`iter` has the wrong type: Received `{type(params.get("iter", None))}` expected `int | 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("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:
+        dwi2tensor_fslgrad_validate(params["fslgrad"])
+    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[Dwi2tensorConfigParamsDict] | None`')
+        for e in params["config"]:
+            dwi2tensor_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("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("dt", None) is None:
+        raise StyxValidationError("`dt` must not be None")
+    if not isinstance(params["dt"], str):
+        raise StyxValidationError(f'`dt` has the wrong type: Received `{type(params.get("dt", None))}` expected `str`')
+
+
+def dwi2tensor_cargs(
+    params: Dwi2tensorParamsDict,
+    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("dwi2tensor")
+    if params.get("ols", False):
+        cargs.append("-ols")
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", None))
+        ])
+    if params.get("b0", None) is not None:
+        cargs.extend([
+            "-b0",
+            params.get("b0", None)
+        ])
+    if params.get("dkt", None) is not None:
+        cargs.extend([
+            "-dkt",
+            params.get("dkt", None)
+        ])
+    if params.get("iter", None) is not None:
+        cargs.extend([
+            "-iter",
+            str(params.get("iter", None))
+        ])
+    if params.get("predicted_signal", None) is not None:
+        cargs.extend([
+            "-predicted_signal",
+            params.get("predicted_signal", None)
+        ])
+    if params.get("grad", None) is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad", None))
+        ])
+    if params.get("fslgrad", None) is not None:
+        cargs.extend(dwi2tensor_fslgrad_cargs(params.get("fslgrad", 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 [dwi2tensor_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("dwi", None)))
+    cargs.append(params.get("dt", None))
+    return cargs
+
+
+def dwi2tensor_outputs(
+    params: Dwi2tensorParamsDict,
+    execution: Execution,
+) -> Dwi2tensorOutputs:
+    """
+    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 = Dwi2tensorOutputs(
+        root=execution.output_file("."),
+        dt=execution.output_file(params.get("dt", None)),
+        b0=execution.output_file(params.get("b0", None)) if (params.get("b0") is not None) else None,
+        dkt=execution.output_file(params.get("dkt", None)) if (params.get("dkt") is not None) else None,
+        predicted_signal=execution.output_file(params.get("predicted_signal", None)) if (params.get("predicted_signal") is not None) else None,
+    )
+    return ret
+
+
+def dwi2tensor_execute(
+    params: Dwi2tensorParamsDict,
+    runner: Runner | None = None,
+) -> Dwi2tensorOutputs:
+    """
+    dwi2tensor
+    
+    Diffusion (kurtosis) tensor estimation.
+    
+    By default, the diffusion tensor (and optionally its kurtosis) is fitted to
+    the log-signal in two steps: firstly, using weighted least-squares (WLS)
+    with weights based on the empirical signal intensities; secondly, by further
+    iterated weighted least-squares (IWLS) with weights determined by the signal
+    predictions from the previous iteration (by default, 2 iterations will be
+    performed). This behaviour can be altered in two ways:
+    
+    * The -ols option will cause the first fitting step to be performed using
+    ordinary least-squares (OLS); that is, all measurements contribute equally
+    to the fit, instead of the default behaviour of weighting based on the
+    empirical signal intensities.
+    
+    * The -iter option controls the number of iterations of the IWLS prodedure.
+    If this is set to zero, then the output model parameters will be those
+    resulting from the first fitting step only: either WLS by default, or OLS if
+    the -ols option is used in conjunction with -iter 0.
+    
+    The tensor coefficients are stored in the output image as follows:
+    volumes 0-5: D11, D22, D33, D12, D13, D23
+    
+    If diffusion kurtosis is estimated using the -dkt option, these are stored
+    as follows:
+    volumes 0-2: W1111, W2222, W3333
+    volumes 3-8: W1112, W1113, W1222, W1333, W2223, W2333
+    volumes 9-11: W1122, W1133, W2233
+    volumes 12-14: W1123, W1223, W1233
+    
+    References:
+    
+    References based on fitting algorithm used:
+    
+    * OLS, WLS:
+    Basser, P.J.; Mattiello, J.; LeBihan, D. Estimation of the effective
+    self-diffusion tensor from the NMR spin echo. J Magn Reson B., 1994, 103,
+    247–254.
+    
+    * IWLS:
+    Veraart, J.; Sijbers, J.; Sunaert, S.; Leemans, A. & Jeurissen, B. Weighted
+    linear least squares estimation of diffusion MRI parameters: strengths,
+    limitations, and pitfalls. NeuroImage, 2013, 81, 335-346.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Dwi2tensorOutputs`).
+    """
+    dwi2tensor_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DWI2TENSOR_METADATA)
+    params = execution.params(params)
+    cargs = dwi2tensor_cargs(params, execution)
+    ret = dwi2tensor_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dwi2tensor(
+    dwi: InputPathType,
+    dt: str,
+    ols: bool = False,
+    mask: InputPathType | None = None,
+    b0: str | None = None,
+    dkt: str | None = None,
+    iter_: int | None = None,
+    predicted_signal: str | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Dwi2tensorFslgradParamsDict | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Dwi2tensorConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Dwi2tensorOutputs:
+    """
+    dwi2tensor
+    
+    Diffusion (kurtosis) tensor estimation.
+    
+    By default, the diffusion tensor (and optionally its kurtosis) is fitted to
+    the log-signal in two steps: firstly, using weighted least-squares (WLS)
+    with weights based on the empirical signal intensities; secondly, by further
+    iterated weighted least-squares (IWLS) with weights determined by the signal
+    predictions from the previous iteration (by default, 2 iterations will be
+    performed). This behaviour can be altered in two ways:
+    
+    * The -ols option will cause the first fitting step to be performed using
+    ordinary least-squares (OLS); that is, all measurements contribute equally
+    to the fit, instead of the default behaviour of weighting based on the
+    empirical signal intensities.
+    
+    * The -iter option controls the number of iterations of the IWLS prodedure.
+    If this is set to zero, then the output model parameters will be those
+    resulting from the first fitting step only: either WLS by default, or OLS if
+    the -ols option is used in conjunction with -iter 0.
+    
+    The tensor coefficients are stored in the output image as follows:
+    volumes 0-5: D11, D22, D33, D12, D13, D23
+    
+    If diffusion kurtosis is estimated using the -dkt option, these are stored
+    as follows:
+    volumes 0-2: W1111, W2222, W3333
+    volumes 3-8: W1112, W1113, W1222, W1333, W2223, W2333
+    volumes 9-11: W1122, W1133, W2233
+    volumes 12-14: W1123, W1223, W1233
+    
+    References:
+    
+    References based on fitting algorithm used:
+    
+    * OLS, WLS:
+    Basser, P.J.; Mattiello, J.; LeBihan, D. Estimation of the effective
+    self-diffusion tensor from the NMR spin echo. J Magn Reson B., 1994, 103,
+    247–254.
+    
+    * IWLS:
+    Veraart, J.; Sijbers, J.; Sunaert, S.; Leemans, A. & Jeurissen, B. Weighted
+    linear least squares estimation of diffusion MRI parameters: strengths,
+    limitations, and pitfalls. NeuroImage, 2013, 81, 335-346.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        dwi: the input dwi image.
+        dt: the output dt image.
+        ols: perform initial fit using an ordinary least-squares (OLS) fit (see\
+            Description).
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        b0: the output b0 image.
+        dkt: the output dkt image.
+        iter_: number of iterative reweightings for IWLS algorithm (default: 2)\
+            (see Description).
+        predicted_signal: the predicted dwi image.
+        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.
+        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 `Dwi2tensorOutputs`).
+    """
+    params = dwi2tensor_params(
+        ols=ols,
+        mask=mask,
+        b0=b0,
+        dkt=dkt,
+        iter_=iter_,
+        predicted_signal=predicted_signal,
+        grad=grad,
+        fslgrad=fslgrad,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        dwi=dwi,
+        dt=dt,
+    )
+    return dwi2tensor_execute(params, runner)
+
+
+__all__ = [
+    "DWI2TENSOR_METADATA",
+    "Dwi2tensorConfigParamsDict",
+    "Dwi2tensorConfigParamsDictTagged",
+    "Dwi2tensorFslgradParamsDict",
+    "Dwi2tensorFslgradParamsDictTagged",
+    "Dwi2tensorOutputs",
+    "Dwi2tensorParamsDict",
+    "Dwi2tensorParamsDictTagged",
+    "dwi2tensor",
+    "dwi2tensor_config",
+    "dwi2tensor_execute",
+    "dwi2tensor_fslgrad",
+    "dwi2tensor_params",
+]