niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tcksift2.py

@@ -0,0 +1,902 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKSIFT2_METADATA = Metadata(
+    id="14aaf15fab77274145a9c252945d1e6493faa9d5.boutiques",
+    name="tcksift2",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Tcksift2ConfigParamsDictNoTag = typing.TypedDict('_Tcksift2ConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Tcksift2ConfigParamsDictTagged = typing.TypedDict('Tcksift2ConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Tcksift2ConfigParamsDict = _Tcksift2ConfigParamsDictNoTag | Tcksift2ConfigParamsDictTagged
+
+
+_Tcksift2ParamsDictNoTag = typing.TypedDict('_Tcksift2ParamsDictNoTag', {
+    "proc_mask": typing.NotRequired[InputPathType | None],
+    "act": typing.NotRequired[InputPathType | None],
+    "fd_scale_gm": bool,
+    "no_dilate_lut": bool,
+    "make_null_lobes": bool,
+    "remove_untracked": bool,
+    "fd_thresh": typing.NotRequired[float | None],
+    "csv": typing.NotRequired[str | None],
+    "out_mu": typing.NotRequired[str | None],
+    "output_debug": bool,
+    "out_coeffs": typing.NotRequired[str | None],
+    "reg_tikhonov": typing.NotRequired[float | None],
+    "reg_tv": typing.NotRequired[float | None],
+    "min_td_frac": typing.NotRequired[float | None],
+    "min_iters": typing.NotRequired[int | None],
+    "max_iters": typing.NotRequired[int | None],
+    "min_factor": typing.NotRequired[float | None],
+    "min_coeff": typing.NotRequired[float | None],
+    "max_factor": typing.NotRequired[float | None],
+    "max_coeff": typing.NotRequired[float | None],
+    "max_coeff_step": typing.NotRequired[float | None],
+    "min_cf_decrease": typing.NotRequired[float | None],
+    "linear": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Tcksift2ConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in_tracks": InputPathType,
+    "in_fod": InputPathType,
+    "out_weights": str,
+})
+Tcksift2ParamsDictTagged = typing.TypedDict('Tcksift2ParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/tcksift2"],
+    "proc_mask": typing.NotRequired[InputPathType | None],
+    "act": typing.NotRequired[InputPathType | None],
+    "fd_scale_gm": bool,
+    "no_dilate_lut": bool,
+    "make_null_lobes": bool,
+    "remove_untracked": bool,
+    "fd_thresh": typing.NotRequired[float | None],
+    "csv": typing.NotRequired[str | None],
+    "out_mu": typing.NotRequired[str | None],
+    "output_debug": bool,
+    "out_coeffs": typing.NotRequired[str | None],
+    "reg_tikhonov": typing.NotRequired[float | None],
+    "reg_tv": typing.NotRequired[float | None],
+    "min_td_frac": typing.NotRequired[float | None],
+    "min_iters": typing.NotRequired[int | None],
+    "max_iters": typing.NotRequired[int | None],
+    "min_factor": typing.NotRequired[float | None],
+    "min_coeff": typing.NotRequired[float | None],
+    "max_factor": typing.NotRequired[float | None],
+    "max_coeff": typing.NotRequired[float | None],
+    "max_coeff_step": typing.NotRequired[float | None],
+    "min_cf_decrease": typing.NotRequired[float | None],
+    "linear": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Tcksift2ConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in_tracks": InputPathType,
+    "in_fod": InputPathType,
+    "out_weights": str,
+})
+Tcksift2ParamsDict = _Tcksift2ParamsDictNoTag | Tcksift2ParamsDictTagged
+
+
+def tcksift2_config(
+    key: str,
+    value: str,
+) -> Tcksift2ConfigParamsDictTagged:
+    """
+    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 tcksift2_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Tcksift2ConfigParamsDict` 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 tcksift2_config_cargs(
+    params: Tcksift2ConfigParamsDict,
+    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 Tcksift2Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Tcksift2ParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_weights: OutputPathType
+    """output text file containing the weighting factor for each streamline"""
+    csv_: OutputPathType | None
+    """output statistics of execution per iteration to a .csv file """
+    out_mu: OutputPathType | None
+    """output the final value of SIFT proportionality coefficient mu to a text
+    file """
+    out_coeffs: OutputPathType | None
+    """output text file containing the weighting coefficient for each streamline
+    """
+
+
+def tcksift2_params(
+    in_tracks: InputPathType,
+    in_fod: InputPathType,
+    out_weights: str,
+    proc_mask: InputPathType | None = None,
+    act: InputPathType | None = None,
+    fd_scale_gm: bool = False,
+    no_dilate_lut: bool = False,
+    make_null_lobes: bool = False,
+    remove_untracked: bool = False,
+    fd_thresh: float | None = None,
+    csv_: str | None = None,
+    out_mu: str | None = None,
+    output_debug: bool = False,
+    out_coeffs: str | None = None,
+    reg_tikhonov: float | None = None,
+    reg_tv: float | None = None,
+    min_td_frac: float | None = None,
+    min_iters: int | None = None,
+    max_iters: int | None = None,
+    min_factor: float | None = None,
+    min_coeff: float | None = None,
+    max_factor: float | None = None,
+    max_coeff: float | None = None,
+    max_coeff_step: float | None = None,
+    min_cf_decrease: float | None = None,
+    linear: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Tcksift2ConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Tcksift2ParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        in_tracks: the input track file.
+        in_fod: input image containing the spherical harmonics of the fibre\
+            orientation distributions.
+        out_weights: output text file containing the weighting factor for each\
+            streamline.
+        proc_mask: provide an image containing the processing mask weights for\
+            the model; image spatial dimensions must match the fixel image.
+        act: use an ACT five-tissue-type segmented anatomical image to derive\
+            the processing mask.
+        fd_scale_gm: provide this option (in conjunction with -act) to\
+            heuristically downsize the fibre density estimates based on the\
+            presence of GM in the voxel. This can assist in reducing tissue\
+            interface effects when using a single-tissue deconvolution algorithm.
+        no_dilate_lut: do NOT dilate FOD lobe lookup tables; only map\
+            streamlines to FOD lobes if the precise tangent lies within the angular\
+            spread of that lobe.
+        make_null_lobes: add an additional FOD lobe to each voxel, with zero\
+            integral, that covers all directions with zero / negative FOD\
+            amplitudes.
+        remove_untracked: remove FOD lobes that do not have any streamline\
+            density attributed to them; this improves filtering slightly, at the\
+            expense of longer computation time (and you can no longer do\
+            quantitative comparisons between reconstructions if this is enabled).
+        fd_thresh: fibre density threshold; exclude an FOD lobe from filtering\
+            processing if its integral is less than this amount (streamlines will\
+            still be mapped to it, but it will not contribute to the cost function\
+            or the filtering).
+        csv_: output statistics of execution per iteration to a .csv file.
+        out_mu: output the final value of SIFT proportionality coefficient mu\
+            to a text file.
+        output_debug: provide various output images for assessing & debugging\
+            performance etc.
+        out_coeffs: output text file containing the weighting coefficient for\
+            each streamline.
+        reg_tikhonov: provide coefficient for regularising streamline weighting\
+            coefficients (Tikhonov regularisation) (default: 0).
+        reg_tv: provide coefficient for regularising variance of streamline\
+            weighting coefficient to fixels along its length (Total Variation\
+            regularisation) (default: 0.1).
+        min_td_frac: minimum fraction of the FOD integral reconstructed by\
+            streamlines; if the reconstructed streamline density is below this\
+            fraction, the fixel is excluded from optimisation (default: 0.1).
+        min_iters: minimum number of iterations to run before testing for\
+            convergence; this can prevent premature termination at early iterations\
+            if the cost function increases slightly (default: 10).
+        max_iters: maximum number of iterations to run before terminating\
+            program.
+        min_factor: minimum weighting factor for an individual streamline; if\
+            the factor falls below this number the streamline will be rejected\
+            entirely (factor set to zero) (default: 0).
+        min_coeff: minimum weighting coefficient for an individual streamline;\
+            similar to the '-min_factor' option, but using the exponential\
+            coefficient basis of the SIFT2 model; these parameters are related as:\
+            factor = e^(coeff). Note that the -min_factor and -min_coeff options\
+            are mutually exclusive - you can only provide one. (default: -inf).
+        max_factor: maximum weighting factor that can be assigned to any one\
+            streamline (default: inf).
+        max_coeff: maximum weighting coefficient for an individual streamline;\
+            similar to the '-max_factor' option, but using the exponential\
+            coefficient basis of the SIFT2 model; these parameters are related as:\
+            factor = e^(coeff). Note that the -max_factor and -max_coeff options\
+            are mutually exclusive - you can only provide one. (default: inf).
+        max_coeff_step: maximum change to a streamline's weighting coefficient\
+            in a single iteration (default: 1).
+        min_cf_decrease: minimum decrease in the cost function (as a fraction\
+            of the initial value) that must occur each iteration for the algorithm\
+            to continue (default: 2.5e-05).
+        linear: perform a linear estimation of streamline weights, rather than\
+            the standard non-linear optimisation (typically does not provide as\
+            accurate a model fit; but only requires a single pass).
+        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/tcksift2",
+        "fd_scale_gm": fd_scale_gm,
+        "no_dilate_lut": no_dilate_lut,
+        "make_null_lobes": make_null_lobes,
+        "remove_untracked": remove_untracked,
+        "output_debug": output_debug,
+        "linear": linear,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in_tracks": in_tracks,
+        "in_fod": in_fod,
+        "out_weights": out_weights,
+    }
+    if proc_mask is not None:
+        params["proc_mask"] = proc_mask
+    if act is not None:
+        params["act"] = act
+    if fd_thresh is not None:
+        params["fd_thresh"] = fd_thresh
+    if csv_ is not None:
+        params["csv"] = csv_
+    if out_mu is not None:
+        params["out_mu"] = out_mu
+    if out_coeffs is not None:
+        params["out_coeffs"] = out_coeffs
+    if reg_tikhonov is not None:
+        params["reg_tikhonov"] = reg_tikhonov
+    if reg_tv is not None:
+        params["reg_tv"] = reg_tv
+    if min_td_frac is not None:
+        params["min_td_frac"] = min_td_frac
+    if min_iters is not None:
+        params["min_iters"] = min_iters
+    if max_iters is not None:
+        params["max_iters"] = max_iters
+    if min_factor is not None:
+        params["min_factor"] = min_factor
+    if min_coeff is not None:
+        params["min_coeff"] = min_coeff
+    if max_factor is not None:
+        params["max_factor"] = max_factor
+    if max_coeff is not None:
+        params["max_coeff"] = max_coeff
+    if max_coeff_step is not None:
+        params["max_coeff_step"] = max_coeff_step
+    if min_cf_decrease is not None:
+        params["min_cf_decrease"] = min_cf_decrease
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tcksift2_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Tcksift2ParamsDict` 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("proc_mask", None) is not None:
+        if not isinstance(params["proc_mask"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`proc_mask` has the wrong type: Received `{type(params.get("proc_mask", None))}` expected `InputPathType | None`')
+    if params.get("act", None) is not None:
+        if not isinstance(params["act"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`act` has the wrong type: Received `{type(params.get("act", None))}` expected `InputPathType | None`')
+    if params.get("fd_scale_gm", False) is None:
+        raise StyxValidationError("`fd_scale_gm` must not be None")
+    if not isinstance(params["fd_scale_gm"], bool):
+        raise StyxValidationError(f'`fd_scale_gm` has the wrong type: Received `{type(params.get("fd_scale_gm", False))}` expected `bool`')
+    if params.get("no_dilate_lut", False) is None:
+        raise StyxValidationError("`no_dilate_lut` must not be None")
+    if not isinstance(params["no_dilate_lut"], bool):
+        raise StyxValidationError(f'`no_dilate_lut` has the wrong type: Received `{type(params.get("no_dilate_lut", False))}` expected `bool`')
+    if params.get("make_null_lobes", False) is None:
+        raise StyxValidationError("`make_null_lobes` must not be None")
+    if not isinstance(params["make_null_lobes"], bool):
+        raise StyxValidationError(f'`make_null_lobes` has the wrong type: Received `{type(params.get("make_null_lobes", False))}` expected `bool`')
+    if params.get("remove_untracked", False) is None:
+        raise StyxValidationError("`remove_untracked` must not be None")
+    if not isinstance(params["remove_untracked"], bool):
+        raise StyxValidationError(f'`remove_untracked` has the wrong type: Received `{type(params.get("remove_untracked", False))}` expected `bool`')
+    if params.get("fd_thresh", None) is not None:
+        if not isinstance(params["fd_thresh"], (float, int)):
+            raise StyxValidationError(f'`fd_thresh` has the wrong type: Received `{type(params.get("fd_thresh", None))}` expected `float | None`')
+    if params.get("csv", None) is not None:
+        if not isinstance(params["csv"], str):
+            raise StyxValidationError(f'`csv` has the wrong type: Received `{type(params.get("csv", None))}` expected `str | None`')
+    if params.get("out_mu", None) is not None:
+        if not isinstance(params["out_mu"], str):
+            raise StyxValidationError(f'`out_mu` has the wrong type: Received `{type(params.get("out_mu", None))}` expected `str | None`')
+    if params.get("output_debug", False) is None:
+        raise StyxValidationError("`output_debug` must not be None")
+    if not isinstance(params["output_debug"], bool):
+        raise StyxValidationError(f'`output_debug` has the wrong type: Received `{type(params.get("output_debug", False))}` expected `bool`')
+    if params.get("out_coeffs", None) is not None:
+        if not isinstance(params["out_coeffs"], str):
+            raise StyxValidationError(f'`out_coeffs` has the wrong type: Received `{type(params.get("out_coeffs", None))}` expected `str | None`')
+    if params.get("reg_tikhonov", None) is not None:
+        if not isinstance(params["reg_tikhonov"], (float, int)):
+            raise StyxValidationError(f'`reg_tikhonov` has the wrong type: Received `{type(params.get("reg_tikhonov", None))}` expected `float | None`')
+    if params.get("reg_tv", None) is not None:
+        if not isinstance(params["reg_tv"], (float, int)):
+            raise StyxValidationError(f'`reg_tv` has the wrong type: Received `{type(params.get("reg_tv", None))}` expected `float | None`')
+    if params.get("min_td_frac", None) is not None:
+        if not isinstance(params["min_td_frac"], (float, int)):
+            raise StyxValidationError(f'`min_td_frac` has the wrong type: Received `{type(params.get("min_td_frac", None))}` expected `float | None`')
+    if params.get("min_iters", None) is not None:
+        if not isinstance(params["min_iters"], int):
+            raise StyxValidationError(f'`min_iters` has the wrong type: Received `{type(params.get("min_iters", None))}` expected `int | None`')
+    if params.get("max_iters", None) is not None:
+        if not isinstance(params["max_iters"], int):
+            raise StyxValidationError(f'`max_iters` has the wrong type: Received `{type(params.get("max_iters", None))}` expected `int | None`')
+    if params.get("min_factor", None) is not None:
+        if not isinstance(params["min_factor"], (float, int)):
+            raise StyxValidationError(f'`min_factor` has the wrong type: Received `{type(params.get("min_factor", None))}` expected `float | None`')
+    if params.get("min_coeff", None) is not None:
+        if not isinstance(params["min_coeff"], (float, int)):
+            raise StyxValidationError(f'`min_coeff` has the wrong type: Received `{type(params.get("min_coeff", None))}` expected `float | None`')
+    if params.get("max_factor", None) is not None:
+        if not isinstance(params["max_factor"], (float, int)):
+            raise StyxValidationError(f'`max_factor` has the wrong type: Received `{type(params.get("max_factor", None))}` expected `float | None`')
+    if params.get("max_coeff", None) is not None:
+        if not isinstance(params["max_coeff"], (float, int)):
+            raise StyxValidationError(f'`max_coeff` has the wrong type: Received `{type(params.get("max_coeff", None))}` expected `float | None`')
+    if params.get("max_coeff_step", None) is not None:
+        if not isinstance(params["max_coeff_step"], (float, int)):
+            raise StyxValidationError(f'`max_coeff_step` has the wrong type: Received `{type(params.get("max_coeff_step", None))}` expected `float | None`')
+    if params.get("min_cf_decrease", None) is not None:
+        if not isinstance(params["min_cf_decrease"], (float, int)):
+            raise StyxValidationError(f'`min_cf_decrease` has the wrong type: Received `{type(params.get("min_cf_decrease", None))}` expected `float | None`')
+    if params.get("linear", False) is None:
+        raise StyxValidationError("`linear` must not be None")
+    if not isinstance(params["linear"], bool):
+        raise StyxValidationError(f'`linear` has the wrong type: Received `{type(params.get("linear", False))}` expected `bool`')
+    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[Tcksift2ConfigParamsDict] | None`')
+        for e in params["config"]:
+            tcksift2_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("in_tracks", None) is None:
+        raise StyxValidationError("`in_tracks` must not be None")
+    if not isinstance(params["in_tracks"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`in_tracks` has the wrong type: Received `{type(params.get("in_tracks", None))}` expected `InputPathType`')
+    if params.get("in_fod", None) is None:
+        raise StyxValidationError("`in_fod` must not be None")
+    if not isinstance(params["in_fod"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`in_fod` has the wrong type: Received `{type(params.get("in_fod", None))}` expected `InputPathType`')
+    if params.get("out_weights", None) is None:
+        raise StyxValidationError("`out_weights` must not be None")
+    if not isinstance(params["out_weights"], str):
+        raise StyxValidationError(f'`out_weights` has the wrong type: Received `{type(params.get("out_weights", None))}` expected `str`')
+
+
+def tcksift2_cargs(
+    params: Tcksift2ParamsDict,
+    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("tcksift2")
+    if params.get("proc_mask", None) is not None:
+        cargs.extend([
+            "-proc_mask",
+            execution.input_file(params.get("proc_mask", None))
+        ])
+    if params.get("act", None) is not None:
+        cargs.extend([
+            "-act",
+            execution.input_file(params.get("act", None))
+        ])
+    if params.get("fd_scale_gm", False):
+        cargs.append("-fd_scale_gm")
+    if params.get("no_dilate_lut", False):
+        cargs.append("-no_dilate_lut")
+    if params.get("make_null_lobes", False):
+        cargs.append("-make_null_lobes")
+    if params.get("remove_untracked", False):
+        cargs.append("-remove_untracked")
+    if params.get("fd_thresh", None) is not None:
+        cargs.extend([
+            "-fd_thresh",
+            str(params.get("fd_thresh", None))
+        ])
+    if params.get("csv", None) is not None:
+        cargs.extend([
+            "-csv",
+            params.get("csv", None)
+        ])
+    if params.get("out_mu", None) is not None:
+        cargs.extend([
+            "-out_mu",
+            params.get("out_mu", None)
+        ])
+    if params.get("output_debug", False):
+        cargs.append("-output_debug")
+    if params.get("out_coeffs", None) is not None:
+        cargs.extend([
+            "-out_coeffs",
+            params.get("out_coeffs", None)
+        ])
+    if params.get("reg_tikhonov", None) is not None:
+        cargs.extend([
+            "-reg_tikhonov",
+            str(params.get("reg_tikhonov", None))
+        ])
+    if params.get("reg_tv", None) is not None:
+        cargs.extend([
+            "-reg_tv",
+            str(params.get("reg_tv", None))
+        ])
+    if params.get("min_td_frac", None) is not None:
+        cargs.extend([
+            "-min_td_frac",
+            str(params.get("min_td_frac", None))
+        ])
+    if params.get("min_iters", None) is not None:
+        cargs.extend([
+            "-min_iters",
+            str(params.get("min_iters", None))
+        ])
+    if params.get("max_iters", None) is not None:
+        cargs.extend([
+            "-max_iters",
+            str(params.get("max_iters", None))
+        ])
+    if params.get("min_factor", None) is not None:
+        cargs.extend([
+            "-min_factor",
+            str(params.get("min_factor", None))
+        ])
+    if params.get("min_coeff", None) is not None:
+        cargs.extend([
+            "-min_coeff",
+            str(params.get("min_coeff", None))
+        ])
+    if params.get("max_factor", None) is not None:
+        cargs.extend([
+            "-max_factor",
+            str(params.get("max_factor", None))
+        ])
+    if params.get("max_coeff", None) is not None:
+        cargs.extend([
+            "-max_coeff",
+            str(params.get("max_coeff", None))
+        ])
+    if params.get("max_coeff_step", None) is not None:
+        cargs.extend([
+            "-max_coeff_step",
+            str(params.get("max_coeff_step", None))
+        ])
+    if params.get("min_cf_decrease", None) is not None:
+        cargs.extend([
+            "-min_cf_decrease",
+            str(params.get("min_cf_decrease", None))
+        ])
+    if params.get("linear", False):
+        cargs.append("-linear")
+    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 [tcksift2_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("in_tracks", None)))
+    cargs.append(execution.input_file(params.get("in_fod", None)))
+    cargs.append(params.get("out_weights", None))
+    return cargs
+
+
+def tcksift2_outputs(
+    params: Tcksift2ParamsDict,
+    execution: Execution,
+) -> Tcksift2Outputs:
+    """
+    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 = Tcksift2Outputs(
+        root=execution.output_file("."),
+        out_weights=execution.output_file(params.get("out_weights", None)),
+        csv_=execution.output_file(params.get("csv", None)) if (params.get("csv") is not None) else None,
+        out_mu=execution.output_file(params.get("out_mu", None)) if (params.get("out_mu") is not None) else None,
+        out_coeffs=execution.output_file(params.get("out_coeffs", None)) if (params.get("out_coeffs") is not None) else None,
+    )
+    return ret
+
+
+def tcksift2_execute(
+    params: Tcksift2ParamsDict,
+    runner: Runner | None = None,
+) -> Tcksift2Outputs:
+    """
+    tcksift2
+    
+    Optimise per-streamline cross-section multipliers to match a whole-brain
+    tractogram to fixel-wise fibre densities.
+    
+    
+    
+    References:
+    
+    Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT2: Enabling
+    dense quantitative assessment of brain white matter connectivity using
+    streamlines tractography. NeuroImage, 2015, 119, 338-351
+    
+    * If using the -linear option:
+    Smith, RE; Raffelt, D; Tournier, J-D; Connelly, A. Quantitative Streamlines
+    Tractography: Methods and Inter-Subject Normalisation. Open Science
+    Framework, https://doi.org/10.31219/osf.io/c67kn.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Tcksift2Outputs`).
+    """
+    tcksift2_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKSIFT2_METADATA)
+    params = execution.params(params)
+    cargs = tcksift2_cargs(params, execution)
+    ret = tcksift2_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tcksift2(
+    in_tracks: InputPathType,
+    in_fod: InputPathType,
+    out_weights: str,
+    proc_mask: InputPathType | None = None,
+    act: InputPathType | None = None,
+    fd_scale_gm: bool = False,
+    no_dilate_lut: bool = False,
+    make_null_lobes: bool = False,
+    remove_untracked: bool = False,
+    fd_thresh: float | None = None,
+    csv_: str | None = None,
+    out_mu: str | None = None,
+    output_debug: bool = False,
+    out_coeffs: str | None = None,
+    reg_tikhonov: float | None = None,
+    reg_tv: float | None = None,
+    min_td_frac: float | None = None,
+    min_iters: int | None = None,
+    max_iters: int | None = None,
+    min_factor: float | None = None,
+    min_coeff: float | None = None,
+    max_factor: float | None = None,
+    max_coeff: float | None = None,
+    max_coeff_step: float | None = None,
+    min_cf_decrease: float | None = None,
+    linear: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Tcksift2ConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Tcksift2Outputs:
+    """
+    tcksift2
+    
+    Optimise per-streamline cross-section multipliers to match a whole-brain
+    tractogram to fixel-wise fibre densities.
+    
+    
+    
+    References:
+    
+    Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT2: Enabling
+    dense quantitative assessment of brain white matter connectivity using
+    streamlines tractography. NeuroImage, 2015, 119, 338-351
+    
+    * If using the -linear option:
+    Smith, RE; Raffelt, D; Tournier, J-D; Connelly, A. Quantitative Streamlines
+    Tractography: Methods and Inter-Subject Normalisation. Open Science
+    Framework, https://doi.org/10.31219/osf.io/c67kn.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_tracks: the input track file.
+        in_fod: input image containing the spherical harmonics of the fibre\
+            orientation distributions.
+        out_weights: output text file containing the weighting factor for each\
+            streamline.
+        proc_mask: provide an image containing the processing mask weights for\
+            the model; image spatial dimensions must match the fixel image.
+        act: use an ACT five-tissue-type segmented anatomical image to derive\
+            the processing mask.
+        fd_scale_gm: provide this option (in conjunction with -act) to\
+            heuristically downsize the fibre density estimates based on the\
+            presence of GM in the voxel. This can assist in reducing tissue\
+            interface effects when using a single-tissue deconvolution algorithm.
+        no_dilate_lut: do NOT dilate FOD lobe lookup tables; only map\
+            streamlines to FOD lobes if the precise tangent lies within the angular\
+            spread of that lobe.
+        make_null_lobes: add an additional FOD lobe to each voxel, with zero\
+            integral, that covers all directions with zero / negative FOD\
+            amplitudes.
+        remove_untracked: remove FOD lobes that do not have any streamline\
+            density attributed to them; this improves filtering slightly, at the\
+            expense of longer computation time (and you can no longer do\
+            quantitative comparisons between reconstructions if this is enabled).
+        fd_thresh: fibre density threshold; exclude an FOD lobe from filtering\
+            processing if its integral is less than this amount (streamlines will\
+            still be mapped to it, but it will not contribute to the cost function\
+            or the filtering).
+        csv_: output statistics of execution per iteration to a .csv file.
+        out_mu: output the final value of SIFT proportionality coefficient mu\
+            to a text file.
+        output_debug: provide various output images for assessing & debugging\
+            performance etc.
+        out_coeffs: output text file containing the weighting coefficient for\
+            each streamline.
+        reg_tikhonov: provide coefficient for regularising streamline weighting\
+            coefficients (Tikhonov regularisation) (default: 0).
+        reg_tv: provide coefficient for regularising variance of streamline\
+            weighting coefficient to fixels along its length (Total Variation\
+            regularisation) (default: 0.1).
+        min_td_frac: minimum fraction of the FOD integral reconstructed by\
+            streamlines; if the reconstructed streamline density is below this\
+            fraction, the fixel is excluded from optimisation (default: 0.1).
+        min_iters: minimum number of iterations to run before testing for\
+            convergence; this can prevent premature termination at early iterations\
+            if the cost function increases slightly (default: 10).
+        max_iters: maximum number of iterations to run before terminating\
+            program.
+        min_factor: minimum weighting factor for an individual streamline; if\
+            the factor falls below this number the streamline will be rejected\
+            entirely (factor set to zero) (default: 0).
+        min_coeff: minimum weighting coefficient for an individual streamline;\
+            similar to the '-min_factor' option, but using the exponential\
+            coefficient basis of the SIFT2 model; these parameters are related as:\
+            factor = e^(coeff). Note that the -min_factor and -min_coeff options\
+            are mutually exclusive - you can only provide one. (default: -inf).
+        max_factor: maximum weighting factor that can be assigned to any one\
+            streamline (default: inf).
+        max_coeff: maximum weighting coefficient for an individual streamline;\
+            similar to the '-max_factor' option, but using the exponential\
+            coefficient basis of the SIFT2 model; these parameters are related as:\
+            factor = e^(coeff). Note that the -max_factor and -max_coeff options\
+            are mutually exclusive - you can only provide one. (default: inf).
+        max_coeff_step: maximum change to a streamline's weighting coefficient\
+            in a single iteration (default: 1).
+        min_cf_decrease: minimum decrease in the cost function (as a fraction\
+            of the initial value) that must occur each iteration for the algorithm\
+            to continue (default: 2.5e-05).
+        linear: perform a linear estimation of streamline weights, rather than\
+            the standard non-linear optimisation (typically does not provide as\
+            accurate a model fit; but only requires a single pass).
+        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 `Tcksift2Outputs`).
+    """
+    params = tcksift2_params(
+        proc_mask=proc_mask,
+        act=act,
+        fd_scale_gm=fd_scale_gm,
+        no_dilate_lut=no_dilate_lut,
+        make_null_lobes=make_null_lobes,
+        remove_untracked=remove_untracked,
+        fd_thresh=fd_thresh,
+        csv_=csv_,
+        out_mu=out_mu,
+        output_debug=output_debug,
+        out_coeffs=out_coeffs,
+        reg_tikhonov=reg_tikhonov,
+        reg_tv=reg_tv,
+        min_td_frac=min_td_frac,
+        min_iters=min_iters,
+        max_iters=max_iters,
+        min_factor=min_factor,
+        min_coeff=min_coeff,
+        max_factor=max_factor,
+        max_coeff=max_coeff,
+        max_coeff_step=max_coeff_step,
+        min_cf_decrease=min_cf_decrease,
+        linear=linear,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_tracks=in_tracks,
+        in_fod=in_fod,
+        out_weights=out_weights,
+    )
+    return tcksift2_execute(params, runner)
+
+
+__all__ = [
+    "TCKSIFT2_METADATA",
+    "Tcksift2ConfigParamsDict",
+    "Tcksift2ConfigParamsDictTagged",
+    "Tcksift2Outputs",
+    "Tcksift2ParamsDict",
+    "Tcksift2ParamsDictTagged",
+    "tcksift2",
+    "tcksift2_config",
+    "tcksift2_execute",
+    "tcksift2_params",
+]