niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tcksift.py

@@ -0,0 +1,739 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKSIFT_METADATA = Metadata(
+    id="7ab67267156023e9057e22433c919ff074901975.boutiques",
+    name="tcksift",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_TcksiftConfigParamsDictNoTag = typing.TypedDict('_TcksiftConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+TcksiftConfigParamsDictTagged = typing.TypedDict('TcksiftConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+TcksiftConfigParamsDict = _TcksiftConfigParamsDictNoTag | TcksiftConfigParamsDictTagged
+
+
+_TcksiftParamsDictNoTag = typing.TypedDict('_TcksiftParamsDictNoTag', {
+    "nofilter": bool,
+    "output_at_counts": typing.NotRequired[list[int] | None],
+    "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_selection": typing.NotRequired[str | None],
+    "term_number": typing.NotRequired[int | None],
+    "term_ratio": typing.NotRequired[float | None],
+    "term_mu": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TcksiftConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in_tracks": InputPathType,
+    "in_fod": InputPathType,
+    "out_tracks": str,
+})
+TcksiftParamsDictTagged = typing.TypedDict('TcksiftParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/tcksift"],
+    "nofilter": bool,
+    "output_at_counts": typing.NotRequired[list[int] | None],
+    "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_selection": typing.NotRequired[str | None],
+    "term_number": typing.NotRequired[int | None],
+    "term_ratio": typing.NotRequired[float | None],
+    "term_mu": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TcksiftConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in_tracks": InputPathType,
+    "in_fod": InputPathType,
+    "out_tracks": str,
+})
+TcksiftParamsDict = _TcksiftParamsDictNoTag | TcksiftParamsDictTagged
+
+
+def tcksift_config(
+    key: str,
+    value: str,
+) -> TcksiftConfigParamsDictTagged:
+    """
+    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 tcksift_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TcksiftConfigParamsDict` 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 tcksift_config_cargs(
+    params: TcksiftConfigParamsDict,
+    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 TcksiftOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `TcksiftParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_tracks: OutputPathType
+    """the output filtered tracks file"""
+    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_selection: OutputPathType | None
+    """output a text file containing the binary selection of streamlines """
+
+
+def tcksift_params(
+    in_tracks: InputPathType,
+    in_fod: InputPathType,
+    out_tracks: str,
+    nofilter: bool = False,
+    output_at_counts: list[int] | None = None,
+    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_selection: str | None = None,
+    term_number: int | None = None,
+    term_ratio: float | None = None,
+    term_mu: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TcksiftConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TcksiftParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        in_tracks: the input track file.
+        in_fod: input image containing the spherical harmonics of the fibre\
+            orientation distributions.
+        out_tracks: the output filtered tracks file.
+        nofilter: do NOT perform track filtering - just construct the model in\
+            order to provide output debugging images.
+        output_at_counts: output filtered track files (and optionally debugging\
+            images if -output_debug is specified) at specific numbers of remaining\
+            streamlines; provide as comma-separated list of integers.
+        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_selection: output a text file containing the binary selection of\
+            streamlines.
+        term_number: number of streamlines - continue filtering until this\
+            number of streamlines remain.
+        term_ratio: termination ratio - defined as the ratio between reduction\
+            in cost function, and reduction in density of streamlines.\
+            Smaller values result in more streamlines being filtered out.
+        term_mu: terminate filtering once the SIFT proportionality coefficient\
+            reaches a given value.
+        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/tcksift",
+        "nofilter": nofilter,
+        "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,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in_tracks": in_tracks,
+        "in_fod": in_fod,
+        "out_tracks": out_tracks,
+    }
+    if output_at_counts is not None:
+        params["output_at_counts"] = output_at_counts
+    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_selection is not None:
+        params["out_selection"] = out_selection
+    if term_number is not None:
+        params["term_number"] = term_number
+    if term_ratio is not None:
+        params["term_ratio"] = term_ratio
+    if term_mu is not None:
+        params["term_mu"] = term_mu
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tcksift_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TcksiftParamsDict` 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("nofilter", False) is None:
+        raise StyxValidationError("`nofilter` must not be None")
+    if not isinstance(params["nofilter"], bool):
+        raise StyxValidationError(f'`nofilter` has the wrong type: Received `{type(params.get("nofilter", False))}` expected `bool`')
+    if params.get("output_at_counts", None) is not None:
+        if not isinstance(params["output_at_counts"], list):
+            raise StyxValidationError(f'`output_at_counts` has the wrong type: Received `{type(params.get("output_at_counts", None))}` expected `list[int] | None`')
+        for e in params["output_at_counts"]:
+            if not isinstance(e, int):
+                raise StyxValidationError(f'`output_at_counts` has the wrong type: Received `{type(params.get("output_at_counts", None))}` expected `list[int] | None`')
+    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_selection", None) is not None:
+        if not isinstance(params["out_selection"], str):
+            raise StyxValidationError(f'`out_selection` has the wrong type: Received `{type(params.get("out_selection", None))}` expected `str | None`')
+    if params.get("term_number", None) is not None:
+        if not isinstance(params["term_number"], int):
+            raise StyxValidationError(f'`term_number` has the wrong type: Received `{type(params.get("term_number", None))}` expected `int | None`')
+    if params.get("term_ratio", None) is not None:
+        if not isinstance(params["term_ratio"], (float, int)):
+            raise StyxValidationError(f'`term_ratio` has the wrong type: Received `{type(params.get("term_ratio", None))}` expected `float | None`')
+    if params.get("term_mu", None) is not None:
+        if not isinstance(params["term_mu"], (float, int)):
+            raise StyxValidationError(f'`term_mu` has the wrong type: Received `{type(params.get("term_mu", None))}` expected `float | None`')
+    if params.get("info", False) is None:
+        raise StyxValidationError("`info` must not be None")
+    if not isinstance(params["info"], bool):
+        raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
+    if params.get("quiet", False) is None:
+        raise StyxValidationError("`quiet` must not be None")
+    if not isinstance(params["quiet"], bool):
+        raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
+    if params.get("debug", False) is None:
+        raise StyxValidationError("`debug` must not be None")
+    if not isinstance(params["debug"], bool):
+        raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
+    if params.get("force", False) is None:
+        raise StyxValidationError("`force` must not be None")
+    if not isinstance(params["force"], bool):
+        raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
+    if params.get("nthreads", None) is not None:
+        if not isinstance(params["nthreads"], int):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
+    if params.get("config", None) is not None:
+        if not isinstance(params["config"], list):
+            raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[TcksiftConfigParamsDict] | None`')
+        for e in params["config"]:
+            tcksift_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_tracks", None) is None:
+        raise StyxValidationError("`out_tracks` must not be None")
+    if not isinstance(params["out_tracks"], str):
+        raise StyxValidationError(f'`out_tracks` has the wrong type: Received `{type(params.get("out_tracks", None))}` expected `str`')
+
+
+def tcksift_cargs(
+    params: TcksiftParamsDict,
+    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("tcksift")
+    if params.get("nofilter", False):
+        cargs.append("-nofilter")
+    if params.get("output_at_counts", None) is not None:
+        cargs.extend([
+            "-output_at_counts",
+            ",".join(map(str, params.get("output_at_counts", None)))
+        ])
+    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_selection", None) is not None:
+        cargs.extend([
+            "-out_selection",
+            params.get("out_selection", None)
+        ])
+    if params.get("term_number", None) is not None:
+        cargs.extend([
+            "-term_number",
+            str(params.get("term_number", None))
+        ])
+    if params.get("term_ratio", None) is not None:
+        cargs.extend([
+            "-term_ratio",
+            str(params.get("term_ratio", None))
+        ])
+    if params.get("term_mu", None) is not None:
+        cargs.extend([
+            "-term_mu",
+            str(params.get("term_mu", None))
+        ])
+    if params.get("info", False):
+        cargs.append("-info")
+    if params.get("quiet", False):
+        cargs.append("-quiet")
+    if params.get("debug", False):
+        cargs.append("-debug")
+    if params.get("force", False):
+        cargs.append("-force")
+    if params.get("nthreads", None) is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads", None))
+        ])
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [tcksift_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_tracks", None))
+    return cargs
+
+
+def tcksift_outputs(
+    params: TcksiftParamsDict,
+    execution: Execution,
+) -> TcksiftOutputs:
+    """
+    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 = TcksiftOutputs(
+        root=execution.output_file("."),
+        out_tracks=execution.output_file(params.get("out_tracks", 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_selection=execution.output_file(params.get("out_selection", None)) if (params.get("out_selection") is not None) else None,
+    )
+    return ret
+
+
+def tcksift_execute(
+    params: TcksiftParamsDict,
+    runner: Runner | None = None,
+) -> TcksiftOutputs:
+    """
+    tcksift
+    
+    Filter a whole-brain fibre-tracking data set such that the streamline
+    densities match the FOD lobe integrals.
+    
+    
+    
+    References:
+    
+    Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT:
+    Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013,
+    67, 298-312.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TcksiftOutputs`).
+    """
+    tcksift_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKSIFT_METADATA)
+    params = execution.params(params)
+    cargs = tcksift_cargs(params, execution)
+    ret = tcksift_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tcksift(
+    in_tracks: InputPathType,
+    in_fod: InputPathType,
+    out_tracks: str,
+    nofilter: bool = False,
+    output_at_counts: list[int] | None = None,
+    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_selection: str | None = None,
+    term_number: int | None = None,
+    term_ratio: float | None = None,
+    term_mu: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TcksiftConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TcksiftOutputs:
+    """
+    tcksift
+    
+    Filter a whole-brain fibre-tracking data set such that the streamline
+    densities match the FOD lobe integrals.
+    
+    
+    
+    References:
+    
+    Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT:
+    Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013,
+    67, 298-312.
+    
+    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_tracks: the output filtered tracks file.
+        nofilter: do NOT perform track filtering - just construct the model in\
+            order to provide output debugging images.
+        output_at_counts: output filtered track files (and optionally debugging\
+            images if -output_debug is specified) at specific numbers of remaining\
+            streamlines; provide as comma-separated list of integers.
+        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_selection: output a text file containing the binary selection of\
+            streamlines.
+        term_number: number of streamlines - continue filtering until this\
+            number of streamlines remain.
+        term_ratio: termination ratio - defined as the ratio between reduction\
+            in cost function, and reduction in density of streamlines.\
+            Smaller values result in more streamlines being filtered out.
+        term_mu: terminate filtering once the SIFT proportionality coefficient\
+            reaches a given value.
+        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 `TcksiftOutputs`).
+    """
+    params = tcksift_params(
+        nofilter=nofilter,
+        output_at_counts=output_at_counts,
+        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_selection=out_selection,
+        term_number=term_number,
+        term_ratio=term_ratio,
+        term_mu=term_mu,
+        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_tracks=out_tracks,
+    )
+    return tcksift_execute(params, runner)
+
+
+__all__ = [
+    "TCKSIFT_METADATA",
+    "TcksiftConfigParamsDict",
+    "TcksiftConfigParamsDictTagged",
+    "TcksiftOutputs",
+    "TcksiftParamsDict",
+    "TcksiftParamsDictTagged",
+    "tcksift",
+    "tcksift_config",
+    "tcksift_execute",
+    "tcksift_params",
+]