niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tck2connectome.py

@@ -0,0 +1,727 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCK2CONNECTOME_METADATA = Metadata(
+    id="a66d5312bce1284177c4cf9ad60b3718c4a1a2b0.boutiques",
+    name="tck2connectome",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Tck2connectomeConfigParamsDictNoTag = typing.TypedDict('_Tck2connectomeConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Tck2connectomeConfigParamsDictTagged = typing.TypedDict('Tck2connectomeConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Tck2connectomeConfigParamsDict = _Tck2connectomeConfigParamsDictNoTag | Tck2connectomeConfigParamsDictTagged
+
+
+_Tck2connectomeParamsDictNoTag = typing.TypedDict('_Tck2connectomeParamsDictNoTag', {
+    "assignment_end_voxels": bool,
+    "assignment_radial_search": typing.NotRequired[float | None],
+    "assignment_reverse_search": typing.NotRequired[float | None],
+    "assignment_forward_search": typing.NotRequired[float | None],
+    "assignment_all_voxels": bool,
+    "scale_length": bool,
+    "scale_invlength": bool,
+    "scale_invnodevol": bool,
+    "scale_file": typing.NotRequired[InputPathType | None],
+    "symmetric": bool,
+    "zero_diagonal": bool,
+    "stat_edge": typing.NotRequired[str | None],
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "keep_unassigned": bool,
+    "out_assignments": typing.NotRequired[str | None],
+    "vector": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Tck2connectomeConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+    "nodes_in": InputPathType,
+    "connectome_out": str,
+})
+Tck2connectomeParamsDictTagged = typing.TypedDict('Tck2connectomeParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/tck2connectome"],
+    "assignment_end_voxels": bool,
+    "assignment_radial_search": typing.NotRequired[float | None],
+    "assignment_reverse_search": typing.NotRequired[float | None],
+    "assignment_forward_search": typing.NotRequired[float | None],
+    "assignment_all_voxels": bool,
+    "scale_length": bool,
+    "scale_invlength": bool,
+    "scale_invnodevol": bool,
+    "scale_file": typing.NotRequired[InputPathType | None],
+    "symmetric": bool,
+    "zero_diagonal": bool,
+    "stat_edge": typing.NotRequired[str | None],
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "keep_unassigned": bool,
+    "out_assignments": typing.NotRequired[str | None],
+    "vector": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Tck2connectomeConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+    "nodes_in": InputPathType,
+    "connectome_out": str,
+})
+Tck2connectomeParamsDict = _Tck2connectomeParamsDictNoTag | Tck2connectomeParamsDictTagged
+
+
+def tck2connectome_config(
+    key: str,
+    value: str,
+) -> Tck2connectomeConfigParamsDictTagged:
+    """
+    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 tck2connectome_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Tck2connectomeConfigParamsDict` 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 tck2connectome_config_cargs(
+    params: Tck2connectomeConfigParamsDict,
+    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 Tck2connectomeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Tck2connectomeParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    connectome_out: OutputPathType
+    """the output .csv file containing edge weights"""
+    out_assignments: OutputPathType | None
+    """output the node assignments of each streamline to a file; this can be
+    used subsequently e.g. by the command connectome2tck """
+
+
+def tck2connectome_params(
+    tracks_in: InputPathType,
+    nodes_in: InputPathType,
+    connectome_out: str,
+    assignment_end_voxels: bool = False,
+    assignment_radial_search: float | None = None,
+    assignment_reverse_search: float | None = None,
+    assignment_forward_search: float | None = None,
+    assignment_all_voxels: bool = False,
+    scale_length: bool = False,
+    scale_invlength: bool = False,
+    scale_invnodevol: bool = False,
+    scale_file: InputPathType | None = None,
+    symmetric: bool = False,
+    zero_diagonal: bool = False,
+    stat_edge: str | None = None,
+    tck_weights_in: InputPathType | None = None,
+    keep_unassigned: bool = False,
+    out_assignments: str | None = None,
+    vector: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Tck2connectomeConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Tck2connectomeParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        tracks_in: the input track file.
+        nodes_in: the input node parcellation image.
+        connectome_out: the output .csv file containing edge weights.
+        assignment_end_voxels: use a simple voxel lookup value at each\
+            streamline endpoint.
+        assignment_radial_search: perform a radial search from each streamline\
+            endpoint to locate the nearest node. Argument is the maximum radius in\
+            mm; if no node is found within this radius, the streamline endpoint is\
+            not assigned to any node. Default search distance is 4mm.
+        assignment_reverse_search: traverse from each streamline endpoint\
+            inwards along the streamline, in search of the last node traversed by\
+            the streamline. Argument is the maximum traversal length in mm (set to\
+            0 to allow search to continue to the streamline midpoint).
+        assignment_forward_search: project the streamline forwards from the\
+            endpoint in search of a parcellation node voxel. Argument is the\
+            maximum traversal length in mm.
+        assignment_all_voxels: assign the streamline to all nodes it intersects\
+            along its length (note that this means a streamline may be assigned to\
+            more than two nodes, or indeed none at all).
+        scale_length: scale each contribution to the connectome edge by the\
+            length of the streamline.
+        scale_invlength: scale each contribution to the connectome edge by the\
+            inverse of the streamline length.
+        scale_invnodevol: scale each contribution to the connectome edge by the\
+            inverse of the two node volumes.
+        scale_file: scale each contribution to the connectome edge according to\
+            the values in a vector file.
+        symmetric: Make matrices symmetric on output.
+        zero_diagonal: Set matrix diagonal to zero on output.
+        stat_edge: statistic for combining the values from all streamlines in\
+            an edge into a single scale value for that edge (options are:\
+            sum,mean,min,max; default=sum).
+        tck_weights_in: specify a text scalar file containing the streamline\
+            weights.
+        keep_unassigned: By default, the program discards the information\
+            regarding those streamlines that are not successfully assigned to a\
+            node pair. Set this option to keep these values (will be the first\
+            row/column in the output matrix).
+        out_assignments: output the node assignments of each streamline to a\
+            file; this can be used subsequently e.g. by the command connectome2tck.
+        vector: output a vector representing connectivities from a given seed\
+            point to target nodes, rather than a matrix of node-node connectivities.
+        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/tck2connectome",
+        "assignment_end_voxels": assignment_end_voxels,
+        "assignment_all_voxels": assignment_all_voxels,
+        "scale_length": scale_length,
+        "scale_invlength": scale_invlength,
+        "scale_invnodevol": scale_invnodevol,
+        "symmetric": symmetric,
+        "zero_diagonal": zero_diagonal,
+        "keep_unassigned": keep_unassigned,
+        "vector": vector,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "tracks_in": tracks_in,
+        "nodes_in": nodes_in,
+        "connectome_out": connectome_out,
+    }
+    if assignment_radial_search is not None:
+        params["assignment_radial_search"] = assignment_radial_search
+    if assignment_reverse_search is not None:
+        params["assignment_reverse_search"] = assignment_reverse_search
+    if assignment_forward_search is not None:
+        params["assignment_forward_search"] = assignment_forward_search
+    if scale_file is not None:
+        params["scale_file"] = scale_file
+    if stat_edge is not None:
+        params["stat_edge"] = stat_edge
+    if tck_weights_in is not None:
+        params["tck_weights_in"] = tck_weights_in
+    if out_assignments is not None:
+        params["out_assignments"] = out_assignments
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tck2connectome_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Tck2connectomeParamsDict` 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("assignment_end_voxels", False) is None:
+        raise StyxValidationError("`assignment_end_voxels` must not be None")
+    if not isinstance(params["assignment_end_voxels"], bool):
+        raise StyxValidationError(f'`assignment_end_voxels` has the wrong type: Received `{type(params.get("assignment_end_voxels", False))}` expected `bool`')
+    if params.get("assignment_radial_search", None) is not None:
+        if not isinstance(params["assignment_radial_search"], (float, int)):
+            raise StyxValidationError(f'`assignment_radial_search` has the wrong type: Received `{type(params.get("assignment_radial_search", None))}` expected `float | None`')
+    if params.get("assignment_reverse_search", None) is not None:
+        if not isinstance(params["assignment_reverse_search"], (float, int)):
+            raise StyxValidationError(f'`assignment_reverse_search` has the wrong type: Received `{type(params.get("assignment_reverse_search", None))}` expected `float | None`')
+    if params.get("assignment_forward_search", None) is not None:
+        if not isinstance(params["assignment_forward_search"], (float, int)):
+            raise StyxValidationError(f'`assignment_forward_search` has the wrong type: Received `{type(params.get("assignment_forward_search", None))}` expected `float | None`')
+    if params.get("assignment_all_voxels", False) is None:
+        raise StyxValidationError("`assignment_all_voxels` must not be None")
+    if not isinstance(params["assignment_all_voxels"], bool):
+        raise StyxValidationError(f'`assignment_all_voxels` has the wrong type: Received `{type(params.get("assignment_all_voxels", False))}` expected `bool`')
+    if params.get("scale_length", False) is None:
+        raise StyxValidationError("`scale_length` must not be None")
+    if not isinstance(params["scale_length"], bool):
+        raise StyxValidationError(f'`scale_length` has the wrong type: Received `{type(params.get("scale_length", False))}` expected `bool`')
+    if params.get("scale_invlength", False) is None:
+        raise StyxValidationError("`scale_invlength` must not be None")
+    if not isinstance(params["scale_invlength"], bool):
+        raise StyxValidationError(f'`scale_invlength` has the wrong type: Received `{type(params.get("scale_invlength", False))}` expected `bool`')
+    if params.get("scale_invnodevol", False) is None:
+        raise StyxValidationError("`scale_invnodevol` must not be None")
+    if not isinstance(params["scale_invnodevol"], bool):
+        raise StyxValidationError(f'`scale_invnodevol` has the wrong type: Received `{type(params.get("scale_invnodevol", False))}` expected `bool`')
+    if params.get("scale_file", None) is not None:
+        if not isinstance(params["scale_file"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`scale_file` has the wrong type: Received `{type(params.get("scale_file", None))}` expected `InputPathType | None`')
+    if params.get("symmetric", False) is None:
+        raise StyxValidationError("`symmetric` must not be None")
+    if not isinstance(params["symmetric"], bool):
+        raise StyxValidationError(f'`symmetric` has the wrong type: Received `{type(params.get("symmetric", False))}` expected `bool`')
+    if params.get("zero_diagonal", False) is None:
+        raise StyxValidationError("`zero_diagonal` must not be None")
+    if not isinstance(params["zero_diagonal"], bool):
+        raise StyxValidationError(f'`zero_diagonal` has the wrong type: Received `{type(params.get("zero_diagonal", False))}` expected `bool`')
+    if params.get("stat_edge", None) is not None:
+        if not isinstance(params["stat_edge"], str):
+            raise StyxValidationError(f'`stat_edge` has the wrong type: Received `{type(params.get("stat_edge", None))}` expected `str | None`')
+    if params.get("tck_weights_in", None) is not None:
+        if not isinstance(params["tck_weights_in"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`tck_weights_in` has the wrong type: Received `{type(params.get("tck_weights_in", None))}` expected `InputPathType | None`')
+    if params.get("keep_unassigned", False) is None:
+        raise StyxValidationError("`keep_unassigned` must not be None")
+    if not isinstance(params["keep_unassigned"], bool):
+        raise StyxValidationError(f'`keep_unassigned` has the wrong type: Received `{type(params.get("keep_unassigned", False))}` expected `bool`')
+    if params.get("out_assignments", None) is not None:
+        if not isinstance(params["out_assignments"], str):
+            raise StyxValidationError(f'`out_assignments` has the wrong type: Received `{type(params.get("out_assignments", None))}` expected `str | None`')
+    if params.get("vector", False) is None:
+        raise StyxValidationError("`vector` must not be None")
+    if not isinstance(params["vector"], bool):
+        raise StyxValidationError(f'`vector` has the wrong type: Received `{type(params.get("vector", 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[Tck2connectomeConfigParamsDict] | None`')
+        for e in params["config"]:
+            tck2connectome_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("tracks_in", None) is None:
+        raise StyxValidationError("`tracks_in` must not be None")
+    if not isinstance(params["tracks_in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`tracks_in` has the wrong type: Received `{type(params.get("tracks_in", None))}` expected `InputPathType`')
+    if params.get("nodes_in", None) is None:
+        raise StyxValidationError("`nodes_in` must not be None")
+    if not isinstance(params["nodes_in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`nodes_in` has the wrong type: Received `{type(params.get("nodes_in", None))}` expected `InputPathType`')
+    if params.get("connectome_out", None) is None:
+        raise StyxValidationError("`connectome_out` must not be None")
+    if not isinstance(params["connectome_out"], str):
+        raise StyxValidationError(f'`connectome_out` has the wrong type: Received `{type(params.get("connectome_out", None))}` expected `str`')
+
+
+def tck2connectome_cargs(
+    params: Tck2connectomeParamsDict,
+    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("tck2connectome")
+    if params.get("assignment_end_voxels", False):
+        cargs.append("-assignment_end_voxels")
+    if params.get("assignment_radial_search", None) is not None:
+        cargs.extend([
+            "-assignment_radial_search",
+            str(params.get("assignment_radial_search", None))
+        ])
+    if params.get("assignment_reverse_search", None) is not None:
+        cargs.extend([
+            "-assignment_reverse_search",
+            str(params.get("assignment_reverse_search", None))
+        ])
+    if params.get("assignment_forward_search", None) is not None:
+        cargs.extend([
+            "-assignment_forward_search",
+            str(params.get("assignment_forward_search", None))
+        ])
+    if params.get("assignment_all_voxels", False):
+        cargs.append("-assignment_all_voxels")
+    if params.get("scale_length", False):
+        cargs.append("-scale_length")
+    if params.get("scale_invlength", False):
+        cargs.append("-scale_invlength")
+    if params.get("scale_invnodevol", False):
+        cargs.append("-scale_invnodevol")
+    if params.get("scale_file", None) is not None:
+        cargs.extend([
+            "-scale_file",
+            execution.input_file(params.get("scale_file", None))
+        ])
+    if params.get("symmetric", False):
+        cargs.append("-symmetric")
+    if params.get("zero_diagonal", False):
+        cargs.append("-zero_diagonal")
+    if params.get("stat_edge", None) is not None:
+        cargs.extend([
+            "-stat_edge",
+            params.get("stat_edge", None)
+        ])
+    if params.get("tck_weights_in", None) is not None:
+        cargs.extend([
+            "-tck_weights_in",
+            execution.input_file(params.get("tck_weights_in", None))
+        ])
+    if params.get("keep_unassigned", False):
+        cargs.append("-keep_unassigned")
+    if params.get("out_assignments", None) is not None:
+        cargs.extend([
+            "-out_assignments",
+            params.get("out_assignments", None)
+        ])
+    if params.get("vector", False):
+        cargs.append("-vector")
+    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 [tck2connectome_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("tracks_in", None)))
+    cargs.append(execution.input_file(params.get("nodes_in", None)))
+    cargs.append(params.get("connectome_out", None))
+    return cargs
+
+
+def tck2connectome_outputs(
+    params: Tck2connectomeParamsDict,
+    execution: Execution,
+) -> Tck2connectomeOutputs:
+    """
+    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 = Tck2connectomeOutputs(
+        root=execution.output_file("."),
+        connectome_out=execution.output_file(params.get("connectome_out", None)),
+        out_assignments=execution.output_file(params.get("out_assignments", None)) if (params.get("out_assignments") is not None) else None,
+    )
+    return ret
+
+
+def tck2connectome_execute(
+    params: Tck2connectomeParamsDict,
+    runner: Runner | None = None,
+) -> Tck2connectomeOutputs:
+    """
+    tck2connectome
+    
+    Generate a connectome matrix from a streamlines file and a node parcellation
+    image.
+    
+    
+    
+    References:
+    
+    If using the default streamline-parcel assignment mechanism (or
+    -assignment_radial_search option): Smith, R. E.; Tournier, J.-D.; Calamante,
+    F. & Connelly, A. The effects of SIFT on the reproducibility and biological
+    accuracy of the structural connectome. NeuroImage, 2015, 104, 253-265
+    
+    If using -scale_invlength or -scale_invnodevol options: Hagmann, P.;
+    Cammoun, L.; Gigandet, X.; Meuli, R.; Honey, C.; Wedeen, V. & Sporns, O.
+    Mapping the Structural Core of Human Cerebral Cortex. PLoS Biology 6(7),
+    e159.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Tck2connectomeOutputs`).
+    """
+    tck2connectome_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCK2CONNECTOME_METADATA)
+    params = execution.params(params)
+    cargs = tck2connectome_cargs(params, execution)
+    ret = tck2connectome_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tck2connectome(
+    tracks_in: InputPathType,
+    nodes_in: InputPathType,
+    connectome_out: str,
+    assignment_end_voxels: bool = False,
+    assignment_radial_search: float | None = None,
+    assignment_reverse_search: float | None = None,
+    assignment_forward_search: float | None = None,
+    assignment_all_voxels: bool = False,
+    scale_length: bool = False,
+    scale_invlength: bool = False,
+    scale_invnodevol: bool = False,
+    scale_file: InputPathType | None = None,
+    symmetric: bool = False,
+    zero_diagonal: bool = False,
+    stat_edge: str | None = None,
+    tck_weights_in: InputPathType | None = None,
+    keep_unassigned: bool = False,
+    out_assignments: str | None = None,
+    vector: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Tck2connectomeConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Tck2connectomeOutputs:
+    """
+    tck2connectome
+    
+    Generate a connectome matrix from a streamlines file and a node parcellation
+    image.
+    
+    
+    
+    References:
+    
+    If using the default streamline-parcel assignment mechanism (or
+    -assignment_radial_search option): Smith, R. E.; Tournier, J.-D.; Calamante,
+    F. & Connelly, A. The effects of SIFT on the reproducibility and biological
+    accuracy of the structural connectome. NeuroImage, 2015, 104, 253-265
+    
+    If using -scale_invlength or -scale_invnodevol options: Hagmann, P.;
+    Cammoun, L.; Gigandet, X.; Meuli, R.; Honey, C.; Wedeen, V. & Sporns, O.
+    Mapping the Structural Core of Human Cerebral Cortex. PLoS Biology 6(7),
+    e159.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        tracks_in: the input track file.
+        nodes_in: the input node parcellation image.
+        connectome_out: the output .csv file containing edge weights.
+        assignment_end_voxels: use a simple voxel lookup value at each\
+            streamline endpoint.
+        assignment_radial_search: perform a radial search from each streamline\
+            endpoint to locate the nearest node. Argument is the maximum radius in\
+            mm; if no node is found within this radius, the streamline endpoint is\
+            not assigned to any node. Default search distance is 4mm.
+        assignment_reverse_search: traverse from each streamline endpoint\
+            inwards along the streamline, in search of the last node traversed by\
+            the streamline. Argument is the maximum traversal length in mm (set to\
+            0 to allow search to continue to the streamline midpoint).
+        assignment_forward_search: project the streamline forwards from the\
+            endpoint in search of a parcellation node voxel. Argument is the\
+            maximum traversal length in mm.
+        assignment_all_voxels: assign the streamline to all nodes it intersects\
+            along its length (note that this means a streamline may be assigned to\
+            more than two nodes, or indeed none at all).
+        scale_length: scale each contribution to the connectome edge by the\
+            length of the streamline.
+        scale_invlength: scale each contribution to the connectome edge by the\
+            inverse of the streamline length.
+        scale_invnodevol: scale each contribution to the connectome edge by the\
+            inverse of the two node volumes.
+        scale_file: scale each contribution to the connectome edge according to\
+            the values in a vector file.
+        symmetric: Make matrices symmetric on output.
+        zero_diagonal: Set matrix diagonal to zero on output.
+        stat_edge: statistic for combining the values from all streamlines in\
+            an edge into a single scale value for that edge (options are:\
+            sum,mean,min,max; default=sum).
+        tck_weights_in: specify a text scalar file containing the streamline\
+            weights.
+        keep_unassigned: By default, the program discards the information\
+            regarding those streamlines that are not successfully assigned to a\
+            node pair. Set this option to keep these values (will be the first\
+            row/column in the output matrix).
+        out_assignments: output the node assignments of each streamline to a\
+            file; this can be used subsequently e.g. by the command connectome2tck.
+        vector: output a vector representing connectivities from a given seed\
+            point to target nodes, rather than a matrix of node-node connectivities.
+        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 `Tck2connectomeOutputs`).
+    """
+    params = tck2connectome_params(
+        assignment_end_voxels=assignment_end_voxels,
+        assignment_radial_search=assignment_radial_search,
+        assignment_reverse_search=assignment_reverse_search,
+        assignment_forward_search=assignment_forward_search,
+        assignment_all_voxels=assignment_all_voxels,
+        scale_length=scale_length,
+        scale_invlength=scale_invlength,
+        scale_invnodevol=scale_invnodevol,
+        scale_file=scale_file,
+        symmetric=symmetric,
+        zero_diagonal=zero_diagonal,
+        stat_edge=stat_edge,
+        tck_weights_in=tck_weights_in,
+        keep_unassigned=keep_unassigned,
+        out_assignments=out_assignments,
+        vector=vector,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        tracks_in=tracks_in,
+        nodes_in=nodes_in,
+        connectome_out=connectome_out,
+    )
+    return tck2connectome_execute(params, runner)
+
+
+__all__ = [
+    "TCK2CONNECTOME_METADATA",
+    "Tck2connectomeConfigParamsDict",
+    "Tck2connectomeConfigParamsDictTagged",
+    "Tck2connectomeOutputs",
+    "Tck2connectomeParamsDict",
+    "Tck2connectomeParamsDictTagged",
+    "tck2connectome",
+    "tck2connectome_config",
+    "tck2connectome_execute",
+    "tck2connectome_params",
+]