niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tckglobal.py

@@ -0,0 +1,944 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKGLOBAL_METADATA = Metadata(
+    id="31e24266a6d4374cd9c0a8ed5d9d697b1c511208.boutiques",
+    name="tckglobal",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_TckglobalRisoParamsDictNoTag = typing.TypedDict('_TckglobalRisoParamsDictNoTag', {
+    "response": InputPathType,
+})
+TckglobalRisoParamsDictTagged = typing.TypedDict('TckglobalRisoParamsDictTagged', {
+    "@type": typing.Literal["riso"],
+    "response": InputPathType,
+})
+TckglobalRisoParamsDict = _TckglobalRisoParamsDictNoTag | TckglobalRisoParamsDictTagged
+
+
+_TckglobalConfigParamsDictNoTag = typing.TypedDict('_TckglobalConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+TckglobalConfigParamsDictTagged = typing.TypedDict('TckglobalConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+TckglobalConfigParamsDict = _TckglobalConfigParamsDictNoTag | TckglobalConfigParamsDictTagged
+
+
+_TckglobalParamsDictNoTag = typing.TypedDict('_TckglobalParamsDictNoTag', {
+    "grad": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "riso": typing.NotRequired[list[TckglobalRisoParamsDict] | None],
+    "lmax": typing.NotRequired[int | None],
+    "length": typing.NotRequired[float | None],
+    "weight": typing.NotRequired[float | None],
+    "ppot": typing.NotRequired[float | None],
+    "cpot": typing.NotRequired[float | None],
+    "t0": typing.NotRequired[float | None],
+    "t1": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[int | None],
+    "fod": typing.NotRequired[str | None],
+    "noapo": bool,
+    "fiso": typing.NotRequired[str | None],
+    "eext": typing.NotRequired[str | None],
+    "etrend": typing.NotRequired[str | None],
+    "balance": typing.NotRequired[float | None],
+    "density": typing.NotRequired[float | None],
+    "prob": typing.NotRequired[list[float] | None],
+    "beta": typing.NotRequired[float | None],
+    "lambda": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckglobalConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "source": InputPathType,
+    "response": InputPathType,
+    "tracks": str,
+})
+TckglobalParamsDictTagged = typing.TypedDict('TckglobalParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/tckglobal"],
+    "grad": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "riso": typing.NotRequired[list[TckglobalRisoParamsDict] | None],
+    "lmax": typing.NotRequired[int | None],
+    "length": typing.NotRequired[float | None],
+    "weight": typing.NotRequired[float | None],
+    "ppot": typing.NotRequired[float | None],
+    "cpot": typing.NotRequired[float | None],
+    "t0": typing.NotRequired[float | None],
+    "t1": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[int | None],
+    "fod": typing.NotRequired[str | None],
+    "noapo": bool,
+    "fiso": typing.NotRequired[str | None],
+    "eext": typing.NotRequired[str | None],
+    "etrend": typing.NotRequired[str | None],
+    "balance": typing.NotRequired[float | None],
+    "density": typing.NotRequired[float | None],
+    "prob": typing.NotRequired[list[float] | None],
+    "beta": typing.NotRequired[float | None],
+    "lambda": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckglobalConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "source": InputPathType,
+    "response": InputPathType,
+    "tracks": str,
+})
+TckglobalParamsDict = _TckglobalParamsDictNoTag | TckglobalParamsDictTagged
+
+
+def tckglobal_riso(
+    response: InputPathType,
+) -> TckglobalRisoParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        response: set one or more isotropic response functions. (multiple\
+            allowed).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "riso",
+        "response": response,
+    }
+    return params
+
+
+def tckglobal_riso_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckglobalRisoParamsDict` 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("response", None) is None:
+        raise StyxValidationError("`response` must not be None")
+    if not isinstance(params["response"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`response` has the wrong type: Received `{type(params.get("response", None))}` expected `InputPathType`')
+
+
+def tckglobal_riso_cargs(
+    params: TckglobalRisoParamsDict,
+    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("-riso")
+    cargs.append(execution.input_file(params.get("response", None)))
+    return cargs
+
+
+def tckglobal_config(
+    key: str,
+    value: str,
+) -> TckglobalConfigParamsDictTagged:
+    """
+    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 tckglobal_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckglobalConfigParamsDict` 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 tckglobal_config_cargs(
+    params: TckglobalConfigParamsDict,
+    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 TckglobalOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `TckglobalParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    tracks: OutputPathType
+    """the output file containing the tracks generated."""
+    fod: OutputPathType | None
+    """Predicted fibre orientation distribution function (fODF).
+    This fODF is estimated as part of the global track optimization, and
+    therefore incorporates the spatial regularization that it imposes.
+    Internally, the fODF is represented as a discrete sum of apodized point
+    spread functions (aPSF) oriented along the directions of all particles in
+    the voxel, used to predict the DWI signal from the particle configuration.
+    """
+    fiso: OutputPathType | None
+    """Predicted isotropic fractions of the tissues for which response functions
+    were provided with -riso. Typically, these are CSF and GM. """
+    eext: OutputPathType | None
+    """Residual external energy in every voxel. """
+    etrend: OutputPathType | None
+    """internal and external energy trend and cooling statistics. """
+
+
+def tckglobal_params(
+    source: InputPathType,
+    response: InputPathType,
+    tracks: str,
+    grad: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    riso: list[TckglobalRisoParamsDict] | None = None,
+    lmax: int | None = None,
+    length: float | None = None,
+    weight: float | None = None,
+    ppot: float | None = None,
+    cpot: float | None = None,
+    t0: float | None = None,
+    t1: float | None = None,
+    niter: int | None = None,
+    fod: str | None = None,
+    noapo: bool = False,
+    fiso: str | None = None,
+    eext: str | None = None,
+    etrend: str | None = None,
+    balance: float | None = None,
+    density: float | None = None,
+    prob: list[float] | None = None,
+    beta: float | None = None,
+    lambda_: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckglobalConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TckglobalParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        source: the image containing the raw DWI data.
+        response: the response of a track segment on the DWI signal.
+        tracks: the output file containing the tracks generated.
+        grad: specify the diffusion encoding scheme (required if not supplied\
+            in the header).
+        mask: only reconstruct the tractogram within the specified brain mask\
+            image.
+        riso: set one or more isotropic response functions. (multiple allowed).
+        lmax: set the maximum harmonic order for the output series. (default =\
+            8).
+        length: set the length of the particles (fibre segments). (default =\
+            1mm).
+        weight: set the weight by which particles contribute to the model.\
+            (default = 0.1).
+        ppot: set the particle potential, i.e., the cost of adding one segment,\
+            relative to the particle weight. (default = 0.05).
+        cpot: set the connection potential, i.e., the energy term that drives\
+            two segments together. (default = 0.5).
+        t0: set the initial temperature of the metropolis hastings optimizer.\
+            (default = 0.1).
+        t1: set the final temperature of the metropolis hastings optimizer.\
+            (default = 0.001).
+        niter: set the number of iterations of the metropolis hastings\
+            optimizer. (default = 10M).
+        fod: Predicted fibre orientation distribution function (fODF).\
+            This fODF is estimated as part of the global track optimization,\
+            and therefore incorporates the spatial regularization that it\
+            imposes. Internally, the fODF is represented as a discrete sum of\
+            apodized point spread functions (aPSF) oriented along the\
+            directions of all particles in the voxel, used to predict the DWI\
+            signal from the particle configuration.
+        noapo: disable spherical convolution of fODF with apodized PSF, to\
+            output a sum of delta functions rather than a sum of aPSFs.
+        fiso: Predicted isotropic fractions of the tissues for which response\
+            functions were provided with -riso. Typically, these are CSF and GM.
+        eext: Residual external energy in every voxel.
+        etrend: internal and external energy trend and cooling statistics.
+        balance: balance internal and external energy. (default = 0)\
+            Negative values give more weight to the internal energy, positive\
+            to the external energy.
+        density: set the desired density of the free Poisson process. (default\
+            = 1).
+        prob: set the probabilities of generating birth, death, randshift,\
+            optshift and connect proposals respectively. (default =\
+            0.25,0.05,0.25,0.1,0.35).
+        beta: set the width of the Hanning interpolation window. (in [0, 1],\
+            default = 0)\
+            If used, a mask is required, and this mask must keep at least one\
+            voxel distance to the image bounding box.
+        lambda_: set the weight of the internal energy directly. (default = 1)\
+            If provided, any value of -balance will be ignored.
+        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/tckglobal",
+        "noapo": noapo,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "source": source,
+        "response": response,
+        "tracks": tracks,
+    }
+    if grad is not None:
+        params["grad"] = grad
+    if mask is not None:
+        params["mask"] = mask
+    if riso is not None:
+        params["riso"] = riso
+    if lmax is not None:
+        params["lmax"] = lmax
+    if length is not None:
+        params["length"] = length
+    if weight is not None:
+        params["weight"] = weight
+    if ppot is not None:
+        params["ppot"] = ppot
+    if cpot is not None:
+        params["cpot"] = cpot
+    if t0 is not None:
+        params["t0"] = t0
+    if t1 is not None:
+        params["t1"] = t1
+    if niter is not None:
+        params["niter"] = niter
+    if fod is not None:
+        params["fod"] = fod
+    if fiso is not None:
+        params["fiso"] = fiso
+    if eext is not None:
+        params["eext"] = eext
+    if etrend is not None:
+        params["etrend"] = etrend
+    if balance is not None:
+        params["balance"] = balance
+    if density is not None:
+        params["density"] = density
+    if prob is not None:
+        params["prob"] = prob
+    if beta is not None:
+        params["beta"] = beta
+    if lambda_ is not None:
+        params["lambda"] = lambda_
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tckglobal_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckglobalParamsDict` 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("grad", None) is not None:
+        if not isinstance(params["grad"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`grad` has the wrong type: Received `{type(params.get("grad", None))}` expected `InputPathType | None`')
+    if params.get("mask", None) is not None:
+        if not isinstance(params["mask"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask` has the wrong type: Received `{type(params.get("mask", None))}` expected `InputPathType | None`')
+    if params.get("riso", None) is not None:
+        if not isinstance(params["riso"], list):
+            raise StyxValidationError(f'`riso` has the wrong type: Received `{type(params.get("riso", None))}` expected `list[TckglobalRisoParamsDict] | None`')
+        for e in params["riso"]:
+            tckglobal_riso_validate(e)
+    if params.get("lmax", None) is not None:
+        if not isinstance(params["lmax"], int):
+            raise StyxValidationError(f'`lmax` has the wrong type: Received `{type(params.get("lmax", None))}` expected `int | None`')
+    if params.get("length", None) is not None:
+        if not isinstance(params["length"], (float, int)):
+            raise StyxValidationError(f'`length` has the wrong type: Received `{type(params.get("length", None))}` expected `float | None`')
+    if params.get("weight", None) is not None:
+        if not isinstance(params["weight"], (float, int)):
+            raise StyxValidationError(f'`weight` has the wrong type: Received `{type(params.get("weight", None))}` expected `float | None`')
+    if params.get("ppot", None) is not None:
+        if not isinstance(params["ppot"], (float, int)):
+            raise StyxValidationError(f'`ppot` has the wrong type: Received `{type(params.get("ppot", None))}` expected `float | None`')
+    if params.get("cpot", None) is not None:
+        if not isinstance(params["cpot"], (float, int)):
+            raise StyxValidationError(f'`cpot` has the wrong type: Received `{type(params.get("cpot", None))}` expected `float | None`')
+    if params.get("t0", None) is not None:
+        if not isinstance(params["t0"], (float, int)):
+            raise StyxValidationError(f'`t0` has the wrong type: Received `{type(params.get("t0", None))}` expected `float | None`')
+    if params.get("t1", None) is not None:
+        if not isinstance(params["t1"], (float, int)):
+            raise StyxValidationError(f'`t1` has the wrong type: Received `{type(params.get("t1", None))}` expected `float | None`')
+    if params.get("niter", None) is not None:
+        if not isinstance(params["niter"], int):
+            raise StyxValidationError(f'`niter` has the wrong type: Received `{type(params.get("niter", None))}` expected `int | None`')
+    if params.get("fod", None) is not None:
+        if not isinstance(params["fod"], str):
+            raise StyxValidationError(f'`fod` has the wrong type: Received `{type(params.get("fod", None))}` expected `str | None`')
+    if params.get("noapo", False) is None:
+        raise StyxValidationError("`noapo` must not be None")
+    if not isinstance(params["noapo"], bool):
+        raise StyxValidationError(f'`noapo` has the wrong type: Received `{type(params.get("noapo", False))}` expected `bool`')
+    if params.get("fiso", None) is not None:
+        if not isinstance(params["fiso"], str):
+            raise StyxValidationError(f'`fiso` has the wrong type: Received `{type(params.get("fiso", None))}` expected `str | None`')
+    if params.get("eext", None) is not None:
+        if not isinstance(params["eext"], str):
+            raise StyxValidationError(f'`eext` has the wrong type: Received `{type(params.get("eext", None))}` expected `str | None`')
+    if params.get("etrend", None) is not None:
+        if not isinstance(params["etrend"], str):
+            raise StyxValidationError(f'`etrend` has the wrong type: Received `{type(params.get("etrend", None))}` expected `str | None`')
+    if params.get("balance", None) is not None:
+        if not isinstance(params["balance"], (float, int)):
+            raise StyxValidationError(f'`balance` has the wrong type: Received `{type(params.get("balance", None))}` expected `float | None`')
+    if params.get("density", None) is not None:
+        if not isinstance(params["density"], (float, int)):
+            raise StyxValidationError(f'`density` has the wrong type: Received `{type(params.get("density", None))}` expected `float | None`')
+    if params.get("prob", None) is not None:
+        if not isinstance(params["prob"], list):
+            raise StyxValidationError(f'`prob` has the wrong type: Received `{type(params.get("prob", None))}` expected `list[float] | None`')
+        for e in params["prob"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`prob` has the wrong type: Received `{type(params.get("prob", None))}` expected `list[float] | None`')
+    if params.get("beta", None) is not None:
+        if not isinstance(params["beta"], (float, int)):
+            raise StyxValidationError(f'`beta` has the wrong type: Received `{type(params.get("beta", None))}` expected `float | None`')
+    if params.get("lambda", None) is not None:
+        if not isinstance(params["lambda"], (float, int)):
+            raise StyxValidationError(f'`lambda` has the wrong type: Received `{type(params.get("lambda", 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[TckglobalConfigParamsDict] | None`')
+        for e in params["config"]:
+            tckglobal_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("source", None) is None:
+        raise StyxValidationError("`source` must not be None")
+    if not isinstance(params["source"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`source` has the wrong type: Received `{type(params.get("source", None))}` expected `InputPathType`')
+    if params.get("response", None) is None:
+        raise StyxValidationError("`response` must not be None")
+    if not isinstance(params["response"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`response` has the wrong type: Received `{type(params.get("response", None))}` expected `InputPathType`')
+    if params.get("tracks", None) is None:
+        raise StyxValidationError("`tracks` must not be None")
+    if not isinstance(params["tracks"], str):
+        raise StyxValidationError(f'`tracks` has the wrong type: Received `{type(params.get("tracks", None))}` expected `str`')
+
+
+def tckglobal_cargs(
+    params: TckglobalParamsDict,
+    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("tckglobal")
+    if params.get("grad", None) is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad", None))
+        ])
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", None))
+        ])
+    if params.get("riso", None) is not None:
+        cargs.extend([a for c in [tckglobal_riso_cargs(s, execution) for s in params.get("riso", None)] for a in c])
+    if params.get("lmax", None) is not None:
+        cargs.extend([
+            "-lmax",
+            str(params.get("lmax", None))
+        ])
+    if params.get("length", None) is not None:
+        cargs.extend([
+            "-length",
+            str(params.get("length", None))
+        ])
+    if params.get("weight", None) is not None:
+        cargs.extend([
+            "-weight",
+            str(params.get("weight", None))
+        ])
+    if params.get("ppot", None) is not None:
+        cargs.extend([
+            "-ppot",
+            str(params.get("ppot", None))
+        ])
+    if params.get("cpot", None) is not None:
+        cargs.extend([
+            "-cpot",
+            str(params.get("cpot", None))
+        ])
+    if params.get("t0", None) is not None:
+        cargs.extend([
+            "-t0",
+            str(params.get("t0", None))
+        ])
+    if params.get("t1", None) is not None:
+        cargs.extend([
+            "-t1",
+            str(params.get("t1", None))
+        ])
+    if params.get("niter", None) is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("niter", None))
+        ])
+    if params.get("fod", None) is not None:
+        cargs.extend([
+            "-fod",
+            params.get("fod", None)
+        ])
+    if params.get("noapo", False):
+        cargs.append("-noapo")
+    if params.get("fiso", None) is not None:
+        cargs.extend([
+            "-fiso",
+            params.get("fiso", None)
+        ])
+    if params.get("eext", None) is not None:
+        cargs.extend([
+            "-eext",
+            params.get("eext", None)
+        ])
+    if params.get("etrend", None) is not None:
+        cargs.extend([
+            "-etrend",
+            params.get("etrend", None)
+        ])
+    if params.get("balance", None) is not None:
+        cargs.extend([
+            "-balance",
+            str(params.get("balance", None))
+        ])
+    if params.get("density", None) is not None:
+        cargs.extend([
+            "-density",
+            str(params.get("density", None))
+        ])
+    if params.get("prob", None) is not None:
+        cargs.extend([
+            "-prob",
+            *map(str, params.get("prob", None))
+        ])
+    if params.get("beta", None) is not None:
+        cargs.extend([
+            "-beta",
+            str(params.get("beta", None))
+        ])
+    if params.get("lambda", None) is not None:
+        cargs.extend([
+            "-lambda",
+            str(params.get("lambda", 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 [tckglobal_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("source", None)))
+    cargs.append(execution.input_file(params.get("response", None)))
+    cargs.append(params.get("tracks", None))
+    return cargs
+
+
+def tckglobal_outputs(
+    params: TckglobalParamsDict,
+    execution: Execution,
+) -> TckglobalOutputs:
+    """
+    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 = TckglobalOutputs(
+        root=execution.output_file("."),
+        tracks=execution.output_file(params.get("tracks", None)),
+        fod=execution.output_file(params.get("fod", None)) if (params.get("fod") is not None) else None,
+        fiso=execution.output_file(params.get("fiso", None)) if (params.get("fiso") is not None) else None,
+        eext=execution.output_file(params.get("eext", None)) if (params.get("eext") is not None) else None,
+        etrend=execution.output_file(params.get("etrend", None)) if (params.get("etrend") is not None) else None,
+    )
+    return ret
+
+
+def tckglobal_execute(
+    params: TckglobalParamsDict,
+    runner: Runner | None = None,
+) -> TckglobalOutputs:
+    """
+    tckglobal
+    
+    Multi-Shell Multi-Tissue Global Tractography.
+    
+    This command will reconstruct the global white matter fibre tractogram that
+    best explains the input DWI data, using a multi-tissue spherical convolution
+    model.
+    
+    Example use:
+    
+    $ tckglobal dwi.mif wmr.txt -riso csfr.txt -riso gmr.txt -mask mask.mif
+    -niter 1e9 -fod fod.mif -fiso fiso.mif tracks.tck
+    
+    in which dwi.mif is the input image, wmr.txt is an anisotropic, multi-shell
+    response function for WM, and csfr.txt and gmr.txt are isotropic response
+    functions for CSF and GM. The output tractogram is saved to tracks.tck.
+    Optional output images fod.mif and fiso.mif contain the predicted WM fODF
+    and isotropic tissue fractions of CSF and GM respectively, estimated as part
+    of the global optimization and thus affected by spatial regularization.
+    
+    References:
+    
+    Christiaens, D.; Reisert, M.; Dhollander, T.; Sunaert, S.; Suetens, P. &
+    Maes, F. Global tractography of multi-shell diffusion-weighted imaging data
+    using a multi-tissue model. NeuroImage, 2015, 123, 89-101.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TckglobalOutputs`).
+    """
+    tckglobal_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKGLOBAL_METADATA)
+    params = execution.params(params)
+    cargs = tckglobal_cargs(params, execution)
+    ret = tckglobal_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tckglobal(
+    source: InputPathType,
+    response: InputPathType,
+    tracks: str,
+    grad: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    riso: list[TckglobalRisoParamsDict] | None = None,
+    lmax: int | None = None,
+    length: float | None = None,
+    weight: float | None = None,
+    ppot: float | None = None,
+    cpot: float | None = None,
+    t0: float | None = None,
+    t1: float | None = None,
+    niter: int | None = None,
+    fod: str | None = None,
+    noapo: bool = False,
+    fiso: str | None = None,
+    eext: str | None = None,
+    etrend: str | None = None,
+    balance: float | None = None,
+    density: float | None = None,
+    prob: list[float] | None = None,
+    beta: float | None = None,
+    lambda_: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckglobalConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TckglobalOutputs:
+    """
+    tckglobal
+    
+    Multi-Shell Multi-Tissue Global Tractography.
+    
+    This command will reconstruct the global white matter fibre tractogram that
+    best explains the input DWI data, using a multi-tissue spherical convolution
+    model.
+    
+    Example use:
+    
+    $ tckglobal dwi.mif wmr.txt -riso csfr.txt -riso gmr.txt -mask mask.mif
+    -niter 1e9 -fod fod.mif -fiso fiso.mif tracks.tck
+    
+    in which dwi.mif is the input image, wmr.txt is an anisotropic, multi-shell
+    response function for WM, and csfr.txt and gmr.txt are isotropic response
+    functions for CSF and GM. The output tractogram is saved to tracks.tck.
+    Optional output images fod.mif and fiso.mif contain the predicted WM fODF
+    and isotropic tissue fractions of CSF and GM respectively, estimated as part
+    of the global optimization and thus affected by spatial regularization.
+    
+    References:
+    
+    Christiaens, D.; Reisert, M.; Dhollander, T.; Sunaert, S.; Suetens, P. &
+    Maes, F. Global tractography of multi-shell diffusion-weighted imaging data
+    using a multi-tissue model. NeuroImage, 2015, 123, 89-101.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        source: the image containing the raw DWI data.
+        response: the response of a track segment on the DWI signal.
+        tracks: the output file containing the tracks generated.
+        grad: specify the diffusion encoding scheme (required if not supplied\
+            in the header).
+        mask: only reconstruct the tractogram within the specified brain mask\
+            image.
+        riso: set one or more isotropic response functions. (multiple allowed).
+        lmax: set the maximum harmonic order for the output series. (default =\
+            8).
+        length: set the length of the particles (fibre segments). (default =\
+            1mm).
+        weight: set the weight by which particles contribute to the model.\
+            (default = 0.1).
+        ppot: set the particle potential, i.e., the cost of adding one segment,\
+            relative to the particle weight. (default = 0.05).
+        cpot: set the connection potential, i.e., the energy term that drives\
+            two segments together. (default = 0.5).
+        t0: set the initial temperature of the metropolis hastings optimizer.\
+            (default = 0.1).
+        t1: set the final temperature of the metropolis hastings optimizer.\
+            (default = 0.001).
+        niter: set the number of iterations of the metropolis hastings\
+            optimizer. (default = 10M).
+        fod: Predicted fibre orientation distribution function (fODF).\
+            This fODF is estimated as part of the global track optimization,\
+            and therefore incorporates the spatial regularization that it\
+            imposes. Internally, the fODF is represented as a discrete sum of\
+            apodized point spread functions (aPSF) oriented along the\
+            directions of all particles in the voxel, used to predict the DWI\
+            signal from the particle configuration.
+        noapo: disable spherical convolution of fODF with apodized PSF, to\
+            output a sum of delta functions rather than a sum of aPSFs.
+        fiso: Predicted isotropic fractions of the tissues for which response\
+            functions were provided with -riso. Typically, these are CSF and GM.
+        eext: Residual external energy in every voxel.
+        etrend: internal and external energy trend and cooling statistics.
+        balance: balance internal and external energy. (default = 0)\
+            Negative values give more weight to the internal energy, positive\
+            to the external energy.
+        density: set the desired density of the free Poisson process. (default\
+            = 1).
+        prob: set the probabilities of generating birth, death, randshift,\
+            optshift and connect proposals respectively. (default =\
+            0.25,0.05,0.25,0.1,0.35).
+        beta: set the width of the Hanning interpolation window. (in [0, 1],\
+            default = 0)\
+            If used, a mask is required, and this mask must keep at least one\
+            voxel distance to the image bounding box.
+        lambda_: set the weight of the internal energy directly. (default = 1)\
+            If provided, any value of -balance will be ignored.
+        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 `TckglobalOutputs`).
+    """
+    params = tckglobal_params(
+        grad=grad,
+        mask=mask,
+        riso=riso,
+        lmax=lmax,
+        length=length,
+        weight=weight,
+        ppot=ppot,
+        cpot=cpot,
+        t0=t0,
+        t1=t1,
+        niter=niter,
+        fod=fod,
+        noapo=noapo,
+        fiso=fiso,
+        eext=eext,
+        etrend=etrend,
+        balance=balance,
+        density=density,
+        prob=prob,
+        beta=beta,
+        lambda_=lambda_,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        source=source,
+        response=response,
+        tracks=tracks,
+    )
+    return tckglobal_execute(params, runner)
+
+
+__all__ = [
+    "TCKGLOBAL_METADATA",
+    "TckglobalConfigParamsDict",
+    "TckglobalConfigParamsDictTagged",
+    "TckglobalOutputs",
+    "TckglobalParamsDict",
+    "TckglobalParamsDictTagged",
+    "TckglobalRisoParamsDict",
+    "TckglobalRisoParamsDictTagged",
+    "tckglobal",
+    "tckglobal_config",
+    "tckglobal_execute",
+    "tckglobal_params",
+    "tckglobal_riso",
+]