niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/connectomestats.py

@@ -0,0 +1,956 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CONNECTOMESTATS_METADATA = Metadata(
+    id="607b512a43f94c7e5deeb72046391536e66cc167.boutiques",
+    name="connectomestats",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_ConnectomestatsColumnParamsDictNoTag = typing.TypedDict('_ConnectomestatsColumnParamsDictNoTag', {
+    "path": InputPathType,
+})
+ConnectomestatsColumnParamsDictTagged = typing.TypedDict('ConnectomestatsColumnParamsDictTagged', {
+    "@type": typing.Literal["column"],
+    "path": InputPathType,
+})
+ConnectomestatsColumnParamsDict = _ConnectomestatsColumnParamsDictNoTag | ConnectomestatsColumnParamsDictTagged
+
+
+_ConnectomestatsConfigParamsDictNoTag = typing.TypedDict('_ConnectomestatsConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+ConnectomestatsConfigParamsDictTagged = typing.TypedDict('ConnectomestatsConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+ConnectomestatsConfigParamsDict = _ConnectomestatsConfigParamsDictNoTag | ConnectomestatsConfigParamsDictTagged
+
+
+_ConnectomestatsParamsDictNoTag = typing.TypedDict('_ConnectomestatsParamsDictNoTag', {
+    "notest": bool,
+    "errors": typing.NotRequired[str | None],
+    "exchange_within": typing.NotRequired[InputPathType | None],
+    "exchange_whole": typing.NotRequired[InputPathType | None],
+    "strong": bool,
+    "nshuffles": typing.NotRequired[int | None],
+    "permutations": typing.NotRequired[InputPathType | None],
+    "nonstationarity": bool,
+    "skew_nonstationarity": typing.NotRequired[float | None],
+    "nshuffles_nonstationarity": typing.NotRequired[int | None],
+    "permutations_nonstationarity": typing.NotRequired[InputPathType | None],
+    "tfce_dh": typing.NotRequired[float | None],
+    "tfce_e": typing.NotRequired[float | None],
+    "tfce_h": typing.NotRequired[float | None],
+    "variance": typing.NotRequired[InputPathType | None],
+    "ftests": typing.NotRequired[InputPathType | None],
+    "fonly": bool,
+    "column": typing.NotRequired[list[ConnectomestatsColumnParamsDict] | None],
+    "threshold": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ConnectomestatsConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "algorithm": str,
+    "design": InputPathType,
+    "contrast": InputPathType,
+    "output": str,
+})
+ConnectomestatsParamsDictTagged = typing.TypedDict('ConnectomestatsParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/connectomestats"],
+    "notest": bool,
+    "errors": typing.NotRequired[str | None],
+    "exchange_within": typing.NotRequired[InputPathType | None],
+    "exchange_whole": typing.NotRequired[InputPathType | None],
+    "strong": bool,
+    "nshuffles": typing.NotRequired[int | None],
+    "permutations": typing.NotRequired[InputPathType | None],
+    "nonstationarity": bool,
+    "skew_nonstationarity": typing.NotRequired[float | None],
+    "nshuffles_nonstationarity": typing.NotRequired[int | None],
+    "permutations_nonstationarity": typing.NotRequired[InputPathType | None],
+    "tfce_dh": typing.NotRequired[float | None],
+    "tfce_e": typing.NotRequired[float | None],
+    "tfce_h": typing.NotRequired[float | None],
+    "variance": typing.NotRequired[InputPathType | None],
+    "ftests": typing.NotRequired[InputPathType | None],
+    "fonly": bool,
+    "column": typing.NotRequired[list[ConnectomestatsColumnParamsDict] | None],
+    "threshold": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ConnectomestatsConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "algorithm": str,
+    "design": InputPathType,
+    "contrast": InputPathType,
+    "output": str,
+})
+ConnectomestatsParamsDict = _ConnectomestatsParamsDictNoTag | ConnectomestatsParamsDictTagged
+
+
+def connectomestats_column(
+    path: InputPathType,
+) -> ConnectomestatsColumnParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        path: add a column to the design matrix corresponding to subject\
+            edge-wise values (note that the contrast matrix must include an\
+            additional column for each use of this option); the text file provided\
+            via this option should contain a file name for each subject.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "column",
+        "path": path,
+    }
+    return params
+
+
+def connectomestats_column_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ConnectomestatsColumnParamsDict` 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("path", None) is None:
+        raise StyxValidationError("`path` must not be None")
+    if not isinstance(params["path"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`path` has the wrong type: Received `{type(params.get("path", None))}` expected `InputPathType`')
+
+
+def connectomestats_column_cargs(
+    params: ConnectomestatsColumnParamsDict,
+    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("-column")
+    cargs.append(execution.input_file(params.get("path", None)))
+    return cargs
+
+
+def connectomestats_config(
+    key: str,
+    value: str,
+) -> ConnectomestatsConfigParamsDictTagged:
+    """
+    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 connectomestats_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ConnectomestatsConfigParamsDict` 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 connectomestats_config_cargs(
+    params: ConnectomestatsConfigParamsDict,
+    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 ConnectomestatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `ConnectomestatsParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def connectomestats_params(
+    input_: InputPathType,
+    algorithm: str,
+    design: InputPathType,
+    contrast: InputPathType,
+    output: str,
+    notest: bool = False,
+    errors: str | None = None,
+    exchange_within: InputPathType | None = None,
+    exchange_whole: InputPathType | None = None,
+    strong: bool = False,
+    nshuffles: int | None = None,
+    permutations: InputPathType | None = None,
+    nonstationarity: bool = False,
+    skew_nonstationarity: float | None = None,
+    nshuffles_nonstationarity: int | None = None,
+    permutations_nonstationarity: InputPathType | None = None,
+    tfce_dh: float | None = None,
+    tfce_e: float | None = None,
+    tfce_h: float | None = None,
+    variance: InputPathType | None = None,
+    ftests: InputPathType | None = None,
+    fonly: bool = False,
+    column: list[ConnectomestatsColumnParamsDict] | None = None,
+    threshold: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[ConnectomestatsConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> ConnectomestatsParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: a text file listing the file names of the input connectomes.
+        algorithm: the algorithm to use in network-based\
+            clustering/enhancement. Options are: nbs, tfnbs, none.
+        design: the design matrix.
+        contrast: the contrast matrix.
+        output: the filename prefix for all output.
+        notest: don't perform statistical inference; only output population\
+            statistics (effect size, stdev etc).
+        errors: specify nature of errors for shuffling; options are:\
+            ee,ise,both (default: ee).
+        exchange_within: specify blocks of observations within each of which\
+            data may undergo restricted exchange.
+        exchange_whole: specify blocks of observations that may be exchanged\
+            with one another (for independent and symmetric errors, sign-flipping\
+            will occur block-wise).
+        strong: use strong familywise error control across multiple hypotheses.
+        nshuffles: the number of shuffles (default: 5000).
+        permutations: manually define the permutations (relabelling). The input\
+            should be a text file defining a m x n matrix, where each relabelling\
+            is defined as a column vector of size m, and the number of columns, n,\
+            defines the number of permutations. Can be generated with the\
+            palm_quickperms function in PALM\
+            (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM). Overrides the -nshuffles\
+            option.
+        nonstationarity: perform non-stationarity correction.
+        skew_nonstationarity: specify the skew parameter for empirical\
+            statistic calculation (default for this command is 1).
+        nshuffles_nonstationarity: the number of shuffles to use when\
+            precomputing the empirical statistic image for non-stationarity\
+            correction (default: 5000).
+        permutations_nonstationarity: manually define the permutations\
+            (relabelling) for computing the emprical statistics for\
+            non-stationarity correction. The input should be a text file defining a\
+            m x n matrix, where each relabelling is defined as a column vector of\
+            size m, and the number of columns, n, defines the number of\
+            permutations. Can be generated with the palm_quickperms function in\
+            PALM (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM) Overrides the\
+            -nshuffles_nonstationarity option.
+        tfce_dh: the height increment used in the tfce integration (default:\
+            0.1).
+        tfce_e: tfce extent exponent (default: 0.4).
+        tfce_h: tfce height exponent (default: 3).
+        variance: define variance groups for the G-statistic; measurements for\
+            which the expected variance is equivalent should contain the same index.
+        ftests: perform F-tests; input text file should contain, for each\
+            F-test, a row containing ones and zeros, where ones indicate the rows\
+            of the contrast matrix to be included in the F-test.
+        fonly: only assess F-tests; do not perform statistical inference on\
+            entries in the contrast matrix.
+        column: add a column to the design matrix corresponding to subject\
+            edge-wise values (note that the contrast matrix must include an\
+            additional column for each use of this option); the text file provided\
+            via this option should contain a file name for each subject.
+        threshold: the t-statistic value to use in threshold-based clustering\
+            algorithms.
+        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/connectomestats",
+        "notest": notest,
+        "strong": strong,
+        "nonstationarity": nonstationarity,
+        "fonly": fonly,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "algorithm": algorithm,
+        "design": design,
+        "contrast": contrast,
+        "output": output,
+    }
+    if errors is not None:
+        params["errors"] = errors
+    if exchange_within is not None:
+        params["exchange_within"] = exchange_within
+    if exchange_whole is not None:
+        params["exchange_whole"] = exchange_whole
+    if nshuffles is not None:
+        params["nshuffles"] = nshuffles
+    if permutations is not None:
+        params["permutations"] = permutations
+    if skew_nonstationarity is not None:
+        params["skew_nonstationarity"] = skew_nonstationarity
+    if nshuffles_nonstationarity is not None:
+        params["nshuffles_nonstationarity"] = nshuffles_nonstationarity
+    if permutations_nonstationarity is not None:
+        params["permutations_nonstationarity"] = permutations_nonstationarity
+    if tfce_dh is not None:
+        params["tfce_dh"] = tfce_dh
+    if tfce_e is not None:
+        params["tfce_e"] = tfce_e
+    if tfce_h is not None:
+        params["tfce_h"] = tfce_h
+    if variance is not None:
+        params["variance"] = variance
+    if ftests is not None:
+        params["ftests"] = ftests
+    if column is not None:
+        params["column"] = column
+    if threshold is not None:
+        params["threshold"] = threshold
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def connectomestats_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ConnectomestatsParamsDict` 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("notest", False) is None:
+        raise StyxValidationError("`notest` must not be None")
+    if not isinstance(params["notest"], bool):
+        raise StyxValidationError(f'`notest` has the wrong type: Received `{type(params.get("notest", False))}` expected `bool`')
+    if params.get("errors", None) is not None:
+        if not isinstance(params["errors"], str):
+            raise StyxValidationError(f'`errors` has the wrong type: Received `{type(params.get("errors", None))}` expected `str | None`')
+    if params.get("exchange_within", None) is not None:
+        if not isinstance(params["exchange_within"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`exchange_within` has the wrong type: Received `{type(params.get("exchange_within", None))}` expected `InputPathType | None`')
+    if params.get("exchange_whole", None) is not None:
+        if not isinstance(params["exchange_whole"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`exchange_whole` has the wrong type: Received `{type(params.get("exchange_whole", None))}` expected `InputPathType | None`')
+    if params.get("strong", False) is None:
+        raise StyxValidationError("`strong` must not be None")
+    if not isinstance(params["strong"], bool):
+        raise StyxValidationError(f'`strong` has the wrong type: Received `{type(params.get("strong", False))}` expected `bool`')
+    if params.get("nshuffles", None) is not None:
+        if not isinstance(params["nshuffles"], int):
+            raise StyxValidationError(f'`nshuffles` has the wrong type: Received `{type(params.get("nshuffles", None))}` expected `int | None`')
+    if params.get("permutations", None) is not None:
+        if not isinstance(params["permutations"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`permutations` has the wrong type: Received `{type(params.get("permutations", None))}` expected `InputPathType | None`')
+    if params.get("nonstationarity", False) is None:
+        raise StyxValidationError("`nonstationarity` must not be None")
+    if not isinstance(params["nonstationarity"], bool):
+        raise StyxValidationError(f'`nonstationarity` has the wrong type: Received `{type(params.get("nonstationarity", False))}` expected `bool`')
+    if params.get("skew_nonstationarity", None) is not None:
+        if not isinstance(params["skew_nonstationarity"], (float, int)):
+            raise StyxValidationError(f'`skew_nonstationarity` has the wrong type: Received `{type(params.get("skew_nonstationarity", None))}` expected `float | None`')
+    if params.get("nshuffles_nonstationarity", None) is not None:
+        if not isinstance(params["nshuffles_nonstationarity"], int):
+            raise StyxValidationError(f'`nshuffles_nonstationarity` has the wrong type: Received `{type(params.get("nshuffles_nonstationarity", None))}` expected `int | None`')
+    if params.get("permutations_nonstationarity", None) is not None:
+        if not isinstance(params["permutations_nonstationarity"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`permutations_nonstationarity` has the wrong type: Received `{type(params.get("permutations_nonstationarity", None))}` expected `InputPathType | None`')
+    if params.get("tfce_dh", None) is not None:
+        if not isinstance(params["tfce_dh"], (float, int)):
+            raise StyxValidationError(f'`tfce_dh` has the wrong type: Received `{type(params.get("tfce_dh", None))}` expected `float | None`')
+    if params.get("tfce_e", None) is not None:
+        if not isinstance(params["tfce_e"], (float, int)):
+            raise StyxValidationError(f'`tfce_e` has the wrong type: Received `{type(params.get("tfce_e", None))}` expected `float | None`')
+    if params.get("tfce_h", None) is not None:
+        if not isinstance(params["tfce_h"], (float, int)):
+            raise StyxValidationError(f'`tfce_h` has the wrong type: Received `{type(params.get("tfce_h", None))}` expected `float | None`')
+    if params.get("variance", None) is not None:
+        if not isinstance(params["variance"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`variance` has the wrong type: Received `{type(params.get("variance", None))}` expected `InputPathType | None`')
+    if params.get("ftests", None) is not None:
+        if not isinstance(params["ftests"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`ftests` has the wrong type: Received `{type(params.get("ftests", None))}` expected `InputPathType | None`')
+    if params.get("fonly", False) is None:
+        raise StyxValidationError("`fonly` must not be None")
+    if not isinstance(params["fonly"], bool):
+        raise StyxValidationError(f'`fonly` has the wrong type: Received `{type(params.get("fonly", False))}` expected `bool`')
+    if params.get("column", None) is not None:
+        if not isinstance(params["column"], list):
+            raise StyxValidationError(f'`column` has the wrong type: Received `{type(params.get("column", None))}` expected `list[ConnectomestatsColumnParamsDict] | None`')
+        for e in params["column"]:
+            connectomestats_column_validate(e)
+    if params.get("threshold", None) is not None:
+        if not isinstance(params["threshold"], (float, int)):
+            raise StyxValidationError(f'`threshold` has the wrong type: Received `{type(params.get("threshold", 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[ConnectomestatsConfigParamsDict] | None`')
+        for e in params["config"]:
+            connectomestats_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("input", None) is None:
+        raise StyxValidationError("`input` must not be None")
+    if not isinstance(params["input"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `InputPathType`')
+    if params.get("algorithm", None) is None:
+        raise StyxValidationError("`algorithm` must not be None")
+    if not isinstance(params["algorithm"], str):
+        raise StyxValidationError(f'`algorithm` has the wrong type: Received `{type(params.get("algorithm", None))}` expected `str`')
+    if params.get("design", None) is None:
+        raise StyxValidationError("`design` must not be None")
+    if not isinstance(params["design"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`design` has the wrong type: Received `{type(params.get("design", None))}` expected `InputPathType`')
+    if params.get("contrast", None) is None:
+        raise StyxValidationError("`contrast` must not be None")
+    if not isinstance(params["contrast"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`contrast` has the wrong type: Received `{type(params.get("contrast", None))}` expected `InputPathType`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], str):
+        raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str`')
+
+
+def connectomestats_cargs(
+    params: ConnectomestatsParamsDict,
+    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("connectomestats")
+    if params.get("notest", False):
+        cargs.append("-notest")
+    if params.get("errors", None) is not None:
+        cargs.extend([
+            "-errors",
+            params.get("errors", None)
+        ])
+    if params.get("exchange_within", None) is not None:
+        cargs.extend([
+            "-exchange_within",
+            execution.input_file(params.get("exchange_within", None))
+        ])
+    if params.get("exchange_whole", None) is not None:
+        cargs.extend([
+            "-exchange_whole",
+            execution.input_file(params.get("exchange_whole", None))
+        ])
+    if params.get("strong", False):
+        cargs.append("-strong")
+    if params.get("nshuffles", None) is not None:
+        cargs.extend([
+            "-nshuffles",
+            str(params.get("nshuffles", None))
+        ])
+    if params.get("permutations", None) is not None:
+        cargs.extend([
+            "-permutations",
+            execution.input_file(params.get("permutations", None))
+        ])
+    if params.get("nonstationarity", False):
+        cargs.append("-nonstationarity")
+    if params.get("skew_nonstationarity", None) is not None:
+        cargs.extend([
+            "-skew_nonstationarity",
+            str(params.get("skew_nonstationarity", None))
+        ])
+    if params.get("nshuffles_nonstationarity", None) is not None:
+        cargs.extend([
+            "-nshuffles_nonstationarity",
+            str(params.get("nshuffles_nonstationarity", None))
+        ])
+    if params.get("permutations_nonstationarity", None) is not None:
+        cargs.extend([
+            "-permutations_nonstationarity",
+            execution.input_file(params.get("permutations_nonstationarity", None))
+        ])
+    if params.get("tfce_dh", None) is not None:
+        cargs.extend([
+            "-tfce_dh",
+            str(params.get("tfce_dh", None))
+        ])
+    if params.get("tfce_e", None) is not None:
+        cargs.extend([
+            "-tfce_e",
+            str(params.get("tfce_e", None))
+        ])
+    if params.get("tfce_h", None) is not None:
+        cargs.extend([
+            "-tfce_h",
+            str(params.get("tfce_h", None))
+        ])
+    if params.get("variance", None) is not None:
+        cargs.extend([
+            "-variance",
+            execution.input_file(params.get("variance", None))
+        ])
+    if params.get("ftests", None) is not None:
+        cargs.extend([
+            "-ftests",
+            execution.input_file(params.get("ftests", None))
+        ])
+    if params.get("fonly", False):
+        cargs.append("-fonly")
+    if params.get("column", None) is not None:
+        cargs.extend([a for c in [connectomestats_column_cargs(s, execution) for s in params.get("column", None)] for a in c])
+    if params.get("threshold", None) is not None:
+        cargs.extend([
+            "-threshold",
+            str(params.get("threshold", 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 [connectomestats_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("input", None)))
+    cargs.append(params.get("algorithm", None))
+    cargs.append(execution.input_file(params.get("design", None)))
+    cargs.append(execution.input_file(params.get("contrast", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def connectomestats_outputs(
+    params: ConnectomestatsParamsDict,
+    execution: Execution,
+) -> ConnectomestatsOutputs:
+    """
+    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 = ConnectomestatsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def connectomestats_execute(
+    params: ConnectomestatsParamsDict,
+    runner: Runner | None = None,
+) -> ConnectomestatsOutputs:
+    """
+    connectomestats
+    
+    Connectome group-wise statistics at the edge level using non-parametric
+    permutation testing.
+    
+    For the TFNBS algorithm, default parameters for statistical enhancement have
+    been set based on the work in:
+    Vinokur, L.; Zalesky, A.; Raffelt, D.; Smith, R.E. & Connelly, A. A Novel
+    Threshold-Free Network-Based Statistics Method: Demonstration using
+    Simulated Pathology. OHBM, 2015, 4144;
+    and:
+    Vinokur, L.; Zalesky, A.; Raffelt, D.; Smith, R.E. & Connelly, A. A novel
+    threshold-free network-based statistical method: Demonstration and parameter
+    optimisation using in vivo simulated pathology. In Proc ISMRM, 2015, 2846.
+    Note however that not only was the optimisation of these parameters not very
+    precise, but the outcomes of statistical inference (for both this algorithm
+    and the NBS method) can vary markedly for even small changes to enhancement
+    parameters. Therefore the specificity of results obtained using either of
+    these methods should be interpreted with caution.
+    
+    In some software packages, a column of ones is automatically added to the
+    GLM design matrix; the purpose of this column is to estimate the "global
+    intercept", which is the predicted value of the observed variable if all
+    explanatory variables were to be zero. However there are rare situations
+    where including such a column would not be appropriate for a particular
+    experimental design. Hence, in MRtrix3 statistical inference commands, it is
+    up to the user to determine whether or not this column of ones should be
+    included in their design matrix, and add it explicitly if necessary. The
+    contrast matrix must also reflect the presence of this additional column.
+    
+    References:
+    
+    * If using the NBS algorithm:
+    Zalesky, A.; Fornito, A. & Bullmore, E. T. Network-based statistic:
+    Identifying differences in brain networks.
+    NeuroImage, 2010, 53, 1197-1207
+    
+    * If using the TFNBS algorithm:
+    Baggio, H.C.; Abos, A.; Segura, B.; Campabadal, A.; Garcia-Diaz, A.; Uribe,
+    C.; Compta, Y.; Marti, M.J.; Valldeoriola, F.; Junque, C. Statistical
+    inference in brain graphs using threshold-free network-based statistics.HBM,
+    2018, 39, 2289-2302
+    
+    * If using the -nonstationary option:
+    Salimi-Khorshidi, G.; Smith, S.M. & Nichols, T.E. Adjusting the effect of
+    nonstationarity in cluster-based and TFCE inference.
+    Neuroimage, 2011, 54(3), 2006-19.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ConnectomestatsOutputs`).
+    """
+    connectomestats_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONNECTOMESTATS_METADATA)
+    params = execution.params(params)
+    cargs = connectomestats_cargs(params, execution)
+    ret = connectomestats_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def connectomestats(
+    input_: InputPathType,
+    algorithm: str,
+    design: InputPathType,
+    contrast: InputPathType,
+    output: str,
+    notest: bool = False,
+    errors: str | None = None,
+    exchange_within: InputPathType | None = None,
+    exchange_whole: InputPathType | None = None,
+    strong: bool = False,
+    nshuffles: int | None = None,
+    permutations: InputPathType | None = None,
+    nonstationarity: bool = False,
+    skew_nonstationarity: float | None = None,
+    nshuffles_nonstationarity: int | None = None,
+    permutations_nonstationarity: InputPathType | None = None,
+    tfce_dh: float | None = None,
+    tfce_e: float | None = None,
+    tfce_h: float | None = None,
+    variance: InputPathType | None = None,
+    ftests: InputPathType | None = None,
+    fonly: bool = False,
+    column: list[ConnectomestatsColumnParamsDict] | None = None,
+    threshold: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[ConnectomestatsConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> ConnectomestatsOutputs:
+    """
+    connectomestats
+    
+    Connectome group-wise statistics at the edge level using non-parametric
+    permutation testing.
+    
+    For the TFNBS algorithm, default parameters for statistical enhancement have
+    been set based on the work in:
+    Vinokur, L.; Zalesky, A.; Raffelt, D.; Smith, R.E. & Connelly, A. A Novel
+    Threshold-Free Network-Based Statistics Method: Demonstration using
+    Simulated Pathology. OHBM, 2015, 4144;
+    and:
+    Vinokur, L.; Zalesky, A.; Raffelt, D.; Smith, R.E. & Connelly, A. A novel
+    threshold-free network-based statistical method: Demonstration and parameter
+    optimisation using in vivo simulated pathology. In Proc ISMRM, 2015, 2846.
+    Note however that not only was the optimisation of these parameters not very
+    precise, but the outcomes of statistical inference (for both this algorithm
+    and the NBS method) can vary markedly for even small changes to enhancement
+    parameters. Therefore the specificity of results obtained using either of
+    these methods should be interpreted with caution.
+    
+    In some software packages, a column of ones is automatically added to the
+    GLM design matrix; the purpose of this column is to estimate the "global
+    intercept", which is the predicted value of the observed variable if all
+    explanatory variables were to be zero. However there are rare situations
+    where including such a column would not be appropriate for a particular
+    experimental design. Hence, in MRtrix3 statistical inference commands, it is
+    up to the user to determine whether or not this column of ones should be
+    included in their design matrix, and add it explicitly if necessary. The
+    contrast matrix must also reflect the presence of this additional column.
+    
+    References:
+    
+    * If using the NBS algorithm:
+    Zalesky, A.; Fornito, A. & Bullmore, E. T. Network-based statistic:
+    Identifying differences in brain networks.
+    NeuroImage, 2010, 53, 1197-1207
+    
+    * If using the TFNBS algorithm:
+    Baggio, H.C.; Abos, A.; Segura, B.; Campabadal, A.; Garcia-Diaz, A.; Uribe,
+    C.; Compta, Y.; Marti, M.J.; Valldeoriola, F.; Junque, C. Statistical
+    inference in brain graphs using threshold-free network-based statistics.HBM,
+    2018, 39, 2289-2302
+    
+    * If using the -nonstationary option:
+    Salimi-Khorshidi, G.; Smith, S.M. & Nichols, T.E. Adjusting the effect of
+    nonstationarity in cluster-based and TFCE inference.
+    Neuroimage, 2011, 54(3), 2006-19.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: a text file listing the file names of the input connectomes.
+        algorithm: the algorithm to use in network-based\
+            clustering/enhancement. Options are: nbs, tfnbs, none.
+        design: the design matrix.
+        contrast: the contrast matrix.
+        output: the filename prefix for all output.
+        notest: don't perform statistical inference; only output population\
+            statistics (effect size, stdev etc).
+        errors: specify nature of errors for shuffling; options are:\
+            ee,ise,both (default: ee).
+        exchange_within: specify blocks of observations within each of which\
+            data may undergo restricted exchange.
+        exchange_whole: specify blocks of observations that may be exchanged\
+            with one another (for independent and symmetric errors, sign-flipping\
+            will occur block-wise).
+        strong: use strong familywise error control across multiple hypotheses.
+        nshuffles: the number of shuffles (default: 5000).
+        permutations: manually define the permutations (relabelling). The input\
+            should be a text file defining a m x n matrix, where each relabelling\
+            is defined as a column vector of size m, and the number of columns, n,\
+            defines the number of permutations. Can be generated with the\
+            palm_quickperms function in PALM\
+            (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM). Overrides the -nshuffles\
+            option.
+        nonstationarity: perform non-stationarity correction.
+        skew_nonstationarity: specify the skew parameter for empirical\
+            statistic calculation (default for this command is 1).
+        nshuffles_nonstationarity: the number of shuffles to use when\
+            precomputing the empirical statistic image for non-stationarity\
+            correction (default: 5000).
+        permutations_nonstationarity: manually define the permutations\
+            (relabelling) for computing the emprical statistics for\
+            non-stationarity correction. The input should be a text file defining a\
+            m x n matrix, where each relabelling is defined as a column vector of\
+            size m, and the number of columns, n, defines the number of\
+            permutations. Can be generated with the palm_quickperms function in\
+            PALM (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM) Overrides the\
+            -nshuffles_nonstationarity option.
+        tfce_dh: the height increment used in the tfce integration (default:\
+            0.1).
+        tfce_e: tfce extent exponent (default: 0.4).
+        tfce_h: tfce height exponent (default: 3).
+        variance: define variance groups for the G-statistic; measurements for\
+            which the expected variance is equivalent should contain the same index.
+        ftests: perform F-tests; input text file should contain, for each\
+            F-test, a row containing ones and zeros, where ones indicate the rows\
+            of the contrast matrix to be included in the F-test.
+        fonly: only assess F-tests; do not perform statistical inference on\
+            entries in the contrast matrix.
+        column: add a column to the design matrix corresponding to subject\
+            edge-wise values (note that the contrast matrix must include an\
+            additional column for each use of this option); the text file provided\
+            via this option should contain a file name for each subject.
+        threshold: the t-statistic value to use in threshold-based clustering\
+            algorithms.
+        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 `ConnectomestatsOutputs`).
+    """
+    params = connectomestats_params(
+        notest=notest,
+        errors=errors,
+        exchange_within=exchange_within,
+        exchange_whole=exchange_whole,
+        strong=strong,
+        nshuffles=nshuffles,
+        permutations=permutations,
+        nonstationarity=nonstationarity,
+        skew_nonstationarity=skew_nonstationarity,
+        nshuffles_nonstationarity=nshuffles_nonstationarity,
+        permutations_nonstationarity=permutations_nonstationarity,
+        tfce_dh=tfce_dh,
+        tfce_e=tfce_e,
+        tfce_h=tfce_h,
+        variance=variance,
+        ftests=ftests,
+        fonly=fonly,
+        column=column,
+        threshold=threshold,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        algorithm=algorithm,
+        design=design,
+        contrast=contrast,
+        output=output,
+    )
+    return connectomestats_execute(params, runner)
+
+
+__all__ = [
+    "CONNECTOMESTATS_METADATA",
+    "ConnectomestatsColumnParamsDict",
+    "ConnectomestatsColumnParamsDictTagged",
+    "ConnectomestatsConfigParamsDict",
+    "ConnectomestatsConfigParamsDictTagged",
+    "ConnectomestatsOutputs",
+    "ConnectomestatsParamsDict",
+    "ConnectomestatsParamsDictTagged",
+    "connectomestats",
+    "connectomestats_column",
+    "connectomestats_config",
+    "connectomestats_execute",
+    "connectomestats_params",
+]