niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixelcfestats.py

@@ -0,0 +1,893 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELCFESTATS_METADATA = Metadata(
+    id="85b1cb9bb9525faf62a80ea0820d52c7ae94777f.boutiques",
+    name="fixelcfestats",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+FixelcfestatsColumnParameters = typing.TypedDict('FixelcfestatsColumnParameters', {
+    "__STYX_TYPE__": typing.Literal["column"],
+    "path": InputPathType,
+})
+
+
+FixelcfestatsConfigParameters = typing.TypedDict('FixelcfestatsConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+FixelcfestatsVariousStringParameters = typing.TypedDict('FixelcfestatsVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+FixelcfestatsVariousFileParameters = typing.TypedDict('FixelcfestatsVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+FixelcfestatsParameters = typing.TypedDict('FixelcfestatsParameters', {
+    "__STYX_TYPE__": typing.Literal["fixelcfestats"],
+    "mask": typing.NotRequired[InputPathType | None],
+    "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],
+    "cfe_dh": typing.NotRequired[float | None],
+    "cfe_e": typing.NotRequired[float | None],
+    "cfe_h": typing.NotRequired[float | None],
+    "cfe_c": typing.NotRequired[float | None],
+    "cfe_legacy": bool,
+    "variance": typing.NotRequired[InputPathType | None],
+    "ftests": typing.NotRequired[InputPathType | None],
+    "fonly": bool,
+    "column": typing.NotRequired[list[FixelcfestatsColumnParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelcfestatsConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in_fixel_directory": InputPathType,
+    "subjects": InputPathType,
+    "design": InputPathType,
+    "contrast": InputPathType,
+    "connectivity": typing.Union[FixelcfestatsVariousStringParameters, FixelcfestatsVariousFileParameters],
+    "out_fixel_directory": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fixelcfestats": fixelcfestats_cargs,
+        "column": fixelcfestats_column_cargs,
+        "config": fixelcfestats_config_cargs,
+        "VariousString": fixelcfestats_various_string_cargs,
+        "VariousFile": fixelcfestats_various_file_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+def fixelcfestats_column_params(
+    path: InputPathType,
+) -> FixelcfestatsColumnParameters:
+    """
+    Build parameters.
+    
+    Args:
+        path: add a column to the design matrix corresponding to subject\
+            fixel-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 = {
+        "__STYXTYPE__": "column",
+        "path": path,
+    }
+    return params
+
+
+def fixelcfestats_column_cargs(
+    params: FixelcfestatsColumnParameters,
+    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")))
+    return cargs
+
+
+def fixelcfestats_config_params(
+    key: str,
+    value: str,
+) -> FixelcfestatsConfigParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def fixelcfestats_config_cargs(
+    params: FixelcfestatsConfigParameters,
+    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"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+def fixelcfestats_various_string_params(
+    obj: str,
+) -> FixelcfestatsVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelcfestats_various_string_cargs(
+    params: FixelcfestatsVariousStringParameters,
+    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(params.get("obj"))
+    return cargs
+
+
+def fixelcfestats_various_file_params(
+    obj: InputPathType,
+) -> FixelcfestatsVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelcfestats_various_file_cargs(
+    params: FixelcfestatsVariousFileParameters,
+    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(execution.input_file(params.get("obj")))
+    return cargs
+
+
+class FixelcfestatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fixelcfestats(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def fixelcfestats_params(
+    in_fixel_directory: InputPathType,
+    subjects: InputPathType,
+    design: InputPathType,
+    contrast: InputPathType,
+    connectivity: typing.Union[FixelcfestatsVariousStringParameters, FixelcfestatsVariousFileParameters],
+    out_fixel_directory: str,
+    mask: InputPathType | None = None,
+    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,
+    cfe_dh: float | None = None,
+    cfe_e: float | None = None,
+    cfe_h: float | None = None,
+    cfe_c: float | None = None,
+    cfe_legacy: bool = False,
+    variance: InputPathType | None = None,
+    ftests: InputPathType | None = None,
+    fonly: bool = False,
+    column: list[FixelcfestatsColumnParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelcfestatsConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelcfestatsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_fixel_directory: the fixel directory containing the data files for\
+            each subject (after obtaining fixel correspondence.
+        subjects: a text file listing the subject identifiers (one per line).\
+            This should correspond with the filenames in the fixel directory\
+            (including the file extension), and be listed in the same order as the\
+            rows of the design matrix.
+        design: the design matrix.
+        contrast: the contrast matrix, specified as rows of weights.
+        connectivity: the fixel-fixel connectivity matrix.
+        out_fixel_directory: the output directory where results will be saved.\
+            Will be created if it does not exist.
+        mask: provide a fixel data file containing a mask of those fixels to be\
+            used during processing.
+        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.
+        cfe_dh: the height increment used in the cfe integration (default: 0.1).
+        cfe_e: cfe extent exponent (default: 2).
+        cfe_h: cfe height exponent (default: 3).
+        cfe_c: cfe connectivity exponent (default: 0.5).
+        cfe_legacy: use the legacy (non-normalised) form of the cfe equation.
+        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\
+            fixel-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.
+        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 = {
+        "__STYXTYPE__": "fixelcfestats",
+        "notest": notest,
+        "strong": strong,
+        "nonstationarity": nonstationarity,
+        "cfe_legacy": cfe_legacy,
+        "fonly": fonly,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in_fixel_directory": in_fixel_directory,
+        "subjects": subjects,
+        "design": design,
+        "contrast": contrast,
+        "connectivity": connectivity,
+        "out_fixel_directory": out_fixel_directory,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    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 cfe_dh is not None:
+        params["cfe_dh"] = cfe_dh
+    if cfe_e is not None:
+        params["cfe_e"] = cfe_e
+    if cfe_h is not None:
+        params["cfe_h"] = cfe_h
+    if cfe_c is not None:
+        params["cfe_c"] = cfe_c
+    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 nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixelcfestats_cargs(
+    params: FixelcfestatsParameters,
+    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("fixelcfestats")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("notest"):
+        cargs.append("-notest")
+    if params.get("errors") is not None:
+        cargs.extend([
+            "-errors",
+            params.get("errors")
+        ])
+    if params.get("exchange_within") is not None:
+        cargs.extend([
+            "-exchange_within",
+            execution.input_file(params.get("exchange_within"))
+        ])
+    if params.get("exchange_whole") is not None:
+        cargs.extend([
+            "-exchange_whole",
+            execution.input_file(params.get("exchange_whole"))
+        ])
+    if params.get("strong"):
+        cargs.append("-strong")
+    if params.get("nshuffles") is not None:
+        cargs.extend([
+            "-nshuffles",
+            str(params.get("nshuffles"))
+        ])
+    if params.get("permutations") is not None:
+        cargs.extend([
+            "-permutations",
+            execution.input_file(params.get("permutations"))
+        ])
+    if params.get("nonstationarity"):
+        cargs.append("-nonstationarity")
+    if params.get("skew_nonstationarity") is not None:
+        cargs.extend([
+            "-skew_nonstationarity",
+            str(params.get("skew_nonstationarity"))
+        ])
+    if params.get("nshuffles_nonstationarity") is not None:
+        cargs.extend([
+            "-nshuffles_nonstationarity",
+            str(params.get("nshuffles_nonstationarity"))
+        ])
+    if params.get("permutations_nonstationarity") is not None:
+        cargs.extend([
+            "-permutations_nonstationarity",
+            execution.input_file(params.get("permutations_nonstationarity"))
+        ])
+    if params.get("cfe_dh") is not None:
+        cargs.extend([
+            "-cfe_dh",
+            str(params.get("cfe_dh"))
+        ])
+    if params.get("cfe_e") is not None:
+        cargs.extend([
+            "-cfe_e",
+            str(params.get("cfe_e"))
+        ])
+    if params.get("cfe_h") is not None:
+        cargs.extend([
+            "-cfe_h",
+            str(params.get("cfe_h"))
+        ])
+    if params.get("cfe_c") is not None:
+        cargs.extend([
+            "-cfe_c",
+            str(params.get("cfe_c"))
+        ])
+    if params.get("cfe_legacy"):
+        cargs.append("-cfe_legacy")
+    if params.get("variance") is not None:
+        cargs.extend([
+            "-variance",
+            execution.input_file(params.get("variance"))
+        ])
+    if params.get("ftests") is not None:
+        cargs.extend([
+            "-ftests",
+            execution.input_file(params.get("ftests"))
+        ])
+    if params.get("fonly"):
+        cargs.append("-fonly")
+    if params.get("column") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("column")] for a in c])
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("in_fixel_directory")))
+    cargs.append(execution.input_file(params.get("subjects")))
+    cargs.append(execution.input_file(params.get("design")))
+    cargs.append(execution.input_file(params.get("contrast")))
+    cargs.extend(dyn_cargs(params.get("connectivity")["__STYXTYPE__"])(params.get("connectivity"), execution))
+    cargs.append(params.get("out_fixel_directory"))
+    return cargs
+
+
+def fixelcfestats_outputs(
+    params: FixelcfestatsParameters,
+    execution: Execution,
+) -> FixelcfestatsOutputs:
+    """
+    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 = FixelcfestatsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def fixelcfestats_execute(
+    params: FixelcfestatsParameters,
+    execution: Execution,
+) -> FixelcfestatsOutputs:
+    """
+    Fixel-based analysis using connectivity-based fixel enhancement and
+    non-parametric permutation testing.
+    
+    Unlike previous versions of this command, where a whole-brain tractogram
+    file would be provided as input in order to generate the fixel-fixel
+    connectivity matrix and smooth fixel data, this version expects to be
+    provided with the directory path to a pre-calculated fixel-fixel
+    connectivity matrix (likely generated using the MRtrix3 command
+    fixelconnectivity), and for the input fixel data to have already been
+    smoothed (likely using the MRtrix3 command fixelfilter).
+    
+    Note that if the -mask option is used, the output fixel directory will still
+    contain the same set of fixels as that present in the input fixel template,
+    in order to retain fixel correspondence. However a consequence of this is
+    that all fixels in the template will be initialy visible when the output
+    fixel directory is loaded in mrview. Those fixels outside the processing
+    mask will immediately disappear from view as soon as any data-file-based
+    fixel colouring or thresholding is applied.
+    
+    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:
+    
+    Raffelt, D.; Smith, RE.; Ridgway, GR.; Tournier, JD.; Vaughan, DN.; Rose,
+    S.; Henderson, R.; Connelly, A. Connectivity-based fixel enhancement:
+    Whole-brain statistical analysis of diffusion MRI measures in the presence
+    of crossing fibres.Neuroimage, 2015, 15(117):40-55
+    
+    * If not using the -cfe_legacy option:
+    Smith, RE.; Dimond, D; Vaughan, D.; Parker, D.; Dhollander, T.; Jackson, G.;
+    Connelly, A. Intrinsic non-stationarity correction for Fixel-Based Analysis.
+    In Proc OHBM 2019 M789
+    
+    * 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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FixelcfestatsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fixelcfestats_cargs(params, execution)
+    ret = fixelcfestats_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelcfestats(
+    in_fixel_directory: InputPathType,
+    subjects: InputPathType,
+    design: InputPathType,
+    contrast: InputPathType,
+    connectivity: typing.Union[FixelcfestatsVariousStringParameters, FixelcfestatsVariousFileParameters],
+    out_fixel_directory: str,
+    mask: InputPathType | None = None,
+    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,
+    cfe_dh: float | None = None,
+    cfe_e: float | None = None,
+    cfe_h: float | None = None,
+    cfe_c: float | None = None,
+    cfe_legacy: bool = False,
+    variance: InputPathType | None = None,
+    ftests: InputPathType | None = None,
+    fonly: bool = False,
+    column: list[FixelcfestatsColumnParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelcfestatsConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelcfestatsOutputs:
+    """
+    Fixel-based analysis using connectivity-based fixel enhancement and
+    non-parametric permutation testing.
+    
+    Unlike previous versions of this command, where a whole-brain tractogram
+    file would be provided as input in order to generate the fixel-fixel
+    connectivity matrix and smooth fixel data, this version expects to be
+    provided with the directory path to a pre-calculated fixel-fixel
+    connectivity matrix (likely generated using the MRtrix3 command
+    fixelconnectivity), and for the input fixel data to have already been
+    smoothed (likely using the MRtrix3 command fixelfilter).
+    
+    Note that if the -mask option is used, the output fixel directory will still
+    contain the same set of fixels as that present in the input fixel template,
+    in order to retain fixel correspondence. However a consequence of this is
+    that all fixels in the template will be initialy visible when the output
+    fixel directory is loaded in mrview. Those fixels outside the processing
+    mask will immediately disappear from view as soon as any data-file-based
+    fixel colouring or thresholding is applied.
+    
+    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:
+    
+    Raffelt, D.; Smith, RE.; Ridgway, GR.; Tournier, JD.; Vaughan, DN.; Rose,
+    S.; Henderson, R.; Connelly, A. Connectivity-based fixel enhancement:
+    Whole-brain statistical analysis of diffusion MRI measures in the presence
+    of crossing fibres.Neuroimage, 2015, 15(117):40-55
+    
+    * If not using the -cfe_legacy option:
+    Smith, RE.; Dimond, D; Vaughan, D.; Parker, D.; Dhollander, T.; Jackson, G.;
+    Connelly, A. Intrinsic non-stationarity correction for Fixel-Based Analysis.
+    In Proc OHBM 2019 M789
+    
+    * 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:
+        in_fixel_directory: the fixel directory containing the data files for\
+            each subject (after obtaining fixel correspondence.
+        subjects: a text file listing the subject identifiers (one per line).\
+            This should correspond with the filenames in the fixel directory\
+            (including the file extension), and be listed in the same order as the\
+            rows of the design matrix.
+        design: the design matrix.
+        contrast: the contrast matrix, specified as rows of weights.
+        connectivity: the fixel-fixel connectivity matrix.
+        out_fixel_directory: the output directory where results will be saved.\
+            Will be created if it does not exist.
+        mask: provide a fixel data file containing a mask of those fixels to be\
+            used during processing.
+        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.
+        cfe_dh: the height increment used in the cfe integration (default: 0.1).
+        cfe_e: cfe extent exponent (default: 2).
+        cfe_h: cfe height exponent (default: 3).
+        cfe_c: cfe connectivity exponent (default: 0.5).
+        cfe_legacy: use the legacy (non-normalised) form of the cfe equation.
+        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\
+            fixel-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.
+        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 `FixelcfestatsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELCFESTATS_METADATA)
+    params = fixelcfestats_params(
+        mask=mask,
+        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,
+        cfe_dh=cfe_dh,
+        cfe_e=cfe_e,
+        cfe_h=cfe_h,
+        cfe_c=cfe_c,
+        cfe_legacy=cfe_legacy,
+        variance=variance,
+        ftests=ftests,
+        fonly=fonly,
+        column=column,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_fixel_directory=in_fixel_directory,
+        subjects=subjects,
+        design=design,
+        contrast=contrast,
+        connectivity=connectivity,
+        out_fixel_directory=out_fixel_directory,
+    )
+    return fixelcfestats_execute(params, execution)
+
+
+__all__ = [
+    "FIXELCFESTATS_METADATA",
+    "FixelcfestatsColumnParameters",
+    "FixelcfestatsConfigParameters",
+    "FixelcfestatsOutputs",
+    "FixelcfestatsParameters",
+    "FixelcfestatsVariousFileParameters",
+    "FixelcfestatsVariousStringParameters",
+    "fixelcfestats",
+    "fixelcfestats_column_params",
+    "fixelcfestats_config_params",
+    "fixelcfestats_params",
+    "fixelcfestats_various_file_params",
+    "fixelcfestats_various_string_params",
+]