niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_volcluster.py

@@ -0,0 +1,765 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_VOLCLUSTER_METADATA = Metadata(
+    id="86e5f012e8262b1a51728b36e2469f6a4678ccf5.boutiques",
+    name="mri_volcluster",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriVolclusterParameters = typing.TypedDict('MriVolclusterParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_volcluster"],
+    "input_file": InputPathType,
+    "summary_file": typing.NotRequired[str | None],
+    "output_volid": typing.NotRequired[str | None],
+    "output_cluster_num_volid": typing.NotRequired[str | None],
+    "cwsig_volid": typing.NotRequired[str | None],
+    "pointset_file": typing.NotRequired[str | None],
+    "min_threshold": typing.NotRequired[float | None],
+    "max_threshold": typing.NotRequired[float | None],
+    "sign": typing.NotRequired[str | None],
+    "no_adjust_flag": bool,
+    "match_value": typing.NotRequired[float | None],
+    "cwpval_threshold": typing.NotRequired[float | None],
+    "registration_file": typing.NotRequired[InputPathType | None],
+    "mni152reg_flag": bool,
+    "regheader_subject": typing.NotRequired[str | None],
+    "fsaverage_flag": bool,
+    "frame_number": typing.NotRequired[float | None],
+    "csd_files": typing.NotRequired[list[InputPathType] | None],
+    "cwsig_map": typing.NotRequired[str | None],
+    "vwsig_map": typing.NotRequired[str | None],
+    "max_cwpval_file": typing.NotRequired[str | None],
+    "csdpdf_file": typing.NotRequired[str | None],
+    "csdpdf_only_flag": bool,
+    "fwhm_value": typing.NotRequired[float | None],
+    "fwhm_file": typing.NotRequired[InputPathType | None],
+    "min_size": typing.NotRequired[float | None],
+    "min_size_vox": typing.NotRequired[float | None],
+    "min_distance": typing.NotRequired[float | None],
+    "allow_diag_flag": bool,
+    "bonferroni_number": typing.NotRequired[float | None],
+    "bonferroni_max_number": typing.NotRequired[float | None],
+    "sig2p_max_flag": bool,
+    "gte_flag": bool,
+    "mask_volid": typing.NotRequired[InputPathType | None],
+    "mask_type": typing.NotRequired[str | None],
+    "mask_frame": typing.NotRequired[float | None],
+    "mask_threshold": typing.NotRequired[float | None],
+    "mask_sign": typing.NotRequired[str | None],
+    "mask_invert_flag": bool,
+    "out_mask_volid": typing.NotRequired[str | None],
+    "out_mask_type": typing.NotRequired[str | None],
+    "label_file": typing.NotRequired[str | None],
+    "nlabel_cluster": typing.NotRequired[float | None],
+    "label_base": typing.NotRequired[str | None],
+    "synth_func": typing.NotRequired[str | None],
+    "diagnostic_level": typing.NotRequired[float | None],
+    "fill_params": typing.NotRequired[str | None],
+    "help_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_volcluster": mri_volcluster_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 {
+        "mri_volcluster": mri_volcluster_outputs,
+    }.get(t)
+
+
+class MriVolclusterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_volcluster(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume: OutputPathType | None
+    """Output volume after clustering."""
+    output_cluster_number_volume: OutputPathType | None
+    """Output cluster number volume."""
+    output_binary_mask: OutputPathType | None
+    """Final binary mask output."""
+    output_label_file: OutputPathType | None
+    """Saved cluster as label file."""
+
+
+def mri_volcluster_params(
+    input_file: InputPathType,
+    summary_file: str | None = None,
+    output_volid: str | None = None,
+    output_cluster_num_volid: str | None = None,
+    cwsig_volid: str | None = None,
+    pointset_file: str | None = None,
+    min_threshold: float | None = None,
+    max_threshold: float | None = None,
+    sign: str | None = None,
+    no_adjust_flag: bool = False,
+    match_value: float | None = None,
+    cwpval_threshold: float | None = None,
+    registration_file: InputPathType | None = None,
+    mni152reg_flag: bool = False,
+    regheader_subject: str | None = None,
+    fsaverage_flag: bool = False,
+    frame_number: float | None = None,
+    csd_files: list[InputPathType] | None = None,
+    cwsig_map: str | None = None,
+    vwsig_map: str | None = None,
+    max_cwpval_file: str | None = None,
+    csdpdf_file: str | None = None,
+    csdpdf_only_flag: bool = False,
+    fwhm_value: float | None = None,
+    fwhm_file: InputPathType | None = None,
+    min_size: float | None = None,
+    min_size_vox: float | None = None,
+    min_distance: float | None = None,
+    allow_diag_flag: bool = False,
+    bonferroni_number: float | None = None,
+    bonferroni_max_number: float | None = None,
+    sig2p_max_flag: bool = False,
+    gte_flag: bool = False,
+    mask_volid: InputPathType | None = None,
+    mask_type: str | None = None,
+    mask_frame: float | None = None,
+    mask_threshold: float | None = None,
+    mask_sign: str | None = None,
+    mask_invert_flag: bool = False,
+    out_mask_volid: str | None = None,
+    out_mask_type: str | None = None,
+    label_file: str | None = None,
+    nlabel_cluster: float | None = None,
+    label_base: str | None = None,
+    synth_func: str | None = None,
+    diagnostic_level: float | None = None,
+    fill_params: str | None = None,
+    help_flag: bool = False,
+) -> MriVolclusterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Source of volume values.
+        summary_file: Text summary file.
+        output_volid: Output volume ID after clustering.
+        output_cluster_num_volid: Output volume ID with cluster number values.
+        cwsig_volid: Volume ID for clusterwise significance.
+        pointset_file: Create a freeview pointset of the clusters.
+        min_threshold: Minimum intensity threshold.
+        max_threshold: Maximum intensity threshold.
+        sign: Sign for one-sided tests (<abs>, pos, neg).
+        no_adjust_flag: Do not adjust threshold for one-tailed tests.
+        match_value: Set thmin=matchval-0.5 and thmax=matchval+0.5.
+        cwpval_threshold: Require clusters to have cwp < threshold.
+        registration_file: For reporting Talairach coordinates.
+        mni152reg_flag: Input is in MNI152 space.
+        regheader_subject: Use header registration with subject.
+        fsaverage_flag: Assume input is in fsaverage space.
+        frame_number: Perform cluster analysis on the nth frame (0-based).
+        csd_files: Cluster simulation data files.
+        cwsig_map: Map of corrected cluster-wise significances.
+        vwsig_map: Map of corrected voxel-wise significances.
+        max_cwpval_file: Save p-value of the largest cluster.
+        csdpdf_file: PDF/CDF of cluster and max significance.
+        csdpdf_only_flag: Write CSD PDF file and exit.
+        fwhm_value: FWHM in mm^3, forces GRF analysis.
+        fwhm_file: Text file with FWHM in mm^3 for GRF.
+        min_size: Minimum volume (mm^3) for a cluster.
+        min_size_vox: Minimum number of contiguous voxels for a cluster.
+        min_distance: Minimum distance between peak clusters.
+        allow_diag_flag: Allow diagonal adjacency for contiguity.
+        bonferroni_number: Bonferroni correction across spaces.
+        bonferroni_max_number: Bonferroni correction applied to maximum.
+        sig2p_max_flag: Convert maximum significance to p-value.
+        gte_flag: Use >= when computing p-value from CSD.
+        mask_volid: Mask volume ID.
+        mask_type: File type of mask volume.
+        mask_frame: Nth frame of mask to use.
+        mask_threshold: Upper threshold for the mask.
+        mask_sign: Sign in mask thresholding (<abs>, neg, pos).
+        mask_invert_flag: Invert mask after thresholding.
+        out_mask_volid: Path for final binary mask.
+        out_mask_type: File type for output mask.
+        label_file: File to save nth cluster as a label.
+        nlabel_cluster: Save the nth cluster as a label.
+        label_base: Base name for saving clusters as labels.
+        synth_func: Function for synthetic data (uniform, loguniform,\
+            gaussian).
+        diagnostic_level: Set diagnostic level.
+        fill_params: Parameters for fill operation (invol outvol matchval).
+        help_flag: Display help message and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_volcluster",
+        "input_file": input_file,
+        "no_adjust_flag": no_adjust_flag,
+        "mni152reg_flag": mni152reg_flag,
+        "fsaverage_flag": fsaverage_flag,
+        "csdpdf_only_flag": csdpdf_only_flag,
+        "allow_diag_flag": allow_diag_flag,
+        "sig2p_max_flag": sig2p_max_flag,
+        "gte_flag": gte_flag,
+        "mask_invert_flag": mask_invert_flag,
+        "help_flag": help_flag,
+    }
+    if summary_file is not None:
+        params["summary_file"] = summary_file
+    if output_volid is not None:
+        params["output_volid"] = output_volid
+    if output_cluster_num_volid is not None:
+        params["output_cluster_num_volid"] = output_cluster_num_volid
+    if cwsig_volid is not None:
+        params["cwsig_volid"] = cwsig_volid
+    if pointset_file is not None:
+        params["pointset_file"] = pointset_file
+    if min_threshold is not None:
+        params["min_threshold"] = min_threshold
+    if max_threshold is not None:
+        params["max_threshold"] = max_threshold
+    if sign is not None:
+        params["sign"] = sign
+    if match_value is not None:
+        params["match_value"] = match_value
+    if cwpval_threshold is not None:
+        params["cwpval_threshold"] = cwpval_threshold
+    if registration_file is not None:
+        params["registration_file"] = registration_file
+    if regheader_subject is not None:
+        params["regheader_subject"] = regheader_subject
+    if frame_number is not None:
+        params["frame_number"] = frame_number
+    if csd_files is not None:
+        params["csd_files"] = csd_files
+    if cwsig_map is not None:
+        params["cwsig_map"] = cwsig_map
+    if vwsig_map is not None:
+        params["vwsig_map"] = vwsig_map
+    if max_cwpval_file is not None:
+        params["max_cwpval_file"] = max_cwpval_file
+    if csdpdf_file is not None:
+        params["csdpdf_file"] = csdpdf_file
+    if fwhm_value is not None:
+        params["fwhm_value"] = fwhm_value
+    if fwhm_file is not None:
+        params["fwhm_file"] = fwhm_file
+    if min_size is not None:
+        params["min_size"] = min_size
+    if min_size_vox is not None:
+        params["min_size_vox"] = min_size_vox
+    if min_distance is not None:
+        params["min_distance"] = min_distance
+    if bonferroni_number is not None:
+        params["bonferroni_number"] = bonferroni_number
+    if bonferroni_max_number is not None:
+        params["bonferroni_max_number"] = bonferroni_max_number
+    if mask_volid is not None:
+        params["mask_volid"] = mask_volid
+    if mask_type is not None:
+        params["mask_type"] = mask_type
+    if mask_frame is not None:
+        params["mask_frame"] = mask_frame
+    if mask_threshold is not None:
+        params["mask_threshold"] = mask_threshold
+    if mask_sign is not None:
+        params["mask_sign"] = mask_sign
+    if out_mask_volid is not None:
+        params["out_mask_volid"] = out_mask_volid
+    if out_mask_type is not None:
+        params["out_mask_type"] = out_mask_type
+    if label_file is not None:
+        params["label_file"] = label_file
+    if nlabel_cluster is not None:
+        params["nlabel_cluster"] = nlabel_cluster
+    if label_base is not None:
+        params["label_base"] = label_base
+    if synth_func is not None:
+        params["synth_func"] = synth_func
+    if diagnostic_level is not None:
+        params["diagnostic_level"] = diagnostic_level
+    if fill_params is not None:
+        params["fill_params"] = fill_params
+    return params
+
+
+def mri_volcluster_cargs(
+    params: MriVolclusterParameters,
+    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("mri_volcluster")
+    cargs.extend([
+        "--in",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("summary_file") is not None:
+        cargs.extend([
+            "--sum",
+            params.get("summary_file")
+        ])
+    if params.get("output_volid") is not None:
+        cargs.extend([
+            "--out",
+            params.get("output_volid")
+        ])
+    if params.get("output_cluster_num_volid") is not None:
+        cargs.extend([
+            "--ocn",
+            params.get("output_cluster_num_volid")
+        ])
+    if params.get("cwsig_volid") is not None:
+        cargs.extend([
+            "--cwsig",
+            params.get("cwsig_volid")
+        ])
+    if params.get("pointset_file") is not None:
+        cargs.extend([
+            "--pointset",
+            params.get("pointset_file")
+        ])
+    if params.get("min_threshold") is not None:
+        cargs.extend([
+            "--thmin",
+            str(params.get("min_threshold"))
+        ])
+    if params.get("max_threshold") is not None:
+        cargs.extend([
+            "--thmax",
+            str(params.get("max_threshold"))
+        ])
+    if params.get("sign") is not None:
+        cargs.extend([
+            "--sign",
+            params.get("sign")
+        ])
+    if params.get("no_adjust_flag"):
+        cargs.append("--no-adjust")
+    if params.get("match_value") is not None:
+        cargs.extend([
+            "--match",
+            str(params.get("match_value"))
+        ])
+    if params.get("cwpval_threshold") is not None:
+        cargs.extend([
+            "--cwpvalthresh",
+            str(params.get("cwpval_threshold"))
+        ])
+    if params.get("registration_file") is not None:
+        cargs.extend([
+            "--reg",
+            execution.input_file(params.get("registration_file"))
+        ])
+    if params.get("mni152reg_flag"):
+        cargs.append("--mni152reg")
+    if params.get("regheader_subject") is not None:
+        cargs.extend([
+            "--regheader",
+            params.get("regheader_subject")
+        ])
+    if params.get("fsaverage_flag"):
+        cargs.append("--fsaverage")
+    if params.get("frame_number") is not None:
+        cargs.extend([
+            "--frame",
+            str(params.get("frame_number"))
+        ])
+    if params.get("csd_files") is not None:
+        cargs.extend([
+            "--csd",
+            *[execution.input_file(f) for f in params.get("csd_files")]
+        ])
+    if params.get("cwsig_map") is not None:
+        cargs.extend([
+            "--cwsig",
+            params.get("cwsig_map")
+        ])
+    if params.get("vwsig_map") is not None:
+        cargs.extend([
+            "--vwsig",
+            params.get("vwsig_map")
+        ])
+    if params.get("max_cwpval_file") is not None:
+        cargs.extend([
+            "--maxcwpval",
+            params.get("max_cwpval_file")
+        ])
+    if params.get("csdpdf_file") is not None:
+        cargs.extend([
+            "--csdpdf",
+            params.get("csdpdf_file")
+        ])
+    if params.get("csdpdf_only_flag"):
+        cargs.append("--csdpdf-only")
+    if params.get("fwhm_value") is not None:
+        cargs.extend([
+            "--fwhm",
+            str(params.get("fwhm_value"))
+        ])
+    if params.get("fwhm_file") is not None:
+        cargs.extend([
+            "--fwhmdat",
+            execution.input_file(params.get("fwhm_file"))
+        ])
+    if params.get("min_size") is not None:
+        cargs.extend([
+            "--minsize",
+            str(params.get("min_size"))
+        ])
+    if params.get("min_size_vox") is not None:
+        cargs.extend([
+            "--minsizevox",
+            str(params.get("min_size_vox"))
+        ])
+    if params.get("min_distance") is not None:
+        cargs.extend([
+            "--mindist",
+            str(params.get("min_distance"))
+        ])
+    if params.get("allow_diag_flag"):
+        cargs.append("--allowdiag")
+    if params.get("bonferroni_number") is not None:
+        cargs.extend([
+            "--bonferroni",
+            str(params.get("bonferroni_number"))
+        ])
+    if params.get("bonferroni_max_number") is not None:
+        cargs.extend([
+            "--bonferroni-max",
+            str(params.get("bonferroni_max_number"))
+        ])
+    if params.get("sig2p_max_flag"):
+        cargs.append("--sig2p-max")
+    if params.get("gte_flag"):
+        cargs.append("--gte")
+    if params.get("mask_volid") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask_volid"))
+        ])
+    if params.get("mask_type") is not None:
+        cargs.extend([
+            "--mask_type",
+            params.get("mask_type")
+        ])
+    if params.get("mask_frame") is not None:
+        cargs.extend([
+            "--maskframe",
+            str(params.get("mask_frame"))
+        ])
+    if params.get("mask_threshold") is not None:
+        cargs.extend([
+            "--maskthresh",
+            str(params.get("mask_threshold"))
+        ])
+    if params.get("mask_sign") is not None:
+        cargs.extend([
+            "--masksign",
+            params.get("mask_sign")
+        ])
+    if params.get("mask_invert_flag"):
+        cargs.append("--maskinvert")
+    if params.get("out_mask_volid") is not None:
+        cargs.extend([
+            "--outmask",
+            params.get("out_mask_volid")
+        ])
+    if params.get("out_mask_type") is not None:
+        cargs.extend([
+            "--outmask_type",
+            params.get("out_mask_type")
+        ])
+    if params.get("label_file") is not None:
+        cargs.extend([
+            "--label",
+            params.get("label_file")
+        ])
+    if params.get("nlabel_cluster") is not None:
+        cargs.extend([
+            "--nlabelcluster",
+            str(params.get("nlabel_cluster"))
+        ])
+    if params.get("label_base") is not None:
+        cargs.extend([
+            "--labelbase",
+            params.get("label_base")
+        ])
+    if params.get("synth_func") is not None:
+        cargs.extend([
+            "--synth",
+            params.get("synth_func")
+        ])
+    if params.get("diagnostic_level") is not None:
+        cargs.extend([
+            "--diag",
+            str(params.get("diagnostic_level"))
+        ])
+    if params.get("fill_params") is not None:
+        cargs.extend([
+            "--fill",
+            params.get("fill_params")
+        ])
+    if params.get("help_flag"):
+        cargs.append("--help")
+    return cargs
+
+
+def mri_volcluster_outputs(
+    params: MriVolclusterParameters,
+    execution: Execution,
+) -> MriVolclusterOutputs:
+    """
+    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 = MriVolclusterOutputs(
+        root=execution.output_file("."),
+        output_volume=execution.output_file(params.get("output_volid")) if (params.get("output_volid") is not None) else None,
+        output_cluster_number_volume=execution.output_file(params.get("output_cluster_num_volid")) if (params.get("output_cluster_num_volid") is not None) else None,
+        output_binary_mask=execution.output_file(params.get("out_mask_volid")) if (params.get("out_mask_volid") is not None) else None,
+        output_label_file=execution.output_file(params.get("label_file")) if (params.get("label_file") is not None) else None,
+    )
+    return ret
+
+
+def mri_volcluster_execute(
+    params: MriVolclusterParameters,
+    execution: Execution,
+) -> MriVolclusterOutputs:
+    """
+    A tool for finding clusters in a volume, useful for analyzing MRI data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriVolclusterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_volcluster_cargs(params, execution)
+    ret = mri_volcluster_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_volcluster(
+    input_file: InputPathType,
+    summary_file: str | None = None,
+    output_volid: str | None = None,
+    output_cluster_num_volid: str | None = None,
+    cwsig_volid: str | None = None,
+    pointset_file: str | None = None,
+    min_threshold: float | None = None,
+    max_threshold: float | None = None,
+    sign: str | None = None,
+    no_adjust_flag: bool = False,
+    match_value: float | None = None,
+    cwpval_threshold: float | None = None,
+    registration_file: InputPathType | None = None,
+    mni152reg_flag: bool = False,
+    regheader_subject: str | None = None,
+    fsaverage_flag: bool = False,
+    frame_number: float | None = None,
+    csd_files: list[InputPathType] | None = None,
+    cwsig_map: str | None = None,
+    vwsig_map: str | None = None,
+    max_cwpval_file: str | None = None,
+    csdpdf_file: str | None = None,
+    csdpdf_only_flag: bool = False,
+    fwhm_value: float | None = None,
+    fwhm_file: InputPathType | None = None,
+    min_size: float | None = None,
+    min_size_vox: float | None = None,
+    min_distance: float | None = None,
+    allow_diag_flag: bool = False,
+    bonferroni_number: float | None = None,
+    bonferroni_max_number: float | None = None,
+    sig2p_max_flag: bool = False,
+    gte_flag: bool = False,
+    mask_volid: InputPathType | None = None,
+    mask_type: str | None = None,
+    mask_frame: float | None = None,
+    mask_threshold: float | None = None,
+    mask_sign: str | None = None,
+    mask_invert_flag: bool = False,
+    out_mask_volid: str | None = None,
+    out_mask_type: str | None = None,
+    label_file: str | None = None,
+    nlabel_cluster: float | None = None,
+    label_base: str | None = None,
+    synth_func: str | None = None,
+    diagnostic_level: float | None = None,
+    fill_params: str | None = None,
+    help_flag: bool = False,
+    runner: Runner | None = None,
+) -> MriVolclusterOutputs:
+    """
+    A tool for finding clusters in a volume, useful for analyzing MRI data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_file: Source of volume values.
+        summary_file: Text summary file.
+        output_volid: Output volume ID after clustering.
+        output_cluster_num_volid: Output volume ID with cluster number values.
+        cwsig_volid: Volume ID for clusterwise significance.
+        pointset_file: Create a freeview pointset of the clusters.
+        min_threshold: Minimum intensity threshold.
+        max_threshold: Maximum intensity threshold.
+        sign: Sign for one-sided tests (<abs>, pos, neg).
+        no_adjust_flag: Do not adjust threshold for one-tailed tests.
+        match_value: Set thmin=matchval-0.5 and thmax=matchval+0.5.
+        cwpval_threshold: Require clusters to have cwp < threshold.
+        registration_file: For reporting Talairach coordinates.
+        mni152reg_flag: Input is in MNI152 space.
+        regheader_subject: Use header registration with subject.
+        fsaverage_flag: Assume input is in fsaverage space.
+        frame_number: Perform cluster analysis on the nth frame (0-based).
+        csd_files: Cluster simulation data files.
+        cwsig_map: Map of corrected cluster-wise significances.
+        vwsig_map: Map of corrected voxel-wise significances.
+        max_cwpval_file: Save p-value of the largest cluster.
+        csdpdf_file: PDF/CDF of cluster and max significance.
+        csdpdf_only_flag: Write CSD PDF file and exit.
+        fwhm_value: FWHM in mm^3, forces GRF analysis.
+        fwhm_file: Text file with FWHM in mm^3 for GRF.
+        min_size: Minimum volume (mm^3) for a cluster.
+        min_size_vox: Minimum number of contiguous voxels for a cluster.
+        min_distance: Minimum distance between peak clusters.
+        allow_diag_flag: Allow diagonal adjacency for contiguity.
+        bonferroni_number: Bonferroni correction across spaces.
+        bonferroni_max_number: Bonferroni correction applied to maximum.
+        sig2p_max_flag: Convert maximum significance to p-value.
+        gte_flag: Use >= when computing p-value from CSD.
+        mask_volid: Mask volume ID.
+        mask_type: File type of mask volume.
+        mask_frame: Nth frame of mask to use.
+        mask_threshold: Upper threshold for the mask.
+        mask_sign: Sign in mask thresholding (<abs>, neg, pos).
+        mask_invert_flag: Invert mask after thresholding.
+        out_mask_volid: Path for final binary mask.
+        out_mask_type: File type for output mask.
+        label_file: File to save nth cluster as a label.
+        nlabel_cluster: Save the nth cluster as a label.
+        label_base: Base name for saving clusters as labels.
+        synth_func: Function for synthetic data (uniform, loguniform,\
+            gaussian).
+        diagnostic_level: Set diagnostic level.
+        fill_params: Parameters for fill operation (invol outvol matchval).
+        help_flag: Display help message and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriVolclusterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_VOLCLUSTER_METADATA)
+    params = mri_volcluster_params(
+        input_file=input_file,
+        summary_file=summary_file,
+        output_volid=output_volid,
+        output_cluster_num_volid=output_cluster_num_volid,
+        cwsig_volid=cwsig_volid,
+        pointset_file=pointset_file,
+        min_threshold=min_threshold,
+        max_threshold=max_threshold,
+        sign=sign,
+        no_adjust_flag=no_adjust_flag,
+        match_value=match_value,
+        cwpval_threshold=cwpval_threshold,
+        registration_file=registration_file,
+        mni152reg_flag=mni152reg_flag,
+        regheader_subject=regheader_subject,
+        fsaverage_flag=fsaverage_flag,
+        frame_number=frame_number,
+        csd_files=csd_files,
+        cwsig_map=cwsig_map,
+        vwsig_map=vwsig_map,
+        max_cwpval_file=max_cwpval_file,
+        csdpdf_file=csdpdf_file,
+        csdpdf_only_flag=csdpdf_only_flag,
+        fwhm_value=fwhm_value,
+        fwhm_file=fwhm_file,
+        min_size=min_size,
+        min_size_vox=min_size_vox,
+        min_distance=min_distance,
+        allow_diag_flag=allow_diag_flag,
+        bonferroni_number=bonferroni_number,
+        bonferroni_max_number=bonferroni_max_number,
+        sig2p_max_flag=sig2p_max_flag,
+        gte_flag=gte_flag,
+        mask_volid=mask_volid,
+        mask_type=mask_type,
+        mask_frame=mask_frame,
+        mask_threshold=mask_threshold,
+        mask_sign=mask_sign,
+        mask_invert_flag=mask_invert_flag,
+        out_mask_volid=out_mask_volid,
+        out_mask_type=out_mask_type,
+        label_file=label_file,
+        nlabel_cluster=nlabel_cluster,
+        label_base=label_base,
+        synth_func=synth_func,
+        diagnostic_level=diagnostic_level,
+        fill_params=fill_params,
+        help_flag=help_flag,
+    )
+    return mri_volcluster_execute(params, execution)
+
+
+__all__ = [
+    "MRI_VOLCLUSTER_METADATA",
+    "MriVolclusterOutputs",
+    "MriVolclusterParameters",
+    "mri_volcluster",
+    "mri_volcluster_params",
+]