niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_register.py

@@ -0,0 +1,927 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_REGISTER_METADATA = Metadata(
+    id="01ac3575a4acd8aa600baa6d27fee615f0a862c6.boutiques",
+    name="mris_register",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisRegisterParameters = typing.TypedDict('MrisRegisterParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_register"],
+    "surf_fname": InputPathType,
+    "target": InputPathType,
+    "out_fname": str,
+    "one_flag": bool,
+    "addframe": typing.NotRequired[str | None],
+    "annot_name": typing.NotRequired[str | None],
+    "curvature_fname": typing.NotRequired[InputPathType | None],
+    "canonical_name": typing.NotRequired[str | None],
+    "inflated": bool,
+    "inflated_name": typing.NotRequired[str | None],
+    "label_file": typing.NotRequired[str | None],
+    "orig_name": typing.NotRequired[str | None],
+    "overlay_values": typing.NotRequired[str | None],
+    "overlay_dir": typing.NotRequired[str | None],
+    "starting_reg_fname": typing.NotRequired[InputPathType | None],
+    "jacobian_fname": typing.NotRequired[str | None],
+    "n_averages": typing.NotRequired[float | None],
+    "adaptive": bool,
+    "l_area": typing.NotRequired[float | None],
+    "l_corr": typing.NotRequired[float | None],
+    "curvature_flag": bool,
+    "l_dist": typing.NotRequired[float | None],
+    "dt_value": typing.NotRequired[float | None],
+    "dt_decrease": typing.NotRequired[float | None],
+    "dt_increase": typing.NotRequired[float | None],
+    "l_external": typing.NotRequired[float | None],
+    "error_ratio": typing.NotRequired[float | None],
+    "initial_flag": bool,
+    "l_laplacian": typing.NotRequired[float | None],
+    "line_min": bool,
+    "momentum": typing.NotRequired[float | None],
+    "max_degrees": typing.NotRequired[float | None],
+    "median": bool,
+    "min_degrees": typing.NotRequired[float | None],
+    "multi_scale": typing.NotRequired[float | None],
+    "n_iterations": typing.NotRequired[float | None],
+    "n_angles": typing.NotRequired[float | None],
+    "neighborhood_size": typing.NotRequired[float | None],
+    "l_nlarea": typing.NotRequired[float | None],
+    "no_curv": bool,
+    "no_normalization": bool,
+    "no_rotation": bool,
+    "no_sulc": bool,
+    "num_surfaces": typing.NotRequired[float | None],
+    "overlay_corr": typing.NotRequired[float | None],
+    "max_passes": typing.NotRequired[float | None],
+    "l_parea": typing.NotRequired[float | None],
+    "remove_negative": typing.NotRequired[float | None],
+    "reverse": bool,
+    "rotate_values": typing.NotRequired[str | None],
+    "registration_file": typing.NotRequired[InputPathType | None],
+    "scale": typing.NotRequired[float | None],
+    "search_flag": bool,
+    "spring_value": typing.NotRequired[float | None],
+    "tolerance": typing.NotRequired[float | None],
+    "topology_flag": bool,
+    "vnum": typing.NotRequired[str | None],
+    "vsmooth": bool,
+    "write_iterations": typing.NotRequired[float | None],
+    "gdiag_no": typing.NotRequired[float | None],
+    "vector_flag": bool,
+    "threads": typing.NotRequired[float | None],
+    "version_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 {
+        "mris_register": mris_register_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 {
+        "mris_register": mris_register_outputs,
+    }.get(t)
+
+
+class MrisRegisterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_register(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_surface_file: OutputPathType
+    """Output surface file after registration."""
+    jacobian_output: OutputPathType | None
+    """Jacobian output file if specified."""
+
+
+def mris_register_params(
+    surf_fname: InputPathType,
+    target: InputPathType,
+    out_fname: str,
+    one_flag: bool = False,
+    addframe: str | None = None,
+    annot_name: str | None = None,
+    curvature_fname: InputPathType | None = None,
+    canonical_name: str | None = None,
+    inflated: bool = False,
+    inflated_name: str | None = None,
+    label_file: str | None = None,
+    orig_name: str | None = None,
+    overlay_values: str | None = None,
+    overlay_dir: str | None = None,
+    starting_reg_fname: InputPathType | None = None,
+    jacobian_fname: str | None = None,
+    n_averages: float | None = None,
+    adaptive: bool = False,
+    l_area: float | None = None,
+    l_corr: float | None = None,
+    curvature_flag: bool = False,
+    l_dist: float | None = None,
+    dt_value: float | None = None,
+    dt_decrease: float | None = None,
+    dt_increase: float | None = None,
+    l_external: float | None = None,
+    error_ratio: float | None = None,
+    initial_flag: bool = False,
+    l_laplacian: float | None = None,
+    line_min: bool = False,
+    momentum: float | None = None,
+    max_degrees: float | None = None,
+    median: bool = False,
+    min_degrees: float | None = None,
+    multi_scale: float | None = None,
+    n_iterations: float | None = None,
+    n_angles: float | None = None,
+    neighborhood_size: float | None = None,
+    l_nlarea: float | None = None,
+    no_curv: bool = False,
+    no_normalization: bool = False,
+    no_rotation: bool = False,
+    no_sulc: bool = False,
+    num_surfaces: float | None = None,
+    overlay_corr: float | None = None,
+    max_passes: float | None = None,
+    l_parea: float | None = None,
+    remove_negative: float | None = None,
+    reverse: bool = False,
+    rotate_values: str | None = None,
+    registration_file: InputPathType | None = None,
+    scale: float | None = None,
+    search_flag: bool = False,
+    spring_value: float | None = None,
+    tolerance: float | None = None,
+    topology_flag: bool = False,
+    vnum: str | None = None,
+    vsmooth: bool = False,
+    write_iterations: float | None = None,
+    gdiag_no: float | None = None,
+    vector_flag: bool = False,
+    threads: float | None = None,
+    version_flag: bool = False,
+) -> MrisRegisterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surf_fname: Surface to register, often {hemi}.sphere.
+        target: The data to register to. A template file for average surface or\
+            a single-subject's surface.
+        out_fname: Output surface file to capture registration. Example:\
+            {hemi}.sphere.reg.
+        one_flag: Treats target argument as a single subject's surface not a\
+            template file.
+        addframe: Add field with location in the atlas.
+        annot_name: Zeroes medial wall using annotation.
+        curvature_fname: Curvature file name.
+        canonical_name: Use surface for canonical properties.
+        inflated: Use inflated surface for initial alignment.
+        inflated_name: Uses this name for inflated surface for initial\
+            alignment.
+        label_file: Specify a manual label to align with atlas label.
+        orig_name: Use this for original properties.
+        overlay_values: Adds a variable to the atlas from overlay file,\
+            smoothing it specified number of times.
+        overlay_dir: Changes overlay path.
+        starting_reg_fname: Start registration with coordinates from file.
+        jacobian_fname: Write out jacobian of mapping to the specified file.
+        n_averages: Set the number of averages.
+        adaptive: Use adaptive time step integration.
+        l_area: Sets l_area parameter.
+        l_corr: Sets the l_corr parameter.
+        curvature_flag: Use smoothwm curvature for final alignment.
+        l_dist: Specify distance term.
+        dt_value: Sets momentum with specified dt.
+        dt_decrease: Set decrease for dt.
+        dt_increase: Set increase for dt.
+        l_external: Sets l_external parameter.
+        error_ratio: Sets error ratio.
+        initial_flag: Use initial registration.
+        l_laplacian: Sets l_laplacian.
+        line_min: Integrate using line minimization.
+        momentum: Chooses integration_type = INTEGRATE_MOMENTUM and sets\
+            momentum value.
+        max_degrees: Set max angle for search.
+        median: Uses median normalization (instead of mean).
+        min_degrees: Set min angle for search.
+        multi_scale: Use multi_scale scales for morphing.
+        n_iterations: Sets number of iterations.
+        n_angles: Set number of angles/search per scale.
+        neighborhood_size: Use neighborhood size specified.
+        l_nlarea: Sets l_nlarea parameter.
+        no_curv: Do not use smoothwm curvature for final alignment.
+        no_normalization: Disables normalization.
+        no_rotation: Disables initial rigid alignment.
+        no_sulc: Disables initial sulc alignment.
+        num_surfaces: Use specified number of surfaces/curvatures for\
+            alignment.
+        overlay_corr: Sets overlay correlation coefficient.
+        max_passes: Limit unfolding to specified passes.
+        l_parea: Sets l_parea parameter.
+        remove_negative: Remove negative triangles with iterative smoothing if\
+            non-zero.
+        reverse: Mirror image reverse brain before morphing.
+        rotate_values: Rotates brain by specified angles.
+        registration_file: Extract rotational components from registration\
+            file.
+        scale: Scales distances by the specified value.
+        search_flag: Integrate with binary search line minimization.
+        spring_value: Sets the spring parameter.
+        tolerance: Specifies tolerance.
+        topology_flag: Preserves the topology of positive area triangles.
+        vnum: Set neighborhood parameters.
+        vsmooth: Use space/time varying smoothness weighting.
+        write_iterations: Set number of write iterations.
+        gdiag_no: Supplies a vertex number for diagnostics.
+        vector_flag: Prints help for Multiframe mode, listing field names and\
+            numbers.
+        threads: Set number of OMP threads.
+        version_flag: Print the version number.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_register",
+        "surf_fname": surf_fname,
+        "target": target,
+        "out_fname": out_fname,
+        "one_flag": one_flag,
+        "inflated": inflated,
+        "adaptive": adaptive,
+        "curvature_flag": curvature_flag,
+        "initial_flag": initial_flag,
+        "line_min": line_min,
+        "median": median,
+        "no_curv": no_curv,
+        "no_normalization": no_normalization,
+        "no_rotation": no_rotation,
+        "no_sulc": no_sulc,
+        "reverse": reverse,
+        "search_flag": search_flag,
+        "topology_flag": topology_flag,
+        "vsmooth": vsmooth,
+        "vector_flag": vector_flag,
+        "version_flag": version_flag,
+    }
+    if addframe is not None:
+        params["addframe"] = addframe
+    if annot_name is not None:
+        params["annot_name"] = annot_name
+    if curvature_fname is not None:
+        params["curvature_fname"] = curvature_fname
+    if canonical_name is not None:
+        params["canonical_name"] = canonical_name
+    if inflated_name is not None:
+        params["inflated_name"] = inflated_name
+    if label_file is not None:
+        params["label_file"] = label_file
+    if orig_name is not None:
+        params["orig_name"] = orig_name
+    if overlay_values is not None:
+        params["overlay_values"] = overlay_values
+    if overlay_dir is not None:
+        params["overlay_dir"] = overlay_dir
+    if starting_reg_fname is not None:
+        params["starting_reg_fname"] = starting_reg_fname
+    if jacobian_fname is not None:
+        params["jacobian_fname"] = jacobian_fname
+    if n_averages is not None:
+        params["n_averages"] = n_averages
+    if l_area is not None:
+        params["l_area"] = l_area
+    if l_corr is not None:
+        params["l_corr"] = l_corr
+    if l_dist is not None:
+        params["l_dist"] = l_dist
+    if dt_value is not None:
+        params["dt_value"] = dt_value
+    if dt_decrease is not None:
+        params["dt_decrease"] = dt_decrease
+    if dt_increase is not None:
+        params["dt_increase"] = dt_increase
+    if l_external is not None:
+        params["l_external"] = l_external
+    if error_ratio is not None:
+        params["error_ratio"] = error_ratio
+    if l_laplacian is not None:
+        params["l_laplacian"] = l_laplacian
+    if momentum is not None:
+        params["momentum"] = momentum
+    if max_degrees is not None:
+        params["max_degrees"] = max_degrees
+    if min_degrees is not None:
+        params["min_degrees"] = min_degrees
+    if multi_scale is not None:
+        params["multi_scale"] = multi_scale
+    if n_iterations is not None:
+        params["n_iterations"] = n_iterations
+    if n_angles is not None:
+        params["n_angles"] = n_angles
+    if neighborhood_size is not None:
+        params["neighborhood_size"] = neighborhood_size
+    if l_nlarea is not None:
+        params["l_nlarea"] = l_nlarea
+    if num_surfaces is not None:
+        params["num_surfaces"] = num_surfaces
+    if overlay_corr is not None:
+        params["overlay_corr"] = overlay_corr
+    if max_passes is not None:
+        params["max_passes"] = max_passes
+    if l_parea is not None:
+        params["l_parea"] = l_parea
+    if remove_negative is not None:
+        params["remove_negative"] = remove_negative
+    if rotate_values is not None:
+        params["rotate_values"] = rotate_values
+    if registration_file is not None:
+        params["registration_file"] = registration_file
+    if scale is not None:
+        params["scale"] = scale
+    if spring_value is not None:
+        params["spring_value"] = spring_value
+    if tolerance is not None:
+        params["tolerance"] = tolerance
+    if vnum is not None:
+        params["vnum"] = vnum
+    if write_iterations is not None:
+        params["write_iterations"] = write_iterations
+    if gdiag_no is not None:
+        params["gdiag_no"] = gdiag_no
+    if threads is not None:
+        params["threads"] = threads
+    return params
+
+
+def mris_register_cargs(
+    params: MrisRegisterParameters,
+    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("mris_register")
+    cargs.append(execution.input_file(params.get("surf_fname")))
+    cargs.append(execution.input_file(params.get("target")))
+    cargs.append(params.get("out_fname"))
+    if params.get("one_flag"):
+        cargs.append("-1")
+    if params.get("addframe") is not None:
+        cargs.extend([
+            "-addframe",
+            params.get("addframe")
+        ])
+    if params.get("annot_name") is not None:
+        cargs.extend([
+            "-annot",
+            params.get("annot_name")
+        ])
+    if params.get("curvature_fname") is not None:
+        cargs.extend([
+            "-C",
+            execution.input_file(params.get("curvature_fname"))
+        ])
+    if params.get("canonical_name") is not None:
+        cargs.extend([
+            "-canon",
+            params.get("canonical_name")
+        ])
+    if params.get("inflated"):
+        cargs.append("-inflated")
+    if params.get("inflated_name") is not None:
+        cargs.extend([
+            "-infname",
+            params.get("inflated_name")
+        ])
+    if params.get("label_file") is not None:
+        cargs.extend([
+            "-L",
+            params.get("label_file")
+        ])
+    if params.get("orig_name") is not None:
+        cargs.extend([
+            "-O",
+            params.get("orig_name")
+        ])
+    if params.get("overlay_values") is not None:
+        cargs.extend([
+            "-overlay",
+            params.get("overlay_values")
+        ])
+    if params.get("overlay_dir") is not None:
+        cargs.extend([
+            "-overlay-dir",
+            params.get("overlay_dir")
+        ])
+    if params.get("starting_reg_fname") is not None:
+        cargs.extend([
+            "-sreg",
+            execution.input_file(params.get("starting_reg_fname"))
+        ])
+    if params.get("jacobian_fname") is not None:
+        cargs.extend([
+            "-jacobian",
+            params.get("jacobian_fname")
+        ])
+    if params.get("n_averages") is not None:
+        cargs.extend([
+            "-A",
+            str(params.get("n_averages"))
+        ])
+    if params.get("adaptive"):
+        cargs.append("-adaptive")
+    if params.get("l_area") is not None:
+        cargs.extend([
+            "-area",
+            str(params.get("l_area"))
+        ])
+    if params.get("l_corr") is not None:
+        cargs.extend([
+            "-corr",
+            str(params.get("l_corr"))
+        ])
+    if params.get("curvature_flag"):
+        cargs.append("-curv")
+    if params.get("l_dist") is not None:
+        cargs.extend([
+            "-dist",
+            str(params.get("l_dist"))
+        ])
+    if params.get("dt_value") is not None:
+        cargs.extend([
+            "-dt",
+            str(params.get("dt_value"))
+        ])
+    if params.get("dt_decrease") is not None:
+        cargs.extend([
+            "-dt_dec",
+            str(params.get("dt_decrease"))
+        ])
+    if params.get("dt_increase") is not None:
+        cargs.extend([
+            "-dt_inc",
+            str(params.get("dt_increase"))
+        ])
+    if params.get("l_external") is not None:
+        cargs.extend([
+            "-E",
+            str(params.get("l_external"))
+        ])
+    if params.get("error_ratio") is not None:
+        cargs.extend([
+            "-error_ratio",
+            str(params.get("error_ratio"))
+        ])
+    if params.get("initial_flag"):
+        cargs.append("-init")
+    if params.get("l_laplacian") is not None:
+        cargs.extend([
+            "-lap",
+            str(params.get("l_laplacian"))
+        ])
+    if params.get("line_min"):
+        cargs.append("-lm")
+    if params.get("momentum") is not None:
+        cargs.extend([
+            "-M",
+            str(params.get("momentum"))
+        ])
+    if params.get("max_degrees") is not None:
+        cargs.extend([
+            "-max_degrees",
+            str(params.get("max_degrees"))
+        ])
+    if params.get("median"):
+        cargs.append("-median")
+    if params.get("min_degrees") is not None:
+        cargs.extend([
+            "-min_degrees",
+            str(params.get("min_degrees"))
+        ])
+    if params.get("multi_scale") is not None:
+        cargs.extend([
+            "-multi_scale",
+            str(params.get("multi_scale"))
+        ])
+    if params.get("n_iterations") is not None:
+        cargs.extend([
+            "-N",
+            str(params.get("n_iterations"))
+        ])
+    if params.get("n_angles") is not None:
+        cargs.extend([
+            "-nangles",
+            str(params.get("n_angles"))
+        ])
+    if params.get("neighborhood_size") is not None:
+        cargs.extend([
+            "-nbrs",
+            str(params.get("neighborhood_size"))
+        ])
+    if params.get("l_nlarea") is not None:
+        cargs.extend([
+            "-nlarea",
+            str(params.get("l_nlarea"))
+        ])
+    if params.get("no_curv"):
+        cargs.append("-nocurv")
+    if params.get("no_normalization"):
+        cargs.append("-nonorm")
+    if params.get("no_rotation"):
+        cargs.append("-norot")
+    if params.get("no_sulc"):
+        cargs.append("-nosulc")
+    if params.get("num_surfaces") is not None:
+        cargs.extend([
+            "-nsurfaces",
+            str(params.get("num_surfaces"))
+        ])
+    if params.get("overlay_corr") is not None:
+        cargs.extend([
+            "-ocorr",
+            str(params.get("overlay_corr"))
+        ])
+    if params.get("max_passes") is not None:
+        cargs.extend([
+            "-P",
+            str(params.get("max_passes"))
+        ])
+    if params.get("l_parea") is not None:
+        cargs.extend([
+            "-parea",
+            str(params.get("l_parea"))
+        ])
+    if params.get("remove_negative") is not None:
+        cargs.extend([
+            "-remove_negative",
+            str(params.get("remove_negative"))
+        ])
+    if params.get("reverse"):
+        cargs.append("-reverse")
+    if params.get("rotate_values") is not None:
+        cargs.extend([
+            "-rotate",
+            params.get("rotate_values")
+        ])
+    if params.get("registration_file") is not None:
+        cargs.extend([
+            "-reg",
+            execution.input_file(params.get("registration_file"))
+        ])
+    if params.get("scale") is not None:
+        cargs.extend([
+            "-S",
+            str(params.get("scale"))
+        ])
+    if params.get("search_flag"):
+        cargs.append("-search")
+    if params.get("spring_value") is not None:
+        cargs.extend([
+            "-spring",
+            str(params.get("spring_value"))
+        ])
+    if params.get("tolerance") is not None:
+        cargs.extend([
+            "-tol",
+            str(params.get("tolerance"))
+        ])
+    if params.get("topology_flag"):
+        cargs.append("-topology")
+    if params.get("vnum") is not None:
+        cargs.extend([
+            "-vnum",
+            params.get("vnum")
+        ])
+    if params.get("vsmooth"):
+        cargs.append("-vsmooth")
+    if params.get("write_iterations") is not None:
+        cargs.extend([
+            "-W",
+            str(params.get("write_iterations"))
+        ])
+    if params.get("gdiag_no") is not None:
+        cargs.extend([
+            "-V",
+            str(params.get("gdiag_no"))
+        ])
+    if params.get("vector_flag"):
+        cargs.append("-vector")
+    if params.get("threads") is not None:
+        cargs.extend([
+            "-threads",
+            str(params.get("threads"))
+        ])
+    if params.get("version_flag"):
+        cargs.append("--version")
+    return cargs
+
+
+def mris_register_outputs(
+    params: MrisRegisterParameters,
+    execution: Execution,
+) -> MrisRegisterOutputs:
+    """
+    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 = MrisRegisterOutputs(
+        root=execution.output_file("."),
+        output_surface_file=execution.output_file(params.get("out_fname")),
+        jacobian_output=execution.output_file(params.get("jacobian_fname")) if (params.get("jacobian_fname") is not None) else None,
+    )
+    return ret
+
+
+def mris_register_execute(
+    params: MrisRegisterParameters,
+    execution: Execution,
+) -> MrisRegisterOutputs:
+    """
+    This program registers a surface to an average surface template.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisRegisterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_register_cargs(params, execution)
+    ret = mris_register_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_register(
+    surf_fname: InputPathType,
+    target: InputPathType,
+    out_fname: str,
+    one_flag: bool = False,
+    addframe: str | None = None,
+    annot_name: str | None = None,
+    curvature_fname: InputPathType | None = None,
+    canonical_name: str | None = None,
+    inflated: bool = False,
+    inflated_name: str | None = None,
+    label_file: str | None = None,
+    orig_name: str | None = None,
+    overlay_values: str | None = None,
+    overlay_dir: str | None = None,
+    starting_reg_fname: InputPathType | None = None,
+    jacobian_fname: str | None = None,
+    n_averages: float | None = None,
+    adaptive: bool = False,
+    l_area: float | None = None,
+    l_corr: float | None = None,
+    curvature_flag: bool = False,
+    l_dist: float | None = None,
+    dt_value: float | None = None,
+    dt_decrease: float | None = None,
+    dt_increase: float | None = None,
+    l_external: float | None = None,
+    error_ratio: float | None = None,
+    initial_flag: bool = False,
+    l_laplacian: float | None = None,
+    line_min: bool = False,
+    momentum: float | None = None,
+    max_degrees: float | None = None,
+    median: bool = False,
+    min_degrees: float | None = None,
+    multi_scale: float | None = None,
+    n_iterations: float | None = None,
+    n_angles: float | None = None,
+    neighborhood_size: float | None = None,
+    l_nlarea: float | None = None,
+    no_curv: bool = False,
+    no_normalization: bool = False,
+    no_rotation: bool = False,
+    no_sulc: bool = False,
+    num_surfaces: float | None = None,
+    overlay_corr: float | None = None,
+    max_passes: float | None = None,
+    l_parea: float | None = None,
+    remove_negative: float | None = None,
+    reverse: bool = False,
+    rotate_values: str | None = None,
+    registration_file: InputPathType | None = None,
+    scale: float | None = None,
+    search_flag: bool = False,
+    spring_value: float | None = None,
+    tolerance: float | None = None,
+    topology_flag: bool = False,
+    vnum: str | None = None,
+    vsmooth: bool = False,
+    write_iterations: float | None = None,
+    gdiag_no: float | None = None,
+    vector_flag: bool = False,
+    threads: float | None = None,
+    version_flag: bool = False,
+    runner: Runner | None = None,
+) -> MrisRegisterOutputs:
+    """
+    This program registers a surface to an average surface template.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        surf_fname: Surface to register, often {hemi}.sphere.
+        target: The data to register to. A template file for average surface or\
+            a single-subject's surface.
+        out_fname: Output surface file to capture registration. Example:\
+            {hemi}.sphere.reg.
+        one_flag: Treats target argument as a single subject's surface not a\
+            template file.
+        addframe: Add field with location in the atlas.
+        annot_name: Zeroes medial wall using annotation.
+        curvature_fname: Curvature file name.
+        canonical_name: Use surface for canonical properties.
+        inflated: Use inflated surface for initial alignment.
+        inflated_name: Uses this name for inflated surface for initial\
+            alignment.
+        label_file: Specify a manual label to align with atlas label.
+        orig_name: Use this for original properties.
+        overlay_values: Adds a variable to the atlas from overlay file,\
+            smoothing it specified number of times.
+        overlay_dir: Changes overlay path.
+        starting_reg_fname: Start registration with coordinates from file.
+        jacobian_fname: Write out jacobian of mapping to the specified file.
+        n_averages: Set the number of averages.
+        adaptive: Use adaptive time step integration.
+        l_area: Sets l_area parameter.
+        l_corr: Sets the l_corr parameter.
+        curvature_flag: Use smoothwm curvature for final alignment.
+        l_dist: Specify distance term.
+        dt_value: Sets momentum with specified dt.
+        dt_decrease: Set decrease for dt.
+        dt_increase: Set increase for dt.
+        l_external: Sets l_external parameter.
+        error_ratio: Sets error ratio.
+        initial_flag: Use initial registration.
+        l_laplacian: Sets l_laplacian.
+        line_min: Integrate using line minimization.
+        momentum: Chooses integration_type = INTEGRATE_MOMENTUM and sets\
+            momentum value.
+        max_degrees: Set max angle for search.
+        median: Uses median normalization (instead of mean).
+        min_degrees: Set min angle for search.
+        multi_scale: Use multi_scale scales for morphing.
+        n_iterations: Sets number of iterations.
+        n_angles: Set number of angles/search per scale.
+        neighborhood_size: Use neighborhood size specified.
+        l_nlarea: Sets l_nlarea parameter.
+        no_curv: Do not use smoothwm curvature for final alignment.
+        no_normalization: Disables normalization.
+        no_rotation: Disables initial rigid alignment.
+        no_sulc: Disables initial sulc alignment.
+        num_surfaces: Use specified number of surfaces/curvatures for\
+            alignment.
+        overlay_corr: Sets overlay correlation coefficient.
+        max_passes: Limit unfolding to specified passes.
+        l_parea: Sets l_parea parameter.
+        remove_negative: Remove negative triangles with iterative smoothing if\
+            non-zero.
+        reverse: Mirror image reverse brain before morphing.
+        rotate_values: Rotates brain by specified angles.
+        registration_file: Extract rotational components from registration\
+            file.
+        scale: Scales distances by the specified value.
+        search_flag: Integrate with binary search line minimization.
+        spring_value: Sets the spring parameter.
+        tolerance: Specifies tolerance.
+        topology_flag: Preserves the topology of positive area triangles.
+        vnum: Set neighborhood parameters.
+        vsmooth: Use space/time varying smoothness weighting.
+        write_iterations: Set number of write iterations.
+        gdiag_no: Supplies a vertex number for diagnostics.
+        vector_flag: Prints help for Multiframe mode, listing field names and\
+            numbers.
+        threads: Set number of OMP threads.
+        version_flag: Print the version number.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisRegisterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REGISTER_METADATA)
+    params = mris_register_params(
+        surf_fname=surf_fname,
+        target=target,
+        out_fname=out_fname,
+        one_flag=one_flag,
+        addframe=addframe,
+        annot_name=annot_name,
+        curvature_fname=curvature_fname,
+        canonical_name=canonical_name,
+        inflated=inflated,
+        inflated_name=inflated_name,
+        label_file=label_file,
+        orig_name=orig_name,
+        overlay_values=overlay_values,
+        overlay_dir=overlay_dir,
+        starting_reg_fname=starting_reg_fname,
+        jacobian_fname=jacobian_fname,
+        n_averages=n_averages,
+        adaptive=adaptive,
+        l_area=l_area,
+        l_corr=l_corr,
+        curvature_flag=curvature_flag,
+        l_dist=l_dist,
+        dt_value=dt_value,
+        dt_decrease=dt_decrease,
+        dt_increase=dt_increase,
+        l_external=l_external,
+        error_ratio=error_ratio,
+        initial_flag=initial_flag,
+        l_laplacian=l_laplacian,
+        line_min=line_min,
+        momentum=momentum,
+        max_degrees=max_degrees,
+        median=median,
+        min_degrees=min_degrees,
+        multi_scale=multi_scale,
+        n_iterations=n_iterations,
+        n_angles=n_angles,
+        neighborhood_size=neighborhood_size,
+        l_nlarea=l_nlarea,
+        no_curv=no_curv,
+        no_normalization=no_normalization,
+        no_rotation=no_rotation,
+        no_sulc=no_sulc,
+        num_surfaces=num_surfaces,
+        overlay_corr=overlay_corr,
+        max_passes=max_passes,
+        l_parea=l_parea,
+        remove_negative=remove_negative,
+        reverse=reverse,
+        rotate_values=rotate_values,
+        registration_file=registration_file,
+        scale=scale,
+        search_flag=search_flag,
+        spring_value=spring_value,
+        tolerance=tolerance,
+        topology_flag=topology_flag,
+        vnum=vnum,
+        vsmooth=vsmooth,
+        write_iterations=write_iterations,
+        gdiag_no=gdiag_no,
+        vector_flag=vector_flag,
+        threads=threads,
+        version_flag=version_flag,
+    )
+    return mris_register_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_REGISTER_METADATA",
+    "MrisRegisterOutputs",
+    "MrisRegisterParameters",
+    "mris_register",
+    "mris_register_params",
+]