niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_make_surfaces.py

@@ -0,0 +1,839 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_MAKE_SURFACES_METADATA = Metadata(
+    id="916ed4d56c0e1cd56b8963f58b7e229385c20cb5.boutiques",
+    name="mris_make_surfaces",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisMakeSurfacesParameters = typing.TypedDict('MrisMakeSurfacesParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_make_surfaces"],
+    "subject_name": str,
+    "hemisphere": str,
+    "white": typing.NotRequired[str | None],
+    "pial": typing.NotRequired[str | None],
+    "whiteonly": bool,
+    "nowhite": bool,
+    "orig_white": typing.NotRequired[str | None],
+    "orig_pial": typing.NotRequired[str | None],
+    "q": bool,
+    "max_gray_scale": typing.NotRequired[float | None],
+    "c": bool,
+    "cortex": typing.NotRequired[float | None],
+    "w": typing.NotRequired[float | None],
+    "first_wm_peak": bool,
+    "a_avgs": typing.NotRequired[float | None],
+    "pa_avgs": typing.NotRequired[float | None],
+    "wa_avgs": typing.NotRequired[float | None],
+    "t1_vol": typing.NotRequired[str | None],
+    "w_vol": typing.NotRequired[str | None],
+    "long": bool,
+    "dura_thresh": typing.NotRequired[float | None],
+    "sdir": typing.NotRequired[str | None],
+    "erase_cerebellum": bool,
+    "wm_weight": typing.NotRequired[float | None],
+    "nsigma_above": typing.NotRequired[float | None],
+    "nsigma_below": typing.NotRequired[float | None],
+    "t2_min_inside": typing.NotRequired[float | None],
+    "t2_max_inside": typing.NotRequired[float | None],
+    "t2_outside_min": typing.NotRequired[float | None],
+    "t2_outside_max": typing.NotRequired[float | None],
+    "min_peak_pct": typing.NotRequired[float | None],
+    "border_vals_hires": bool,
+    "no_unitize": bool,
+    "intensity": typing.NotRequired[float | None],
+    "curv": typing.NotRequired[float | None],
+    "tspring": typing.NotRequired[float | None],
+    "nspring": typing.NotRequired[float | None],
+    "repulse": typing.NotRequired[float | None],
+    "save_target": bool,
+    "save_res": bool,
+    "v_vertexno": typing.NotRequired[float | None],
+    "diag_vertex": typing.NotRequired[float | None],
+    "rip": typing.NotRequired[str | None],
+    "sigma_white": typing.NotRequired[str | None],
+    "sigma_pial": typing.NotRequired[str | None],
+    "output": typing.NotRequired[str | None],
+    "min_border_white": typing.NotRequired[float | None],
+    "max_border_white": typing.NotRequired[float | None],
+    "min_gray_white_border": typing.NotRequired[float | None],
+    "max_gray": typing.NotRequired[float | None],
+    "max_gray_csf_border": typing.NotRequired[float | None],
+    "min_gray_csf_border": typing.NotRequired[float | None],
+    "max_csf": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_make_surfaces": mris_make_surfaces_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)
+
+
+class MrisMakeSurfacesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_make_surfaces(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_make_surfaces_params(
+    subject_name: str,
+    hemisphere: str,
+    white: str | None = None,
+    pial: str | None = None,
+    whiteonly: bool = False,
+    nowhite: bool = False,
+    orig_white: str | None = None,
+    orig_pial: str | None = None,
+    q: bool = False,
+    max_gray_scale: float | None = None,
+    c: bool = False,
+    cortex: float | None = None,
+    w: float | None = None,
+    first_wm_peak: bool = False,
+    a_avgs: float | None = None,
+    pa_avgs: float | None = None,
+    wa_avgs: float | None = None,
+    t1_vol: str | None = None,
+    w_vol: str | None = None,
+    long: bool = False,
+    dura_thresh: float | None = None,
+    sdir: str | None = None,
+    erase_cerebellum: bool = False,
+    wm_weight: float | None = None,
+    nsigma_above: float | None = None,
+    nsigma_below: float | None = None,
+    t2_min_inside: float | None = None,
+    t2_max_inside: float | None = None,
+    t2_outside_min: float | None = None,
+    t2_outside_max: float | None = None,
+    min_peak_pct: float | None = None,
+    border_vals_hires: bool = False,
+    no_unitize: bool = False,
+    intensity: float | None = None,
+    curv: float | None = None,
+    tspring: float | None = None,
+    nspring: float | None = None,
+    repulse: float | None = None,
+    save_target: bool = False,
+    save_res: bool = False,
+    v_vertexno: float | None = None,
+    diag_vertex: float | None = None,
+    rip: str | None = None,
+    sigma_white: str | None = None,
+    sigma_pial: str | None = None,
+    output: str | None = None,
+    min_border_white: float | None = None,
+    max_border_white: float | None = None,
+    min_gray_white_border: float | None = None,
+    max_gray: float | None = None,
+    max_gray_csf_border: float | None = None,
+    min_gray_csf_border: float | None = None,
+    max_csf: float | None = None,
+) -> MrisMakeSurfacesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_name: Name of the subject.
+        hemisphere: Brain hemisphere (r or l).
+        white: Output name for white surface (default is 'white'). Set to\
+            NOWHITE to generate but not save white surface.
+        pial: Output name for pial surface (default is 'pial').
+        whiteonly: Only generate white matter surface.
+        nowhite: Only generate pial surface.
+        orig_white: Specify a white surface to start with.
+        orig_pial: Specify a pial surface to start with.
+        q: Omit self-intersection and only generate gray/white surface.
+        max_gray_scale: Set maximum gray scale value.
+        c: Do not create curvature and area files from white matter surface.
+        cortex: Set to 0 to turn off creation of cortex label file.
+        w: Unused argument.
+        first_wm_peak: Settle WM surface at first peak in intensity profile\
+            instead of highest.
+        a_avgs: Average curvature values a number of times (default=10).
+        pa_avgs: Average pial curvature values a max of a number of times\
+            (default=16).
+        wa_avgs: Average white curvature values a max of a number of times\
+            (default=4).
+        t1_vol: Specify T1 volume (default is brain).
+        w_vol: Specify white volume and <hires> option.
+        long: Run longitudinal analysis.
+        dura_thresh: Set a threshold for the multi-echo mprage dura avoidance.
+        sdir: Specify SUBJECTS_DIR.
+        erase_cerebellum: Erase cerebellar labeled voxels if aseg is loaded.
+        wm_weight: Weighting of WM mean in calculating T2 threshold of\
+            disallowed GM values, default=3.
+        nsigma_above: # of sigmas above the mean to allow gray matter T2\
+            intensities.
+        nsigma_below: # of sigmas below the mean to allow gray matter T2\
+            intensities.
+        t2_min_inside: Specify threshold for min T2 value allowed to be\
+            interior to the cortical ribbon.
+        t2_max_inside: Specify threshold for max T2 value allowed to be\
+            interior to the cortical ribbon.
+        t2_outside_min: Specify threshold for min T2 value outside of pial\
+            surface that will cause surface to deform outwards.
+        t2_outside_max: Specify threshold for max T2 value outside of pial\
+            surface that will cause surface to deform outwards.
+        min_peak_pct: Specify the pct of the histo peak in the local gm\
+            histogram to use as threshold for finding the local inside and outside\
+            gm thresholds.
+        border_vals_hires: Turn on hires options in\
+            MRIScomputeBorderValues_new(). May not be helpful.
+        no_unitize: Turn off face normal unitization.
+        intensity: Set weight of intensity cost.
+        curv: Set weight of curvature cost.
+        tspring: Set weight of tangential spring cost.
+        nspring: Set weight of normal spring cost.
+        repulse: Set weight of repulsion force.
+        save_target: Save target surface for debugging.
+        save_res: Save residual for debugging.
+        v_vertexno: Set Gdiag_no to vertex number.
+        diag_vertex: Set Gdiag_no to vertex number and turn off writing of\
+            cortex label or curvature files.
+        rip: Save ripflag as overlay. Specify full path including hemi, suffix,\
+            etc.
+        sigma_white: Save white surface sigma as overlay. Specify full path\
+            including hemi, suffix, etc.
+        sigma_pial: Save pial surface sigma as overlay. Specify full path\
+            including hemi, suffix, etc.
+        output: Append suffix to all outputs to prevent over-writing.
+        min_border_white: Minimum border white.
+        max_border_white: Maximum border white.
+        min_gray_white_border: Minimum gray at white border.
+        max_gray: Maximum gray value.
+        max_gray_csf_border: Maximum gray at CSF border.
+        min_gray_csf_border: Minimum gray at CSF border.
+        max_csf: Maximum CSF value.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_make_surfaces",
+        "subject_name": subject_name,
+        "hemisphere": hemisphere,
+        "whiteonly": whiteonly,
+        "nowhite": nowhite,
+        "q": q,
+        "c": c,
+        "first_wm_peak": first_wm_peak,
+        "long": long,
+        "erase_cerebellum": erase_cerebellum,
+        "border_vals_hires": border_vals_hires,
+        "no_unitize": no_unitize,
+        "save_target": save_target,
+        "save_res": save_res,
+    }
+    if white is not None:
+        params["white"] = white
+    if pial is not None:
+        params["pial"] = pial
+    if orig_white is not None:
+        params["orig_white"] = orig_white
+    if orig_pial is not None:
+        params["orig_pial"] = orig_pial
+    if max_gray_scale is not None:
+        params["max_gray_scale"] = max_gray_scale
+    if cortex is not None:
+        params["cortex"] = cortex
+    if w is not None:
+        params["w"] = w
+    if a_avgs is not None:
+        params["a_avgs"] = a_avgs
+    if pa_avgs is not None:
+        params["pa_avgs"] = pa_avgs
+    if wa_avgs is not None:
+        params["wa_avgs"] = wa_avgs
+    if t1_vol is not None:
+        params["t1_vol"] = t1_vol
+    if w_vol is not None:
+        params["w_vol"] = w_vol
+    if dura_thresh is not None:
+        params["dura_thresh"] = dura_thresh
+    if sdir is not None:
+        params["sdir"] = sdir
+    if wm_weight is not None:
+        params["wm_weight"] = wm_weight
+    if nsigma_above is not None:
+        params["nsigma_above"] = nsigma_above
+    if nsigma_below is not None:
+        params["nsigma_below"] = nsigma_below
+    if t2_min_inside is not None:
+        params["t2_min_inside"] = t2_min_inside
+    if t2_max_inside is not None:
+        params["t2_max_inside"] = t2_max_inside
+    if t2_outside_min is not None:
+        params["t2_outside_min"] = t2_outside_min
+    if t2_outside_max is not None:
+        params["t2_outside_max"] = t2_outside_max
+    if min_peak_pct is not None:
+        params["min_peak_pct"] = min_peak_pct
+    if intensity is not None:
+        params["intensity"] = intensity
+    if curv is not None:
+        params["curv"] = curv
+    if tspring is not None:
+        params["tspring"] = tspring
+    if nspring is not None:
+        params["nspring"] = nspring
+    if repulse is not None:
+        params["repulse"] = repulse
+    if v_vertexno is not None:
+        params["v_vertexno"] = v_vertexno
+    if diag_vertex is not None:
+        params["diag_vertex"] = diag_vertex
+    if rip is not None:
+        params["rip"] = rip
+    if sigma_white is not None:
+        params["sigma_white"] = sigma_white
+    if sigma_pial is not None:
+        params["sigma_pial"] = sigma_pial
+    if output is not None:
+        params["output"] = output
+    if min_border_white is not None:
+        params["min_border_white"] = min_border_white
+    if max_border_white is not None:
+        params["max_border_white"] = max_border_white
+    if min_gray_white_border is not None:
+        params["min_gray_white_border"] = min_gray_white_border
+    if max_gray is not None:
+        params["max_gray"] = max_gray
+    if max_gray_csf_border is not None:
+        params["max_gray_csf_border"] = max_gray_csf_border
+    if min_gray_csf_border is not None:
+        params["min_gray_csf_border"] = min_gray_csf_border
+    if max_csf is not None:
+        params["max_csf"] = max_csf
+    return params
+
+
+def mris_make_surfaces_cargs(
+    params: MrisMakeSurfacesParameters,
+    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_make_surfaces")
+    cargs.append(params.get("subject_name"))
+    cargs.append(params.get("hemisphere"))
+    if params.get("white") is not None:
+        cargs.extend([
+            "-white",
+            params.get("white")
+        ])
+    if params.get("pial") is not None:
+        cargs.extend([
+            "-pial",
+            params.get("pial")
+        ])
+    if params.get("whiteonly"):
+        cargs.append("-whiteonly")
+    if params.get("nowhite"):
+        cargs.append("-nowhite")
+    if params.get("orig_white") is not None:
+        cargs.extend([
+            "-orig_white",
+            params.get("orig_white")
+        ])
+    if params.get("orig_pial") is not None:
+        cargs.extend([
+            "-orig_pial",
+            params.get("orig_pial")
+        ])
+    if params.get("q"):
+        cargs.append("-q")
+    if params.get("max_gray_scale") is not None:
+        cargs.extend([
+            "-max_gray_scale",
+            str(params.get("max_gray_scale"))
+        ])
+    if params.get("c"):
+        cargs.append("-c")
+    if params.get("cortex") is not None:
+        cargs.extend([
+            "-cortex",
+            str(params.get("cortex"))
+        ])
+    if params.get("w") is not None:
+        cargs.extend([
+            "-w",
+            str(params.get("w"))
+        ])
+    if params.get("first_wm_peak"):
+        cargs.append("-first_wm_peak")
+    if params.get("a_avgs") is not None:
+        cargs.extend([
+            "-a",
+            str(params.get("a_avgs"))
+        ])
+    if params.get("pa_avgs") is not None:
+        cargs.extend([
+            "-pa",
+            str(params.get("pa_avgs"))
+        ])
+    if params.get("wa_avgs") is not None:
+        cargs.extend([
+            "-wa",
+            str(params.get("wa_avgs"))
+        ])
+    if params.get("t1_vol") is not None:
+        cargs.extend([
+            "-T1",
+            params.get("t1_vol")
+        ])
+    if params.get("w_vol") is not None:
+        cargs.extend([
+            "-wvol",
+            params.get("w_vol")
+        ])
+    if params.get("long"):
+        cargs.append("-long")
+    if params.get("dura_thresh") is not None:
+        cargs.extend([
+            "-dura_thresh",
+            str(params.get("dura_thresh"))
+        ])
+    if params.get("sdir") is not None:
+        cargs.extend([
+            "-SDIR",
+            params.get("sdir")
+        ])
+    if params.get("erase_cerebellum"):
+        cargs.append("-erase_cerebellum")
+    if params.get("wm_weight") is not None:
+        cargs.extend([
+            "-wm_weight",
+            str(params.get("wm_weight"))
+        ])
+    if params.get("nsigma_above") is not None:
+        cargs.extend([
+            "-nsigma_above",
+            str(params.get("nsigma_above"))
+        ])
+    if params.get("nsigma_below") is not None:
+        cargs.extend([
+            "-nsigma_below",
+            str(params.get("nsigma_below"))
+        ])
+    if params.get("t2_min_inside") is not None:
+        cargs.extend([
+            "-T2_min_inside",
+            str(params.get("t2_min_inside"))
+        ])
+    if params.get("t2_max_inside") is not None:
+        cargs.extend([
+            "-T2_max_inside",
+            str(params.get("t2_max_inside"))
+        ])
+    if params.get("t2_outside_min") is not None:
+        cargs.extend([
+            "-T2_outside_min",
+            str(params.get("t2_outside_min"))
+        ])
+    if params.get("t2_outside_max") is not None:
+        cargs.extend([
+            "-T2_outside_max",
+            str(params.get("t2_outside_max"))
+        ])
+    if params.get("min_peak_pct") is not None:
+        cargs.extend([
+            "-min_peak_pct",
+            str(params.get("min_peak_pct"))
+        ])
+    if params.get("border_vals_hires"):
+        cargs.append("-border-vals-hires")
+    if params.get("no_unitize"):
+        cargs.append("-no-unitize")
+    if params.get("intensity") is not None:
+        cargs.extend([
+            "-intensity",
+            str(params.get("intensity"))
+        ])
+    if params.get("curv") is not None:
+        cargs.extend([
+            "-curv",
+            str(params.get("curv"))
+        ])
+    if params.get("tspring") is not None:
+        cargs.extend([
+            "-tspring",
+            str(params.get("tspring"))
+        ])
+    if params.get("nspring") is not None:
+        cargs.extend([
+            "-nspring",
+            str(params.get("nspring"))
+        ])
+    if params.get("repulse") is not None:
+        cargs.extend([
+            "-repulse",
+            str(params.get("repulse"))
+        ])
+    if params.get("save_target"):
+        cargs.append("-save-target")
+    if params.get("save_res"):
+        cargs.append("-save-res")
+    if params.get("v_vertexno") is not None:
+        cargs.extend([
+            "-v",
+            str(params.get("v_vertexno"))
+        ])
+    if params.get("diag_vertex") is not None:
+        cargs.extend([
+            "-diag-vertex",
+            str(params.get("diag_vertex"))
+        ])
+    if params.get("rip") is not None:
+        cargs.extend([
+            "-rip",
+            params.get("rip")
+        ])
+    if params.get("sigma_white") is not None:
+        cargs.extend([
+            "-sigma-white",
+            params.get("sigma_white")
+        ])
+    if params.get("sigma_pial") is not None:
+        cargs.extend([
+            "-sigma-pial",
+            params.get("sigma_pial")
+        ])
+    if params.get("output") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output")
+        ])
+    if params.get("min_border_white") is not None:
+        cargs.extend([
+            "-min_border_white",
+            str(params.get("min_border_white"))
+        ])
+    if params.get("max_border_white") is not None:
+        cargs.extend([
+            "-max_border_white",
+            str(params.get("max_border_white"))
+        ])
+    if params.get("min_gray_white_border") is not None:
+        cargs.extend([
+            "-min_gray_at_white_border",
+            str(params.get("min_gray_white_border"))
+        ])
+    if params.get("max_gray") is not None:
+        cargs.extend([
+            "-max_gray",
+            str(params.get("max_gray"))
+        ])
+    if params.get("max_gray_csf_border") is not None:
+        cargs.extend([
+            "-max_gray_at_csf_border",
+            str(params.get("max_gray_csf_border"))
+        ])
+    if params.get("min_gray_csf_border") is not None:
+        cargs.extend([
+            "-min_gray_at_csf_border",
+            str(params.get("min_gray_csf_border"))
+        ])
+    if params.get("max_csf") is not None:
+        cargs.extend([
+            "-max_csf",
+            str(params.get("max_csf"))
+        ])
+    return cargs
+
+
+def mris_make_surfaces_outputs(
+    params: MrisMakeSurfacesParameters,
+    execution: Execution,
+) -> MrisMakeSurfacesOutputs:
+    """
+    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 = MrisMakeSurfacesOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_make_surfaces_execute(
+    params: MrisMakeSurfacesParameters,
+    execution: Execution,
+) -> MrisMakeSurfacesOutputs:
+    """
+    Positions the tessellation of the cortical surface at the white matter surface,
+    then the gray matter surface, generating surface files along with a curvature
+    file and a surface file for cortical thickness.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisMakeSurfacesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_make_surfaces_cargs(params, execution)
+    ret = mris_make_surfaces_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_make_surfaces(
+    subject_name: str,
+    hemisphere: str,
+    white: str | None = None,
+    pial: str | None = None,
+    whiteonly: bool = False,
+    nowhite: bool = False,
+    orig_white: str | None = None,
+    orig_pial: str | None = None,
+    q: bool = False,
+    max_gray_scale: float | None = None,
+    c: bool = False,
+    cortex: float | None = None,
+    w: float | None = None,
+    first_wm_peak: bool = False,
+    a_avgs: float | None = None,
+    pa_avgs: float | None = None,
+    wa_avgs: float | None = None,
+    t1_vol: str | None = None,
+    w_vol: str | None = None,
+    long: bool = False,
+    dura_thresh: float | None = None,
+    sdir: str | None = None,
+    erase_cerebellum: bool = False,
+    wm_weight: float | None = None,
+    nsigma_above: float | None = None,
+    nsigma_below: float | None = None,
+    t2_min_inside: float | None = None,
+    t2_max_inside: float | None = None,
+    t2_outside_min: float | None = None,
+    t2_outside_max: float | None = None,
+    min_peak_pct: float | None = None,
+    border_vals_hires: bool = False,
+    no_unitize: bool = False,
+    intensity: float | None = None,
+    curv: float | None = None,
+    tspring: float | None = None,
+    nspring: float | None = None,
+    repulse: float | None = None,
+    save_target: bool = False,
+    save_res: bool = False,
+    v_vertexno: float | None = None,
+    diag_vertex: float | None = None,
+    rip: str | None = None,
+    sigma_white: str | None = None,
+    sigma_pial: str | None = None,
+    output: str | None = None,
+    min_border_white: float | None = None,
+    max_border_white: float | None = None,
+    min_gray_white_border: float | None = None,
+    max_gray: float | None = None,
+    max_gray_csf_border: float | None = None,
+    min_gray_csf_border: float | None = None,
+    max_csf: float | None = None,
+    runner: Runner | None = None,
+) -> MrisMakeSurfacesOutputs:
+    """
+    Positions the tessellation of the cortical surface at the white matter surface,
+    then the gray matter surface, generating surface files along with a curvature
+    file and a surface file for cortical thickness.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_name: Name of the subject.
+        hemisphere: Brain hemisphere (r or l).
+        white: Output name for white surface (default is 'white'). Set to\
+            NOWHITE to generate but not save white surface.
+        pial: Output name for pial surface (default is 'pial').
+        whiteonly: Only generate white matter surface.
+        nowhite: Only generate pial surface.
+        orig_white: Specify a white surface to start with.
+        orig_pial: Specify a pial surface to start with.
+        q: Omit self-intersection and only generate gray/white surface.
+        max_gray_scale: Set maximum gray scale value.
+        c: Do not create curvature and area files from white matter surface.
+        cortex: Set to 0 to turn off creation of cortex label file.
+        w: Unused argument.
+        first_wm_peak: Settle WM surface at first peak in intensity profile\
+            instead of highest.
+        a_avgs: Average curvature values a number of times (default=10).
+        pa_avgs: Average pial curvature values a max of a number of times\
+            (default=16).
+        wa_avgs: Average white curvature values a max of a number of times\
+            (default=4).
+        t1_vol: Specify T1 volume (default is brain).
+        w_vol: Specify white volume and <hires> option.
+        long: Run longitudinal analysis.
+        dura_thresh: Set a threshold for the multi-echo mprage dura avoidance.
+        sdir: Specify SUBJECTS_DIR.
+        erase_cerebellum: Erase cerebellar labeled voxels if aseg is loaded.
+        wm_weight: Weighting of WM mean in calculating T2 threshold of\
+            disallowed GM values, default=3.
+        nsigma_above: # of sigmas above the mean to allow gray matter T2\
+            intensities.
+        nsigma_below: # of sigmas below the mean to allow gray matter T2\
+            intensities.
+        t2_min_inside: Specify threshold for min T2 value allowed to be\
+            interior to the cortical ribbon.
+        t2_max_inside: Specify threshold for max T2 value allowed to be\
+            interior to the cortical ribbon.
+        t2_outside_min: Specify threshold for min T2 value outside of pial\
+            surface that will cause surface to deform outwards.
+        t2_outside_max: Specify threshold for max T2 value outside of pial\
+            surface that will cause surface to deform outwards.
+        min_peak_pct: Specify the pct of the histo peak in the local gm\
+            histogram to use as threshold for finding the local inside and outside\
+            gm thresholds.
+        border_vals_hires: Turn on hires options in\
+            MRIScomputeBorderValues_new(). May not be helpful.
+        no_unitize: Turn off face normal unitization.
+        intensity: Set weight of intensity cost.
+        curv: Set weight of curvature cost.
+        tspring: Set weight of tangential spring cost.
+        nspring: Set weight of normal spring cost.
+        repulse: Set weight of repulsion force.
+        save_target: Save target surface for debugging.
+        save_res: Save residual for debugging.
+        v_vertexno: Set Gdiag_no to vertex number.
+        diag_vertex: Set Gdiag_no to vertex number and turn off writing of\
+            cortex label or curvature files.
+        rip: Save ripflag as overlay. Specify full path including hemi, suffix,\
+            etc.
+        sigma_white: Save white surface sigma as overlay. Specify full path\
+            including hemi, suffix, etc.
+        sigma_pial: Save pial surface sigma as overlay. Specify full path\
+            including hemi, suffix, etc.
+        output: Append suffix to all outputs to prevent over-writing.
+        min_border_white: Minimum border white.
+        max_border_white: Maximum border white.
+        min_gray_white_border: Minimum gray at white border.
+        max_gray: Maximum gray value.
+        max_gray_csf_border: Maximum gray at CSF border.
+        min_gray_csf_border: Minimum gray at CSF border.
+        max_csf: Maximum CSF value.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisMakeSurfacesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MAKE_SURFACES_METADATA)
+    params = mris_make_surfaces_params(
+        subject_name=subject_name,
+        hemisphere=hemisphere,
+        white=white,
+        pial=pial,
+        whiteonly=whiteonly,
+        nowhite=nowhite,
+        orig_white=orig_white,
+        orig_pial=orig_pial,
+        q=q,
+        max_gray_scale=max_gray_scale,
+        c=c,
+        cortex=cortex,
+        w=w,
+        first_wm_peak=first_wm_peak,
+        a_avgs=a_avgs,
+        pa_avgs=pa_avgs,
+        wa_avgs=wa_avgs,
+        t1_vol=t1_vol,
+        w_vol=w_vol,
+        long=long,
+        dura_thresh=dura_thresh,
+        sdir=sdir,
+        erase_cerebellum=erase_cerebellum,
+        wm_weight=wm_weight,
+        nsigma_above=nsigma_above,
+        nsigma_below=nsigma_below,
+        t2_min_inside=t2_min_inside,
+        t2_max_inside=t2_max_inside,
+        t2_outside_min=t2_outside_min,
+        t2_outside_max=t2_outside_max,
+        min_peak_pct=min_peak_pct,
+        border_vals_hires=border_vals_hires,
+        no_unitize=no_unitize,
+        intensity=intensity,
+        curv=curv,
+        tspring=tspring,
+        nspring=nspring,
+        repulse=repulse,
+        save_target=save_target,
+        save_res=save_res,
+        v_vertexno=v_vertexno,
+        diag_vertex=diag_vertex,
+        rip=rip,
+        sigma_white=sigma_white,
+        sigma_pial=sigma_pial,
+        output=output,
+        min_border_white=min_border_white,
+        max_border_white=max_border_white,
+        min_gray_white_border=min_gray_white_border,
+        max_gray=max_gray,
+        max_gray_csf_border=max_gray_csf_border,
+        min_gray_csf_border=min_gray_csf_border,
+        max_csf=max_csf,
+    )
+    return mris_make_surfaces_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_MAKE_SURFACES_METADATA",
+    "MrisMakeSurfacesOutputs",
+    "MrisMakeSurfacesParameters",
+    "mris_make_surfaces",
+    "mris_make_surfaces_params",
+]