niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/samseg.py

@@ -0,0 +1,682 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SAMSEG_METADATA = Metadata(
+    id="1947f646fba1c79e354f5efabbda10d0a11595ce.boutiques",
+    name="samseg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+SamsegParameters = typing.TypedDict('SamsegParameters', {
+    "__STYX_TYPE__": typing.Literal["samseg"],
+    "input_files": list[InputPathType],
+    "t1w_files": typing.NotRequired[list[InputPathType] | None],
+    "t2w_files": typing.NotRequired[list[InputPathType] | None],
+    "flair_files": typing.NotRequired[list[InputPathType] | None],
+    "other_modality_files": typing.NotRequired[list[InputPathType] | None],
+    "output_directory": str,
+    "options_file": typing.NotRequired[InputPathType | None],
+    "dissection_photo_mode": typing.NotRequired[str | None],
+    "save_history": bool,
+    "subject": typing.NotRequired[str | None],
+    "save_posteriors": bool,
+    "save_probabilities": bool,
+    "no_save_warp": bool,
+    "mrf": bool,
+    "no_mrf": bool,
+    "threads": typing.NotRequired[float | None],
+    "atlas_directory": typing.NotRequired[str | None],
+    "gmm_file": typing.NotRequired[InputPathType | None],
+    "no_block_coordinate_descent": bool,
+    "logdomain_costandgradient_calculator": bool,
+    "no_logdomain_costandgradient_calculator": bool,
+    "recon": bool,
+    "fill": bool,
+    "normalization2": bool,
+    "use_t2w": bool,
+    "use_flair": bool,
+    "hires": bool,
+    "subjects_directory": typing.NotRequired[str | None],
+    "pallidum_separate": bool,
+    "stiffness": typing.NotRequired[float | None],
+    "lesion": bool,
+    "lesion_mask_pattern": typing.NotRequired[list[float] | None],
+    "bias_field_smoothing_kernel": typing.NotRequired[float | None],
+    "registration_file": typing.NotRequired[InputPathType | None],
+    "regmat_file": typing.NotRequired[InputPathType | None],
+    "init_lta": typing.NotRequired[InputPathType | None],
+    "reg_only": bool,
+    "save_mesh": bool,
+    "max_iters": typing.NotRequired[float | None],
+    "dice_file": typing.NotRequired[InputPathType | None],
+    "ignore_unknown": bool,
+    "smooth_wm_cortex": typing.NotRequired[float | None],
+    "profile_file": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "samseg": samseg_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 {
+        "samseg": samseg_outputs,
+    }.get(t)
+
+
+class SamsegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `samseg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    segmentation_output: OutputPathType
+    """Segmentation output file."""
+    posteriors_output: OutputPathType
+    """Posterior probabilities output file."""
+    probabilities_output: OutputPathType
+    """Probabilities output file, including post, prior, and likelihood."""
+    mesh_output: OutputPathType
+    """Mesh output file (if save-mesh is enabled)."""
+
+
+def samseg_params(
+    input_files: list[InputPathType],
+    output_directory: str,
+    t1w_files: list[InputPathType] | None = None,
+    t2w_files: list[InputPathType] | None = None,
+    flair_files: list[InputPathType] | None = None,
+    other_modality_files: list[InputPathType] | None = None,
+    options_file: InputPathType | None = None,
+    dissection_photo_mode: str | None = None,
+    save_history: bool = False,
+    subject: str | None = None,
+    save_posteriors: bool = False,
+    save_probabilities: bool = False,
+    no_save_warp: bool = False,
+    mrf: bool = False,
+    no_mrf: bool = False,
+    threads: float | None = None,
+    atlas_directory: str | None = None,
+    gmm_file: InputPathType | None = None,
+    no_block_coordinate_descent: bool = False,
+    logdomain_costandgradient_calculator: bool = False,
+    no_logdomain_costandgradient_calculator: bool = False,
+    recon: bool = False,
+    fill: bool = False,
+    normalization2: bool = False,
+    use_t2w: bool = False,
+    use_flair: bool = False,
+    hires: bool = False,
+    subjects_directory: str | None = None,
+    pallidum_separate: bool = False,
+    stiffness: float | None = None,
+    lesion: bool = False,
+    lesion_mask_pattern: list[float] | None = None,
+    bias_field_smoothing_kernel: float | None = None,
+    registration_file: InputPathType | None = None,
+    regmat_file: InputPathType | None = None,
+    init_lta: InputPathType | None = None,
+    reg_only: bool = False,
+    save_mesh: bool = False,
+    max_iters: float | None = None,
+    dice_file: InputPathType | None = None,
+    ignore_unknown: bool = False,
+    smooth_wm_cortex: float | None = None,
+    profile_file: InputPathType | None = None,
+) -> SamsegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input image files, must be in registration with each\
+            other.
+        output_directory: Output directory where results will be saved.
+        t1w_files: T1-weighted input file, causes input to be conformed unless\
+            --hires is used.
+        t2w_files: T2-weighted input file.
+        flair_files: FLAIR-weighted input file.
+        other_modality_files: Specific mode input files, each associated with a\
+            custom modality name.
+        options_file: JSON file for specifying advanced options.
+        dissection_photo_mode: Mode for processing 3D reconstructed dissection\
+            photos, specifying left/right/both.
+        save_history: Turns on saving of processing history.
+        subject: Subject identifier, sets output directory to\
+            subject/mri/samseg. The first input must be the conformed T1 weighted\
+            input.
+        save_posteriors: Save posterior probabilities.
+        save_probabilities: Save posterior, prior, and likelihood as 3-frame\
+            volume for each tissue type.
+        no_save_warp: Do not save m3z-style warp.
+        mrf: Perform Markov Random Field processing.
+        no_mrf: Do not perform Markov Random Field processing.
+        threads: Set the number of CPUs to use.
+        atlas_directory: Path to the SAMSEG atlas directory.
+        gmm_file: Gaussian Mixture Model file.
+        no_block_coordinate_descent: Do not use block coordinate descent.
+        logdomain_costandgradient_calculator: Use log-domain cost and gradient\
+            calculator.
+        no_logdomain_costandgradient_calculator: Do not use log-domain cost and\
+            gradient calculator.
+        recon: Run recon-all.
+        fill: Use samseg to create filled.mgz instead of recon-all.
+        normalization2: Use samseg to create brain.mgz instead of recon-all\
+            (with --recon).
+        use_t2w: Use the T2-weighted input when running recon-all.
+        use_flair: Use the FLAIR-weighted input when running recon-all.
+        hires: Use -hires when running recon-all.
+        subjects_directory: Path to the SUBJECTS_DIR.
+        pallidum_separate: Move pallidum outside of global white matter class,\
+            used for analyzing T2 or FLAIR.
+        stiffness: Set mesh stiffness.
+        lesion: Turn on lesion segmentation.
+        lesion_mask_pattern: Pattern needed when using T2 for lesion mask,\
+            e.g., 0 1.
+        bias_field_smoothing_kernel: Width of bias field smoothness.
+        registration_file: Registration file (LTA or MAT) as output by samseg.
+        regmat_file: Same as --reg.
+        init_lta: Initial registration LTA file.
+        reg_only: Only perform registration.
+        save_mesh: Save the mesh, useful for longitudinal analysis.
+        max_iters: Maximum number of iterations.
+        dice_file: DICE coefficient file for segmentation.
+        ignore_unknown: Ignore unknown flags.
+        smooth_wm_cortex: Smooth white matter and cortex priors using specified\
+            sigma value.
+        profile_file: Run using the cProfile Python profiler, with the\
+            specified profile file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "samseg",
+        "input_files": input_files,
+        "output_directory": output_directory,
+        "save_history": save_history,
+        "save_posteriors": save_posteriors,
+        "save_probabilities": save_probabilities,
+        "no_save_warp": no_save_warp,
+        "mrf": mrf,
+        "no_mrf": no_mrf,
+        "no_block_coordinate_descent": no_block_coordinate_descent,
+        "logdomain_costandgradient_calculator": logdomain_costandgradient_calculator,
+        "no_logdomain_costandgradient_calculator": no_logdomain_costandgradient_calculator,
+        "recon": recon,
+        "fill": fill,
+        "normalization2": normalization2,
+        "use_t2w": use_t2w,
+        "use_flair": use_flair,
+        "hires": hires,
+        "pallidum_separate": pallidum_separate,
+        "lesion": lesion,
+        "reg_only": reg_only,
+        "save_mesh": save_mesh,
+        "ignore_unknown": ignore_unknown,
+    }
+    if t1w_files is not None:
+        params["t1w_files"] = t1w_files
+    if t2w_files is not None:
+        params["t2w_files"] = t2w_files
+    if flair_files is not None:
+        params["flair_files"] = flair_files
+    if other_modality_files is not None:
+        params["other_modality_files"] = other_modality_files
+    if options_file is not None:
+        params["options_file"] = options_file
+    if dissection_photo_mode is not None:
+        params["dissection_photo_mode"] = dissection_photo_mode
+    if subject is not None:
+        params["subject"] = subject
+    if threads is not None:
+        params["threads"] = threads
+    if atlas_directory is not None:
+        params["atlas_directory"] = atlas_directory
+    if gmm_file is not None:
+        params["gmm_file"] = gmm_file
+    if subjects_directory is not None:
+        params["subjects_directory"] = subjects_directory
+    if stiffness is not None:
+        params["stiffness"] = stiffness
+    if lesion_mask_pattern is not None:
+        params["lesion_mask_pattern"] = lesion_mask_pattern
+    if bias_field_smoothing_kernel is not None:
+        params["bias_field_smoothing_kernel"] = bias_field_smoothing_kernel
+    if registration_file is not None:
+        params["registration_file"] = registration_file
+    if regmat_file is not None:
+        params["regmat_file"] = regmat_file
+    if init_lta is not None:
+        params["init_lta"] = init_lta
+    if max_iters is not None:
+        params["max_iters"] = max_iters
+    if dice_file is not None:
+        params["dice_file"] = dice_file
+    if smooth_wm_cortex is not None:
+        params["smooth_wm_cortex"] = smooth_wm_cortex
+    if profile_file is not None:
+        params["profile_file"] = profile_file
+    return params
+
+
+def samseg_cargs(
+    params: SamsegParameters,
+    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("samseg")
+    cargs.extend([
+        "--i",
+        *[execution.input_file(f) for f in params.get("input_files")]
+    ])
+    if params.get("t1w_files") is not None:
+        cargs.extend([
+            "--t1w",
+            *[execution.input_file(f) for f in params.get("t1w_files")]
+        ])
+    if params.get("t2w_files") is not None:
+        cargs.extend([
+            "--t2w",
+            *[execution.input_file(f) for f in params.get("t2w_files")]
+        ])
+    if params.get("flair_files") is not None:
+        cargs.extend([
+            "--flair",
+            *[execution.input_file(f) for f in params.get("flair_files")]
+        ])
+    if params.get("other_modality_files") is not None:
+        cargs.extend([
+            "--mode",
+            *[execution.input_file(f) for f in params.get("other_modality_files")]
+        ])
+    cargs.extend([
+        "--o",
+        params.get("output_directory")
+    ])
+    if params.get("options_file") is not None:
+        cargs.extend([
+            "--options",
+            execution.input_file(params.get("options_file"))
+        ])
+    if params.get("dissection_photo_mode") is not None:
+        cargs.extend([
+            "--dissection-photo",
+            params.get("dissection_photo_mode")
+        ])
+    if params.get("save_history"):
+        cargs.append("--history")
+    if params.get("subject") is not None:
+        cargs.extend([
+            "--s",
+            params.get("subject")
+        ])
+    if params.get("save_posteriors"):
+        cargs.append("--save-posteriors")
+    if params.get("save_probabilities"):
+        cargs.append("--save-probabilities")
+    if params.get("no_save_warp"):
+        cargs.append("--no-save-warp")
+    if params.get("mrf"):
+        cargs.append("--mrf")
+    if params.get("no_mrf"):
+        cargs.append("--no-mrf")
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("atlas_directory") is not None:
+        cargs.extend([
+            "--atlas",
+            params.get("atlas_directory")
+        ])
+    if params.get("gmm_file") is not None:
+        cargs.extend([
+            "--gmm",
+            execution.input_file(params.get("gmm_file"))
+        ])
+    if params.get("no_block_coordinate_descent"):
+        cargs.append("--no-block-coordinate-descent")
+    if params.get("logdomain_costandgradient_calculator"):
+        cargs.append("--logdomain-costandgradient-calculator")
+    if params.get("no_logdomain_costandgradient_calculator"):
+        cargs.append("--no-logdomain-costandgradient-calculator")
+    if params.get("recon"):
+        cargs.append("--recon")
+    if params.get("fill"):
+        cargs.append("--fill")
+    if params.get("normalization2"):
+        cargs.append("--normalization2")
+    if params.get("use_t2w"):
+        cargs.append("--use-t2w")
+    if params.get("use_flair"):
+        cargs.append("--use-flair")
+    if params.get("hires"):
+        cargs.append("--hires")
+    if params.get("subjects_directory") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subjects_directory")
+        ])
+    if params.get("pallidum_separate"):
+        cargs.append("--pallidum-separate")
+    if params.get("stiffness") is not None:
+        cargs.extend([
+            "--stiffness",
+            str(params.get("stiffness"))
+        ])
+    if params.get("lesion"):
+        cargs.append("--lesion")
+    if params.get("lesion_mask_pattern") is not None:
+        cargs.extend([
+            "--lesion-mask-pattern",
+            *map(str, params.get("lesion_mask_pattern"))
+        ])
+    if params.get("bias_field_smoothing_kernel") is not None:
+        cargs.extend([
+            "--bias-field-smoothing-kernel",
+            str(params.get("bias_field_smoothing_kernel"))
+        ])
+    if params.get("registration_file") is not None:
+        cargs.extend([
+            "--reg",
+            execution.input_file(params.get("registration_file"))
+        ])
+    if params.get("regmat_file") is not None:
+        cargs.extend([
+            "--regmat",
+            execution.input_file(params.get("regmat_file"))
+        ])
+    if params.get("init_lta") is not None:
+        cargs.extend([
+            "--initlta",
+            execution.input_file(params.get("init_lta"))
+        ])
+    if params.get("reg_only"):
+        cargs.append("--reg-only")
+    if params.get("save_mesh"):
+        cargs.append("--save-mesh")
+    if params.get("max_iters") is not None:
+        cargs.extend([
+            "--max-iters",
+            str(params.get("max_iters"))
+        ])
+    if params.get("dice_file") is not None:
+        cargs.extend([
+            "--dice",
+            execution.input_file(params.get("dice_file"))
+        ])
+    if params.get("ignore_unknown"):
+        cargs.append("--ignore-unknown")
+    if params.get("smooth_wm_cortex") is not None:
+        cargs.extend([
+            "--smooth-wm-cortex",
+            str(params.get("smooth_wm_cortex"))
+        ])
+    if params.get("profile_file") is not None:
+        cargs.extend([
+            "--profile",
+            execution.input_file(params.get("profile_file"))
+        ])
+    return cargs
+
+
+def samseg_outputs(
+    params: SamsegParameters,
+    execution: Execution,
+) -> SamsegOutputs:
+    """
+    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 = SamsegOutputs(
+        root=execution.output_file("."),
+        segmentation_output=execution.output_file(params.get("output_directory") + "/seg.mgz"),
+        posteriors_output=execution.output_file(params.get("output_directory") + "/posteriors.mgz"),
+        probabilities_output=execution.output_file(params.get("output_directory") + "/probabilities.mgz"),
+        mesh_output=execution.output_file(params.get("output_directory") + "/mesh.stl"),
+    )
+    return ret
+
+
+def samseg_execute(
+    params: SamsegParameters,
+    execution: Execution,
+) -> SamsegOutputs:
+    """
+    SAMSEG (Statistical and Algorithmic Methods for Segmentation) is a tool for
+    segmenting neuroimaging data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SamsegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = samseg_cargs(params, execution)
+    ret = samseg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def samseg(
+    input_files: list[InputPathType],
+    output_directory: str,
+    t1w_files: list[InputPathType] | None = None,
+    t2w_files: list[InputPathType] | None = None,
+    flair_files: list[InputPathType] | None = None,
+    other_modality_files: list[InputPathType] | None = None,
+    options_file: InputPathType | None = None,
+    dissection_photo_mode: str | None = None,
+    save_history: bool = False,
+    subject: str | None = None,
+    save_posteriors: bool = False,
+    save_probabilities: bool = False,
+    no_save_warp: bool = False,
+    mrf: bool = False,
+    no_mrf: bool = False,
+    threads: float | None = None,
+    atlas_directory: str | None = None,
+    gmm_file: InputPathType | None = None,
+    no_block_coordinate_descent: bool = False,
+    logdomain_costandgradient_calculator: bool = False,
+    no_logdomain_costandgradient_calculator: bool = False,
+    recon: bool = False,
+    fill: bool = False,
+    normalization2: bool = False,
+    use_t2w: bool = False,
+    use_flair: bool = False,
+    hires: bool = False,
+    subjects_directory: str | None = None,
+    pallidum_separate: bool = False,
+    stiffness: float | None = None,
+    lesion: bool = False,
+    lesion_mask_pattern: list[float] | None = None,
+    bias_field_smoothing_kernel: float | None = None,
+    registration_file: InputPathType | None = None,
+    regmat_file: InputPathType | None = None,
+    init_lta: InputPathType | None = None,
+    reg_only: bool = False,
+    save_mesh: bool = False,
+    max_iters: float | None = None,
+    dice_file: InputPathType | None = None,
+    ignore_unknown: bool = False,
+    smooth_wm_cortex: float | None = None,
+    profile_file: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> SamsegOutputs:
+    """
+    SAMSEG (Statistical and Algorithmic Methods for Segmentation) is a tool for
+    segmenting neuroimaging data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_files: Input image files, must be in registration with each\
+            other.
+        output_directory: Output directory where results will be saved.
+        t1w_files: T1-weighted input file, causes input to be conformed unless\
+            --hires is used.
+        t2w_files: T2-weighted input file.
+        flair_files: FLAIR-weighted input file.
+        other_modality_files: Specific mode input files, each associated with a\
+            custom modality name.
+        options_file: JSON file for specifying advanced options.
+        dissection_photo_mode: Mode for processing 3D reconstructed dissection\
+            photos, specifying left/right/both.
+        save_history: Turns on saving of processing history.
+        subject: Subject identifier, sets output directory to\
+            subject/mri/samseg. The first input must be the conformed T1 weighted\
+            input.
+        save_posteriors: Save posterior probabilities.
+        save_probabilities: Save posterior, prior, and likelihood as 3-frame\
+            volume for each tissue type.
+        no_save_warp: Do not save m3z-style warp.
+        mrf: Perform Markov Random Field processing.
+        no_mrf: Do not perform Markov Random Field processing.
+        threads: Set the number of CPUs to use.
+        atlas_directory: Path to the SAMSEG atlas directory.
+        gmm_file: Gaussian Mixture Model file.
+        no_block_coordinate_descent: Do not use block coordinate descent.
+        logdomain_costandgradient_calculator: Use log-domain cost and gradient\
+            calculator.
+        no_logdomain_costandgradient_calculator: Do not use log-domain cost and\
+            gradient calculator.
+        recon: Run recon-all.
+        fill: Use samseg to create filled.mgz instead of recon-all.
+        normalization2: Use samseg to create brain.mgz instead of recon-all\
+            (with --recon).
+        use_t2w: Use the T2-weighted input when running recon-all.
+        use_flair: Use the FLAIR-weighted input when running recon-all.
+        hires: Use -hires when running recon-all.
+        subjects_directory: Path to the SUBJECTS_DIR.
+        pallidum_separate: Move pallidum outside of global white matter class,\
+            used for analyzing T2 or FLAIR.
+        stiffness: Set mesh stiffness.
+        lesion: Turn on lesion segmentation.
+        lesion_mask_pattern: Pattern needed when using T2 for lesion mask,\
+            e.g., 0 1.
+        bias_field_smoothing_kernel: Width of bias field smoothness.
+        registration_file: Registration file (LTA or MAT) as output by samseg.
+        regmat_file: Same as --reg.
+        init_lta: Initial registration LTA file.
+        reg_only: Only perform registration.
+        save_mesh: Save the mesh, useful for longitudinal analysis.
+        max_iters: Maximum number of iterations.
+        dice_file: DICE coefficient file for segmentation.
+        ignore_unknown: Ignore unknown flags.
+        smooth_wm_cortex: Smooth white matter and cortex priors using specified\
+            sigma value.
+        profile_file: Run using the cProfile Python profiler, with the\
+            specified profile file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SamsegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SAMSEG_METADATA)
+    params = samseg_params(
+        input_files=input_files,
+        t1w_files=t1w_files,
+        t2w_files=t2w_files,
+        flair_files=flair_files,
+        other_modality_files=other_modality_files,
+        output_directory=output_directory,
+        options_file=options_file,
+        dissection_photo_mode=dissection_photo_mode,
+        save_history=save_history,
+        subject=subject,
+        save_posteriors=save_posteriors,
+        save_probabilities=save_probabilities,
+        no_save_warp=no_save_warp,
+        mrf=mrf,
+        no_mrf=no_mrf,
+        threads=threads,
+        atlas_directory=atlas_directory,
+        gmm_file=gmm_file,
+        no_block_coordinate_descent=no_block_coordinate_descent,
+        logdomain_costandgradient_calculator=logdomain_costandgradient_calculator,
+        no_logdomain_costandgradient_calculator=no_logdomain_costandgradient_calculator,
+        recon=recon,
+        fill=fill,
+        normalization2=normalization2,
+        use_t2w=use_t2w,
+        use_flair=use_flair,
+        hires=hires,
+        subjects_directory=subjects_directory,
+        pallidum_separate=pallidum_separate,
+        stiffness=stiffness,
+        lesion=lesion,
+        lesion_mask_pattern=lesion_mask_pattern,
+        bias_field_smoothing_kernel=bias_field_smoothing_kernel,
+        registration_file=registration_file,
+        regmat_file=regmat_file,
+        init_lta=init_lta,
+        reg_only=reg_only,
+        save_mesh=save_mesh,
+        max_iters=max_iters,
+        dice_file=dice_file,
+        ignore_unknown=ignore_unknown,
+        smooth_wm_cortex=smooth_wm_cortex,
+        profile_file=profile_file,
+    )
+    return samseg_execute(params, execution)
+
+
+__all__ = [
+    "SAMSEG_METADATA",
+    "SamsegOutputs",
+    "SamsegParameters",
+    "samseg",
+    "samseg_params",
+]