niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_segstats.py

@@ -0,0 +1,903 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SEGSTATS_METADATA = Metadata(
+    id="de1b9dfa3f1dac83d5a96b745b8f327109cb07d4.boutiques",
+    name="mri_segstats",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSegstatsParameters = typing.TypedDict('MriSegstatsParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_segstats"],
+    "segvol": InputPathType,
+    "annot_subject": typing.NotRequired[str | None],
+    "annot_hemisphere": typing.NotRequired[str | None],
+    "annot_parcellation": typing.NotRequired[str | None],
+    "slabel_subject": typing.NotRequired[str | None],
+    "slabel_hemisphere": typing.NotRequired[str | None],
+    "slabel_label": typing.NotRequired[InputPathType | None],
+    "output_file": str,
+    "partial_vol_comp": typing.NotRequired[InputPathType | None],
+    "input_volume": typing.NotRequired[InputPathType | None],
+    "seg_erode": typing.NotRequired[float | None],
+    "frame": typing.NotRequired[float | None],
+    "robust": typing.NotRequired[float | None],
+    "square_input": bool,
+    "sqrt_input": bool,
+    "multiply_input": typing.NotRequired[float | None],
+    "divide_input": typing.NotRequired[float | None],
+    "snr_column": bool,
+    "absolute_value": bool,
+    "accumulate_mean": bool,
+    "color_table": typing.NotRequired[InputPathType | None],
+    "default_color_table": bool,
+    "gca_color_table": typing.NotRequired[InputPathType | None],
+    "ids": typing.NotRequired[str | None],
+    "exclude_ids": typing.NotRequired[str | None],
+    "exclude_gm_wm": bool,
+    "surf_wm_vol": bool,
+    "surf_ctx_vol": bool,
+    "no_global_stats": bool,
+    "empty_segments": bool,
+    "ctab_output": typing.NotRequired[str | None],
+    "mask_volume": typing.NotRequired[InputPathType | None],
+    "mask_threshold": typing.NotRequired[float | None],
+    "mask_sign": typing.NotRequired[str | None],
+    "mask_frame": typing.NotRequired[float | None],
+    "invert_mask": bool,
+    "mask_erode": typing.NotRequired[float | None],
+    "brain_vol_seg": bool,
+    "brain_mask_vol": typing.NotRequired[InputPathType | None],
+    "subcortical_gray": bool,
+    "total_gray": bool,
+    "intracranial_volume": bool,
+    "intracranial_volume_only": bool,
+    "old_intracranial_volume_only": bool,
+    "talairach_transform": typing.NotRequired[InputPathType | None],
+    "xfm_to_etiv": typing.NotRequired[str | None],
+    "euler_hole_count": bool,
+    "avg_waveform": typing.NotRequired[str | None],
+    "sum_waveform": typing.NotRequired[str | None],
+    "avg_waveform_vol": typing.NotRequired[str | None],
+    "remove_avgwf_mean": bool,
+    "spatial_frame_avg": typing.NotRequired[str | None],
+    "voxel_crs": typing.NotRequired[str | None],
+    "replace_ids": typing.NotRequired[str | None],
+    "replace_ids_file": typing.NotRequired[InputPathType | None],
+    "gtm_default_seg_merge": bool,
+    "gtm_default_seg_merge_choroid": bool,
+    "qa_stats_file": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "random_seed": 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 {
+        "mri_segstats": mri_segstats_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_segstats": mri_segstats_outputs,
+    }.get(t)
+
+
+class MriSegstatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_segstats(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    summary_output_file: OutputPathType
+    """Output file for summary statistics."""
+    avg_waveform_output: OutputPathType | None
+    """Average waveform output text file."""
+    sum_waveform_output: OutputPathType | None
+    """Sum waveform output text file."""
+    avg_waveform_vol_output: OutputPathType | None
+    """Average waveform volume output file."""
+    spatial_frame_avg_output: OutputPathType | None
+    """Spatial frame average output file."""
+    ctab_output_file: OutputPathType | None
+    """Output color table with the reported segmentations."""
+
+
+def mri_segstats_params(
+    segvol: InputPathType,
+    output_file: str,
+    annot_subject: str | None = None,
+    annot_hemisphere: str | None = None,
+    annot_parcellation: str | None = None,
+    slabel_subject: str | None = None,
+    slabel_hemisphere: str | None = None,
+    slabel_label: InputPathType | None = None,
+    partial_vol_comp: InputPathType | None = None,
+    input_volume: InputPathType | None = None,
+    seg_erode: float | None = None,
+    frame: float | None = None,
+    robust: float | None = None,
+    square_input: bool = False,
+    sqrt_input: bool = False,
+    multiply_input: float | None = None,
+    divide_input: float | None = None,
+    snr_column: bool = False,
+    absolute_value: bool = False,
+    accumulate_mean: bool = False,
+    color_table: InputPathType | None = None,
+    default_color_table: bool = False,
+    gca_color_table: InputPathType | None = None,
+    ids: str | None = None,
+    exclude_ids: str | None = None,
+    exclude_gm_wm: bool = False,
+    surf_wm_vol: bool = False,
+    surf_ctx_vol: bool = False,
+    no_global_stats: bool = False,
+    empty_segments: bool = False,
+    ctab_output: str | None = None,
+    mask_volume: InputPathType | None = None,
+    mask_threshold: float | None = None,
+    mask_sign: str | None = None,
+    mask_frame: float | None = None,
+    invert_mask: bool = False,
+    mask_erode: float | None = None,
+    brain_vol_seg: bool = False,
+    brain_mask_vol: InputPathType | None = None,
+    subcortical_gray: bool = False,
+    total_gray: bool = False,
+    intracranial_volume: bool = False,
+    intracranial_volume_only: bool = False,
+    old_intracranial_volume_only: bool = False,
+    talairach_transform: InputPathType | None = None,
+    xfm_to_etiv: str | None = None,
+    euler_hole_count: bool = False,
+    avg_waveform: str | None = None,
+    sum_waveform: str | None = None,
+    avg_waveform_vol: str | None = None,
+    remove_avgwf_mean: bool = False,
+    spatial_frame_avg: str | None = None,
+    voxel_crs: str | None = None,
+    replace_ids: str | None = None,
+    replace_ids_file: InputPathType | None = None,
+    gtm_default_seg_merge: bool = False,
+    gtm_default_seg_merge_choroid: bool = False,
+    qa_stats_file: str | None = None,
+    subjects_dir: str | None = None,
+    random_seed: float | None = None,
+) -> MriSegstatsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        segvol: Input segmentation volume. This volume's voxel values indicate\
+            a segmentation or class.
+        output_file: ASCII file in which summary statistics are saved.
+        annot_subject: Create a segmentation from hemi.parc.annot. Subject is\
+            the name of the subject.
+        annot_hemisphere:.
+        annot_parcellation:.
+        slabel_subject: Create a segmentation from the given surface label. The\
+            points in the label are given a value of 1; 0 for outside.
+        slabel_hemisphere:.
+        slabel_label:.
+        partial_vol_comp: Use pvvol to compensate for partial voluming,\
+            resulting in more accurate volumes.
+        input_volume: Input volume from which to compute more statistics.
+        seg_erode: Erode segmentation boundaries by Nerodes.
+        frame: Report statistics of the input volume at the specified 0-based\
+            frame number.
+        robust: Compute stats after excluding a percentage of high and low\
+            values.
+        square_input: Compute the square of the input before computing stats.
+        sqrt_input: Compute the square root of the input before computing\
+            stats.
+        multiply_input: Multiply input by value.
+        divide_input: Divide input by value.
+        snr_column: Save mean/std as extra column in output table.
+        absolute_value: Compute absolute value of input before spatial average.
+        accumulate_mean: Save mean*nvoxels instead of mean.
+        color_table: FreeSurfer color table file to specify how each\
+            segmentation index is mapped to a segmentation name and color.
+        default_color_table: Use default color table from\
+            FreeSurferColorLUT.txt.
+        gca_color_table: Get color table from the given GCA file.
+        ids: Specify numeric segmentation ids.
+        exclude_ids: Exclude the given segmentation id(s) from report.
+        exclude_gm_wm: Exclude cortical gray and white matter based on\
+            predefined IDs.
+        surf_wm_vol: Compute cortical matter volume based on the white surface\
+            volume.
+        surf_ctx_vol: Compute cortical volumes from surface.
+        no_global_stats: Turns off computation of global stats.
+        empty_segments: Report on segmentations listed in the color table even\
+            if they are not found in the segmentation volume.
+        ctab_output: Create an output color table with just the segmentations\
+            reported.
+        mask_volume: Exclude voxels that are not in the mask. Voxels to be\
+            excluded are assigned a segid of 0.
+        mask_threshold: Exclude voxels that are below thresh, above -thresh, or\
+            between -thresh and +thresh.
+        mask_sign: Specify sign for masking threshold. Choices are abs, pos,\
+            and neg.
+        mask_frame: Derive the mask volume from the specified 0-based frame.
+        invert_mask: After applying all the masking criteria, invert the mask.
+        mask_erode: Erode mask by specified number of iterations.
+        brain_vol_seg: Get volume of brain as the sum of the volumes of the\
+            segmentations that are in the brain.
+        brain_mask_vol: Load brain mask and compute brain volume from non-zero\
+            voxels.
+        subcortical_gray: Compute volume of subcortical gray matter.
+        total_gray: Compute volume of total gray matter.
+        intracranial_volume: Compute intracranial volume from talairach.xfm.
+        intracranial_volume_only: Compute intracranial volume from\
+            talairach.xfm and exit.
+        old_intracranial_volume_only: Compute intracranial volume from\
+            talairach_with_skull.lta and exit.
+        talairach_transform: Specify path to talairach.xfm file for eTIV.
+        xfm_to_etiv: Convert xfm to eTIV and write to output file.
+        euler_hole_count: Write out number of defect holes based on the Euler\
+            number.
+        avg_waveform: Compute the average waveform and save to text file.
+        sum_waveform: Compute the sum waveform and save to text file.
+        avg_waveform_vol: Compute average waveform and save to MRI volume.
+        remove_avgwf_mean: Remove temporal mean from avgwf and avgwfvol.
+        spatial_frame_avg: Save mean across space and frame.
+        voxel_crs: Replace segmentation with all 0s except at specified voxel.
+        replace_ids: Replace segmentation ID1 with ID2.
+        replace_ids_file: Replace segmentations based on pairs in file.
+        gtm_default_seg_merge: Replace segmentations based on GTM default.
+        gtm_default_seg_merge_choroid: Replace segmentations based on GTM\
+            default excluding choroid.
+        qa_stats_file: Compute stats useful for quality control.
+        subjects_dir: Set SUBJECTS_DIR environment variable.
+        random_seed: Set random number generator seed value.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_segstats",
+        "segvol": segvol,
+        "output_file": output_file,
+        "square_input": square_input,
+        "sqrt_input": sqrt_input,
+        "snr_column": snr_column,
+        "absolute_value": absolute_value,
+        "accumulate_mean": accumulate_mean,
+        "default_color_table": default_color_table,
+        "exclude_gm_wm": exclude_gm_wm,
+        "surf_wm_vol": surf_wm_vol,
+        "surf_ctx_vol": surf_ctx_vol,
+        "no_global_stats": no_global_stats,
+        "empty_segments": empty_segments,
+        "invert_mask": invert_mask,
+        "brain_vol_seg": brain_vol_seg,
+        "subcortical_gray": subcortical_gray,
+        "total_gray": total_gray,
+        "intracranial_volume": intracranial_volume,
+        "intracranial_volume_only": intracranial_volume_only,
+        "old_intracranial_volume_only": old_intracranial_volume_only,
+        "euler_hole_count": euler_hole_count,
+        "remove_avgwf_mean": remove_avgwf_mean,
+        "gtm_default_seg_merge": gtm_default_seg_merge,
+        "gtm_default_seg_merge_choroid": gtm_default_seg_merge_choroid,
+    }
+    if annot_subject is not None:
+        params["annot_subject"] = annot_subject
+    if annot_hemisphere is not None:
+        params["annot_hemisphere"] = annot_hemisphere
+    if annot_parcellation is not None:
+        params["annot_parcellation"] = annot_parcellation
+    if slabel_subject is not None:
+        params["slabel_subject"] = slabel_subject
+    if slabel_hemisphere is not None:
+        params["slabel_hemisphere"] = slabel_hemisphere
+    if slabel_label is not None:
+        params["slabel_label"] = slabel_label
+    if partial_vol_comp is not None:
+        params["partial_vol_comp"] = partial_vol_comp
+    if input_volume is not None:
+        params["input_volume"] = input_volume
+    if seg_erode is not None:
+        params["seg_erode"] = seg_erode
+    if frame is not None:
+        params["frame"] = frame
+    if robust is not None:
+        params["robust"] = robust
+    if multiply_input is not None:
+        params["multiply_input"] = multiply_input
+    if divide_input is not None:
+        params["divide_input"] = divide_input
+    if color_table is not None:
+        params["color_table"] = color_table
+    if gca_color_table is not None:
+        params["gca_color_table"] = gca_color_table
+    if ids is not None:
+        params["ids"] = ids
+    if exclude_ids is not None:
+        params["exclude_ids"] = exclude_ids
+    if ctab_output is not None:
+        params["ctab_output"] = ctab_output
+    if mask_volume is not None:
+        params["mask_volume"] = mask_volume
+    if mask_threshold is not None:
+        params["mask_threshold"] = mask_threshold
+    if mask_sign is not None:
+        params["mask_sign"] = mask_sign
+    if mask_frame is not None:
+        params["mask_frame"] = mask_frame
+    if mask_erode is not None:
+        params["mask_erode"] = mask_erode
+    if brain_mask_vol is not None:
+        params["brain_mask_vol"] = brain_mask_vol
+    if talairach_transform is not None:
+        params["talairach_transform"] = talairach_transform
+    if xfm_to_etiv is not None:
+        params["xfm_to_etiv"] = xfm_to_etiv
+    if avg_waveform is not None:
+        params["avg_waveform"] = avg_waveform
+    if sum_waveform is not None:
+        params["sum_waveform"] = sum_waveform
+    if avg_waveform_vol is not None:
+        params["avg_waveform_vol"] = avg_waveform_vol
+    if spatial_frame_avg is not None:
+        params["spatial_frame_avg"] = spatial_frame_avg
+    if voxel_crs is not None:
+        params["voxel_crs"] = voxel_crs
+    if replace_ids is not None:
+        params["replace_ids"] = replace_ids
+    if replace_ids_file is not None:
+        params["replace_ids_file"] = replace_ids_file
+    if qa_stats_file is not None:
+        params["qa_stats_file"] = qa_stats_file
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if random_seed is not None:
+        params["random_seed"] = random_seed
+    return params
+
+
+def mri_segstats_cargs(
+    params: MriSegstatsParameters,
+    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_segstats")
+    cargs.extend([
+        "--seg",
+        execution.input_file(params.get("segvol"))
+    ])
+    if params.get("annot_subject") is not None:
+        cargs.extend([
+            "--annot",
+            params.get("annot_subject")
+        ])
+    if params.get("annot_hemisphere") is not None:
+        cargs.append(params.get("annot_hemisphere"))
+    if params.get("annot_parcellation") is not None:
+        cargs.append(params.get("annot_parcellation"))
+    if params.get("slabel_subject") is not None:
+        cargs.extend([
+            "--slabel",
+            params.get("slabel_subject")
+        ])
+    if params.get("slabel_hemisphere") is not None:
+        cargs.append(params.get("slabel_hemisphere"))
+    if params.get("slabel_label") is not None:
+        cargs.append(execution.input_file(params.get("slabel_label")))
+    cargs.extend([
+        "--o",
+        params.get("output_file")
+    ])
+    if params.get("partial_vol_comp") is not None:
+        cargs.extend([
+            "--pv",
+            execution.input_file(params.get("partial_vol_comp"))
+        ])
+    if params.get("input_volume") is not None:
+        cargs.extend([
+            "--i",
+            execution.input_file(params.get("input_volume"))
+        ])
+    if params.get("seg_erode") is not None:
+        cargs.extend([
+            "--seg-erode",
+            str(params.get("seg_erode"))
+        ])
+    if params.get("frame") is not None:
+        cargs.extend([
+            "--frame",
+            str(params.get("frame"))
+        ])
+    if params.get("robust") is not None:
+        cargs.extend([
+            "--robust",
+            str(params.get("robust"))
+        ])
+    if params.get("square_input"):
+        cargs.append("--sqr")
+    if params.get("sqrt_input"):
+        cargs.append("--sqrt")
+    if params.get("multiply_input") is not None:
+        cargs.extend([
+            "--mul",
+            str(params.get("multiply_input"))
+        ])
+    if params.get("divide_input") is not None:
+        cargs.extend([
+            "--div",
+            str(params.get("divide_input"))
+        ])
+    if params.get("snr_column"):
+        cargs.append("--snr")
+    if params.get("absolute_value"):
+        cargs.append("--abs")
+    if params.get("accumulate_mean"):
+        cargs.append("--accumulate")
+    if params.get("color_table") is not None:
+        cargs.extend([
+            "--ctab",
+            execution.input_file(params.get("color_table"))
+        ])
+    if params.get("default_color_table"):
+        cargs.append("--ctab-default")
+    if params.get("gca_color_table") is not None:
+        cargs.extend([
+            "--ctab-gca",
+            execution.input_file(params.get("gca_color_table"))
+        ])
+    if params.get("ids") is not None:
+        cargs.extend([
+            "--id",
+            params.get("ids")
+        ])
+    if params.get("exclude_ids") is not None:
+        cargs.extend([
+            "--excludeid",
+            params.get("exclude_ids")
+        ])
+    if params.get("exclude_gm_wm"):
+        cargs.append("--excl-ctxgmwm")
+    if params.get("surf_wm_vol"):
+        cargs.append("--surf-wm-vol")
+    if params.get("surf_ctx_vol"):
+        cargs.append("--surf-ctx-vol")
+    if params.get("no_global_stats"):
+        cargs.append("--no-global-stats")
+    if params.get("empty_segments"):
+        cargs.append("--empty")
+    if params.get("ctab_output") is not None:
+        cargs.extend([
+            "--ctab-out",
+            params.get("ctab_output")
+        ])
+    if params.get("mask_volume") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask_volume"))
+        ])
+    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_frame") is not None:
+        cargs.extend([
+            "--maskframe",
+            str(params.get("mask_frame"))
+        ])
+    if params.get("invert_mask"):
+        cargs.append("--maskinvert")
+    if params.get("mask_erode") is not None:
+        cargs.extend([
+            "--maskerode",
+            str(params.get("mask_erode"))
+        ])
+    if params.get("brain_vol_seg"):
+        cargs.append("--brain-vol-from-seg")
+    if params.get("brain_mask_vol") is not None:
+        cargs.extend([
+            "--brainmask",
+            execution.input_file(params.get("brain_mask_vol"))
+        ])
+    if params.get("subcortical_gray"):
+        cargs.append("--subcortgray")
+    if params.get("total_gray"):
+        cargs.append("--totalgray")
+    if params.get("intracranial_volume"):
+        cargs.append("--etiv")
+    if params.get("intracranial_volume_only"):
+        cargs.append("--etiv-only")
+    if params.get("old_intracranial_volume_only"):
+        cargs.append("--old-etiv-only")
+    if params.get("talairach_transform") is not None:
+        cargs.extend([
+            "--talxfm",
+            execution.input_file(params.get("talairach_transform"))
+        ])
+    if params.get("xfm_to_etiv") is not None:
+        cargs.extend([
+            "--xfm2etiv",
+            params.get("xfm_to_etiv")
+        ])
+    if params.get("euler_hole_count"):
+        cargs.append("--euler")
+    if params.get("avg_waveform") is not None:
+        cargs.extend([
+            "--avgwf",
+            params.get("avg_waveform")
+        ])
+    if params.get("sum_waveform") is not None:
+        cargs.extend([
+            "--sumwf",
+            params.get("sum_waveform")
+        ])
+    if params.get("avg_waveform_vol") is not None:
+        cargs.extend([
+            "--avgwfvol",
+            params.get("avg_waveform_vol")
+        ])
+    if params.get("remove_avgwf_mean"):
+        cargs.append("--avgwf-remove-mean")
+    if params.get("spatial_frame_avg") is not None:
+        cargs.extend([
+            "--sfavg",
+            params.get("spatial_frame_avg")
+        ])
+    if params.get("voxel_crs") is not None:
+        cargs.extend([
+            "--vox",
+            params.get("voxel_crs")
+        ])
+    if params.get("replace_ids") is not None:
+        cargs.extend([
+            "--replace",
+            params.get("replace_ids")
+        ])
+    if params.get("replace_ids_file") is not None:
+        cargs.extend([
+            "--replace-file",
+            execution.input_file(params.get("replace_ids_file"))
+        ])
+    if params.get("gtm_default_seg_merge"):
+        cargs.append("--gtm-default-seg-merge")
+    if params.get("gtm_default_seg_merge_choroid"):
+        cargs.append("--gtm-default-seg-merge-choroid")
+    if params.get("qa_stats_file") is not None:
+        cargs.extend([
+            "--qa-stats",
+            params.get("qa_stats_file")
+        ])
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subjects_dir")
+        ])
+    if params.get("random_seed") is not None:
+        cargs.extend([
+            "--seed",
+            str(params.get("random_seed"))
+        ])
+    return cargs
+
+
+def mri_segstats_outputs(
+    params: MriSegstatsParameters,
+    execution: Execution,
+) -> MriSegstatsOutputs:
+    """
+    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 = MriSegstatsOutputs(
+        root=execution.output_file("."),
+        summary_output_file=execution.output_file(params.get("output_file")),
+        avg_waveform_output=execution.output_file(params.get("avg_waveform")) if (params.get("avg_waveform") is not None) else None,
+        sum_waveform_output=execution.output_file(params.get("sum_waveform")) if (params.get("sum_waveform") is not None) else None,
+        avg_waveform_vol_output=execution.output_file(params.get("avg_waveform_vol")) if (params.get("avg_waveform_vol") is not None) else None,
+        spatial_frame_avg_output=execution.output_file(params.get("spatial_frame_avg")) if (params.get("spatial_frame_avg") is not None) else None,
+        ctab_output_file=execution.output_file(params.get("ctab_output")) if (params.get("ctab_output") is not None) else None,
+    )
+    return ret
+
+
+def mri_segstats_execute(
+    params: MriSegstatsParameters,
+    execution: Execution,
+) -> MriSegstatsOutputs:
+    """
+    Calculates measures and stats derived from brain segmentation data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSegstatsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_segstats_cargs(params, execution)
+    ret = mri_segstats_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_segstats(
+    segvol: InputPathType,
+    output_file: str,
+    annot_subject: str | None = None,
+    annot_hemisphere: str | None = None,
+    annot_parcellation: str | None = None,
+    slabel_subject: str | None = None,
+    slabel_hemisphere: str | None = None,
+    slabel_label: InputPathType | None = None,
+    partial_vol_comp: InputPathType | None = None,
+    input_volume: InputPathType | None = None,
+    seg_erode: float | None = None,
+    frame: float | None = None,
+    robust: float | None = None,
+    square_input: bool = False,
+    sqrt_input: bool = False,
+    multiply_input: float | None = None,
+    divide_input: float | None = None,
+    snr_column: bool = False,
+    absolute_value: bool = False,
+    accumulate_mean: bool = False,
+    color_table: InputPathType | None = None,
+    default_color_table: bool = False,
+    gca_color_table: InputPathType | None = None,
+    ids: str | None = None,
+    exclude_ids: str | None = None,
+    exclude_gm_wm: bool = False,
+    surf_wm_vol: bool = False,
+    surf_ctx_vol: bool = False,
+    no_global_stats: bool = False,
+    empty_segments: bool = False,
+    ctab_output: str | None = None,
+    mask_volume: InputPathType | None = None,
+    mask_threshold: float | None = None,
+    mask_sign: str | None = None,
+    mask_frame: float | None = None,
+    invert_mask: bool = False,
+    mask_erode: float | None = None,
+    brain_vol_seg: bool = False,
+    brain_mask_vol: InputPathType | None = None,
+    subcortical_gray: bool = False,
+    total_gray: bool = False,
+    intracranial_volume: bool = False,
+    intracranial_volume_only: bool = False,
+    old_intracranial_volume_only: bool = False,
+    talairach_transform: InputPathType | None = None,
+    xfm_to_etiv: str | None = None,
+    euler_hole_count: bool = False,
+    avg_waveform: str | None = None,
+    sum_waveform: str | None = None,
+    avg_waveform_vol: str | None = None,
+    remove_avgwf_mean: bool = False,
+    spatial_frame_avg: str | None = None,
+    voxel_crs: str | None = None,
+    replace_ids: str | None = None,
+    replace_ids_file: InputPathType | None = None,
+    gtm_default_seg_merge: bool = False,
+    gtm_default_seg_merge_choroid: bool = False,
+    qa_stats_file: str | None = None,
+    subjects_dir: str | None = None,
+    random_seed: float | None = None,
+    runner: Runner | None = None,
+) -> MriSegstatsOutputs:
+    """
+    Calculates measures and stats derived from brain segmentation data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        segvol: Input segmentation volume. This volume's voxel values indicate\
+            a segmentation or class.
+        output_file: ASCII file in which summary statistics are saved.
+        annot_subject: Create a segmentation from hemi.parc.annot. Subject is\
+            the name of the subject.
+        annot_hemisphere:.
+        annot_parcellation:.
+        slabel_subject: Create a segmentation from the given surface label. The\
+            points in the label are given a value of 1; 0 for outside.
+        slabel_hemisphere:.
+        slabel_label:.
+        partial_vol_comp: Use pvvol to compensate for partial voluming,\
+            resulting in more accurate volumes.
+        input_volume: Input volume from which to compute more statistics.
+        seg_erode: Erode segmentation boundaries by Nerodes.
+        frame: Report statistics of the input volume at the specified 0-based\
+            frame number.
+        robust: Compute stats after excluding a percentage of high and low\
+            values.
+        square_input: Compute the square of the input before computing stats.
+        sqrt_input: Compute the square root of the input before computing\
+            stats.
+        multiply_input: Multiply input by value.
+        divide_input: Divide input by value.
+        snr_column: Save mean/std as extra column in output table.
+        absolute_value: Compute absolute value of input before spatial average.
+        accumulate_mean: Save mean*nvoxels instead of mean.
+        color_table: FreeSurfer color table file to specify how each\
+            segmentation index is mapped to a segmentation name and color.
+        default_color_table: Use default color table from\
+            FreeSurferColorLUT.txt.
+        gca_color_table: Get color table from the given GCA file.
+        ids: Specify numeric segmentation ids.
+        exclude_ids: Exclude the given segmentation id(s) from report.
+        exclude_gm_wm: Exclude cortical gray and white matter based on\
+            predefined IDs.
+        surf_wm_vol: Compute cortical matter volume based on the white surface\
+            volume.
+        surf_ctx_vol: Compute cortical volumes from surface.
+        no_global_stats: Turns off computation of global stats.
+        empty_segments: Report on segmentations listed in the color table even\
+            if they are not found in the segmentation volume.
+        ctab_output: Create an output color table with just the segmentations\
+            reported.
+        mask_volume: Exclude voxels that are not in the mask. Voxels to be\
+            excluded are assigned a segid of 0.
+        mask_threshold: Exclude voxels that are below thresh, above -thresh, or\
+            between -thresh and +thresh.
+        mask_sign: Specify sign for masking threshold. Choices are abs, pos,\
+            and neg.
+        mask_frame: Derive the mask volume from the specified 0-based frame.
+        invert_mask: After applying all the masking criteria, invert the mask.
+        mask_erode: Erode mask by specified number of iterations.
+        brain_vol_seg: Get volume of brain as the sum of the volumes of the\
+            segmentations that are in the brain.
+        brain_mask_vol: Load brain mask and compute brain volume from non-zero\
+            voxels.
+        subcortical_gray: Compute volume of subcortical gray matter.
+        total_gray: Compute volume of total gray matter.
+        intracranial_volume: Compute intracranial volume from talairach.xfm.
+        intracranial_volume_only: Compute intracranial volume from\
+            talairach.xfm and exit.
+        old_intracranial_volume_only: Compute intracranial volume from\
+            talairach_with_skull.lta and exit.
+        talairach_transform: Specify path to talairach.xfm file for eTIV.
+        xfm_to_etiv: Convert xfm to eTIV and write to output file.
+        euler_hole_count: Write out number of defect holes based on the Euler\
+            number.
+        avg_waveform: Compute the average waveform and save to text file.
+        sum_waveform: Compute the sum waveform and save to text file.
+        avg_waveform_vol: Compute average waveform and save to MRI volume.
+        remove_avgwf_mean: Remove temporal mean from avgwf and avgwfvol.
+        spatial_frame_avg: Save mean across space and frame.
+        voxel_crs: Replace segmentation with all 0s except at specified voxel.
+        replace_ids: Replace segmentation ID1 with ID2.
+        replace_ids_file: Replace segmentations based on pairs in file.
+        gtm_default_seg_merge: Replace segmentations based on GTM default.
+        gtm_default_seg_merge_choroid: Replace segmentations based on GTM\
+            default excluding choroid.
+        qa_stats_file: Compute stats useful for quality control.
+        subjects_dir: Set SUBJECTS_DIR environment variable.
+        random_seed: Set random number generator seed value.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSegstatsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SEGSTATS_METADATA)
+    params = mri_segstats_params(
+        segvol=segvol,
+        annot_subject=annot_subject,
+        annot_hemisphere=annot_hemisphere,
+        annot_parcellation=annot_parcellation,
+        slabel_subject=slabel_subject,
+        slabel_hemisphere=slabel_hemisphere,
+        slabel_label=slabel_label,
+        output_file=output_file,
+        partial_vol_comp=partial_vol_comp,
+        input_volume=input_volume,
+        seg_erode=seg_erode,
+        frame=frame,
+        robust=robust,
+        square_input=square_input,
+        sqrt_input=sqrt_input,
+        multiply_input=multiply_input,
+        divide_input=divide_input,
+        snr_column=snr_column,
+        absolute_value=absolute_value,
+        accumulate_mean=accumulate_mean,
+        color_table=color_table,
+        default_color_table=default_color_table,
+        gca_color_table=gca_color_table,
+        ids=ids,
+        exclude_ids=exclude_ids,
+        exclude_gm_wm=exclude_gm_wm,
+        surf_wm_vol=surf_wm_vol,
+        surf_ctx_vol=surf_ctx_vol,
+        no_global_stats=no_global_stats,
+        empty_segments=empty_segments,
+        ctab_output=ctab_output,
+        mask_volume=mask_volume,
+        mask_threshold=mask_threshold,
+        mask_sign=mask_sign,
+        mask_frame=mask_frame,
+        invert_mask=invert_mask,
+        mask_erode=mask_erode,
+        brain_vol_seg=brain_vol_seg,
+        brain_mask_vol=brain_mask_vol,
+        subcortical_gray=subcortical_gray,
+        total_gray=total_gray,
+        intracranial_volume=intracranial_volume,
+        intracranial_volume_only=intracranial_volume_only,
+        old_intracranial_volume_only=old_intracranial_volume_only,
+        talairach_transform=talairach_transform,
+        xfm_to_etiv=xfm_to_etiv,
+        euler_hole_count=euler_hole_count,
+        avg_waveform=avg_waveform,
+        sum_waveform=sum_waveform,
+        avg_waveform_vol=avg_waveform_vol,
+        remove_avgwf_mean=remove_avgwf_mean,
+        spatial_frame_avg=spatial_frame_avg,
+        voxel_crs=voxel_crs,
+        replace_ids=replace_ids,
+        replace_ids_file=replace_ids_file,
+        gtm_default_seg_merge=gtm_default_seg_merge,
+        gtm_default_seg_merge_choroid=gtm_default_seg_merge_choroid,
+        qa_stats_file=qa_stats_file,
+        subjects_dir=subjects_dir,
+        random_seed=random_seed,
+    )
+    return mri_segstats_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SEGSTATS_METADATA",
+    "MriSegstatsOutputs",
+    "MriSegstatsParameters",
+    "mri_segstats",
+    "mri_segstats_params",
+]