niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_gtmpvc.py

@@ -0,0 +1,861 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_GTMPVC_METADATA = Metadata(
+    id="fd930d51e0a8f5012076ae523ec1cb2238ba47c5.boutiques",
+    name="mri_gtmpvc",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriGtmpvcParameters = typing.TypedDict('MriGtmpvcParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_gtmpvc"],
+    "input_volume": InputPathType,
+    "frame": typing.NotRequired[float | None],
+    "psf": float,
+    "segmentation": InputPathType,
+    "registration": typing.NotRequired[InputPathType | None],
+    "output_directory": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "auto_mask": typing.NotRequired[int | None],
+    "no_reduce_fov": bool,
+    "reduce_fov_eqodd": bool,
+    "contrast_matrix": typing.NotRequired[InputPathType | None],
+    "default_seg_merge": bool,
+    "merge_hypos": bool,
+    "merge_cblum_wm_gyri": bool,
+    "tt_reduce": bool,
+    "replace_seg": typing.NotRequired[str | None],
+    "replace_file": typing.NotRequired[InputPathType | None],
+    "rescale": typing.NotRequired[str | None],
+    "no_rescale": bool,
+    "scale_refval": typing.NotRequired[float | None],
+    "ctab": typing.NotRequired[InputPathType | None],
+    "ctab_default": bool,
+    "tt_update": bool,
+    "lateralization": bool,
+    "no_tfe": bool,
+    "no_pvc": bool,
+    "segpvfres": typing.NotRequired[float | None],
+    "rbv": bool,
+    "rbv_res": typing.NotRequired[float | None],
+    "mueller_pvc": typing.NotRequired[str | None],
+    "mg_ref_cerebral_wm": bool,
+    "mg_ref_lobes_wm": bool,
+    "glm_mg_pvc": typing.NotRequired[float | None],
+    "km_ref": typing.NotRequired[str | None],
+    "km_hb": typing.NotRequired[str | None],
+    "steady_state": typing.NotRequired[str | None],
+    "save_x": bool,
+    "save_y": bool,
+    "save_beta": bool,
+    "save_x0": bool,
+    "save_input": bool,
+    "save_eres": bool,
+    "save_yhat": bool,
+    "save_yhat_noise": typing.NotRequired[str | None],
+    "save_yhat_full_fov": bool,
+    "save_yhat0": bool,
+    "synth": typing.NotRequired[str | None],
+    "synth_only": bool,
+    "synth_save": bool,
+    "save_text": bool,
+    "threads": typing.NotRequired[float | None],
+    "max_threads": bool,
+    "max_threads_minus_one": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+    "vg_thresh": typing.NotRequired[float | None],
+    "gdiag": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": bool,
+    "help": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_gtmpvc": mri_gtmpvc_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_gtmpvc": mri_gtmpvc_outputs,
+    }.get(t)
+
+
+class MriGtmpvcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_gtmpvc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    synthesized_volume: OutputPathType
+    """Synthesized volume"""
+    rescaled_input: OutputPathType
+    """Rescaled input volume"""
+    eresiduals: OutputPathType
+    """Residual errors volume"""
+    yhat: OutputPathType
+    """Yhat volume"""
+    yhat_with_noise: OutputPathType
+    """Yhat with noise volume"""
+    yhat_full_fov: OutputPathType
+    """Yhat full FoV volume"""
+    yhat_prior: OutputPathType
+    """Yhat prior to smoothing volume"""
+    x_matrix: OutputPathType
+    """X matrix in matlab4 format"""
+    y_matrix: OutputPathType
+    """Y matrix in matlab4 format"""
+    beta_matrix: OutputPathType
+    """Beta matrix in matlab4 format"""
+    x0_matrix: OutputPathType
+    """X0 matrix in matlab4 format"""
+    gtm_values_text: OutputPathType
+    """Demeaned GTM values as text file"""
+
+
+def mri_gtmpvc_params(
+    input_volume: InputPathType,
+    psf: float,
+    segmentation: InputPathType,
+    output_directory: str,
+    frame: float | None = None,
+    registration: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    auto_mask: int | None = None,
+    no_reduce_fov: bool = False,
+    reduce_fov_eqodd: bool = False,
+    contrast_matrix: InputPathType | None = None,
+    default_seg_merge: bool = False,
+    merge_hypos: bool = False,
+    merge_cblum_wm_gyri: bool = False,
+    tt_reduce: bool = False,
+    replace_seg: str | None = None,
+    replace_file: InputPathType | None = None,
+    rescale: str | None = None,
+    no_rescale: bool = False,
+    scale_refval: float | None = None,
+    ctab: InputPathType | None = None,
+    ctab_default: bool = False,
+    tt_update: bool = False,
+    lateralization: bool = False,
+    no_tfe: bool = False,
+    no_pvc: bool = False,
+    segpvfres: float | None = None,
+    rbv: bool = False,
+    rbv_res: float | None = None,
+    mueller_pvc: str | None = None,
+    mg_ref_cerebral_wm: bool = False,
+    mg_ref_lobes_wm: bool = False,
+    glm_mg_pvc: float | None = None,
+    km_ref: str | None = None,
+    km_hb: str | None = None,
+    steady_state: str | None = None,
+    save_x: bool = False,
+    save_y: bool = False,
+    save_beta: bool = False,
+    save_x0: bool = False,
+    save_input: bool = False,
+    save_eres: bool = False,
+    save_yhat: bool = False,
+    save_yhat_noise: str | None = None,
+    save_yhat_full_fov: bool = False,
+    save_yhat0: bool = False,
+    synth: str | None = None,
+    synth_only: bool = False,
+    synth_save: bool = False,
+    save_text: bool = False,
+    threads: float | None = None,
+    max_threads: bool = False,
+    max_threads_minus_one: bool = False,
+    subjects_dir: str | None = None,
+    vg_thresh: float | None = None,
+    gdiag: float | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    help_: bool = False,
+    version: bool = False,
+) -> MriGtmpvcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volume: Input volume: source data to PVC.
+        psf: Scanner PSF FWHM in mm.
+        segmentation: Anatomical segmentation to define regions for GTM.
+        output_directory: Output directory.
+        frame: Only process 0-based frame F from input volume.
+        registration: LTA registration file that maps PET to anatomical.
+        mask: Ignore areas outside of the mask (in input vol space).
+        auto_mask: Automatically compute mask with FWHM and threshold.
+        no_reduce_fov: Do not reduce FoV to encompass mask.
+        reduce_fov_eqodd: Reduce FoV to encompass mask but force nc=nr and ns\
+            to be odd.
+        contrast_matrix: Univariate contrast to test.
+        default_seg_merge: Default schema for merging ROIs.
+        merge_hypos: Merge left and right hypointensites into ROI.
+        merge_cblum_wm_gyri: Cerebellum WM gyri back into cerebellum WM.
+        tt_reduce: Reduce segmentation to that of a tissue type.
+        replace_seg: Replace seg Id1 with seg Id2.
+        replace_file: File with a list of Ids to replace.
+        rescale: Specify reference region(s) used to rescale (default is pons).
+        no_rescale: Do not global rescale such that mean of reference region is\
+            scaleref.
+        scale_refval: Scale such that mean in reference region is refval.
+        ctab: Specify color table explicitly.
+        ctab_default: Use default color table.
+        tt_update: Changes tissue type of VentralDC, BrainStem, and Pons to be\
+            SubcortGM.
+        lateralization: Lateralize tissue types.
+        no_tfe: Do not correct for tissue fraction effect.
+        no_pvc: Turns off PVC entirely.
+        segpvfres: Set the tissue fraction resolution parameter (default is\
+            0.5).
+        rbv: Perform RBV PVC.
+        rbv_res: Set RBV voxel resolution.
+        mueller_pvc: Perform Mueller-Gaertner PVC.
+        mg_ref_cerebral_wm: Set MG RefIds to 2 and 41.
+        mg_ref_lobes_wm: Set MG RefIds to those for lobes when using wm subseg.
+        glm_mg_pvc: GLM-based Mueller-Gaertner PVC.
+        km_ref: Compute reference TAC for KM as mean of given RefIds.
+        km_hb: Compute HiBinding TAC for KM as mean of given RefIds.
+        steady_state: Steady-state analysis spec blood plasma concentration,\
+            unit scale, and decay correction factor.
+        save_x: Save X matrix in matlab4 format as X.mat.
+        save_y: Save y matrix in matlab4 format as y.mat.
+        save_beta: Save beta matrix in matlab4 format as beta.mat.
+        save_x0: Save X0 matrix in matlab4 format as X0.mat.
+        save_input: Saves rescaled input as input.rescaled.nii.gz.
+        save_eres: Saves residual error.
+        save_yhat: Saves yhat.
+        save_yhat_noise: Saves yhat with noise, seed < 0 for TOD.
+        save_yhat_full_fov: Saves yhat in full FoV (if FoV was reduced).
+        save_yhat0: Saves yhat prior to smoothing.
+        synth: Synthesize volume with gtmbeta as input.
+        synth_only: Exit after doing synthesis (implies --synth-save).
+        synth_save: With --synth saves synthesized volume to\
+            outdir/synth.nii.gz.
+        save_text: Save demeaned GTM values out to text files named after the\
+            seg.
+        threads: Use N threads (with Open MP).
+        max_threads: Use the maximum allowable number of threads for this\
+            computer.
+        max_threads_minus_one: Use one less than the maximum allowable number\
+            of threads for this computer.
+        subjects_dir: Specify SUBJECTS_DIR.
+        vg_thresh: Threshold for LTAconcat error.
+        gdiag: Set diagnostic level.
+        debug: Turn on debugging.
+        checkopts: Don't run anything, just check options and exit.
+        help_: Print out information on how to use this program.
+        version: Print out version and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_gtmpvc",
+        "input_volume": input_volume,
+        "psf": psf,
+        "segmentation": segmentation,
+        "output_directory": output_directory,
+        "no_reduce_fov": no_reduce_fov,
+        "reduce_fov_eqodd": reduce_fov_eqodd,
+        "default_seg_merge": default_seg_merge,
+        "merge_hypos": merge_hypos,
+        "merge_cblum_wm_gyri": merge_cblum_wm_gyri,
+        "tt_reduce": tt_reduce,
+        "no_rescale": no_rescale,
+        "ctab_default": ctab_default,
+        "tt_update": tt_update,
+        "lateralization": lateralization,
+        "no_tfe": no_tfe,
+        "no_pvc": no_pvc,
+        "rbv": rbv,
+        "mg_ref_cerebral_wm": mg_ref_cerebral_wm,
+        "mg_ref_lobes_wm": mg_ref_lobes_wm,
+        "save_x": save_x,
+        "save_y": save_y,
+        "save_beta": save_beta,
+        "save_x0": save_x0,
+        "save_input": save_input,
+        "save_eres": save_eres,
+        "save_yhat": save_yhat,
+        "save_yhat_full_fov": save_yhat_full_fov,
+        "save_yhat0": save_yhat0,
+        "synth_only": synth_only,
+        "synth_save": synth_save,
+        "save_text": save_text,
+        "max_threads": max_threads,
+        "max_threads_minus_one": max_threads_minus_one,
+        "debug": debug,
+        "checkopts": checkopts,
+        "help": help_,
+        "version": version,
+    }
+    if frame is not None:
+        params["frame"] = frame
+    if registration is not None:
+        params["registration"] = registration
+    if mask is not None:
+        params["mask"] = mask
+    if auto_mask is not None:
+        params["auto_mask"] = auto_mask
+    if contrast_matrix is not None:
+        params["contrast_matrix"] = contrast_matrix
+    if replace_seg is not None:
+        params["replace_seg"] = replace_seg
+    if replace_file is not None:
+        params["replace_file"] = replace_file
+    if rescale is not None:
+        params["rescale"] = rescale
+    if scale_refval is not None:
+        params["scale_refval"] = scale_refval
+    if ctab is not None:
+        params["ctab"] = ctab
+    if segpvfres is not None:
+        params["segpvfres"] = segpvfres
+    if rbv_res is not None:
+        params["rbv_res"] = rbv_res
+    if mueller_pvc is not None:
+        params["mueller_pvc"] = mueller_pvc
+    if glm_mg_pvc is not None:
+        params["glm_mg_pvc"] = glm_mg_pvc
+    if km_ref is not None:
+        params["km_ref"] = km_ref
+    if km_hb is not None:
+        params["km_hb"] = km_hb
+    if steady_state is not None:
+        params["steady_state"] = steady_state
+    if save_yhat_noise is not None:
+        params["save_yhat_noise"] = save_yhat_noise
+    if synth is not None:
+        params["synth"] = synth
+    if threads is not None:
+        params["threads"] = threads
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if vg_thresh is not None:
+        params["vg_thresh"] = vg_thresh
+    if gdiag is not None:
+        params["gdiag"] = gdiag
+    return params
+
+
+def mri_gtmpvc_cargs(
+    params: MriGtmpvcParameters,
+    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_gtmpvc")
+    cargs.extend([
+        "--i",
+        execution.input_file(params.get("input_volume"))
+    ])
+    if params.get("frame") is not None:
+        cargs.extend([
+            "--frame",
+            str(params.get("frame"))
+        ])
+    cargs.extend([
+        "--psf",
+        str(params.get("psf"))
+    ])
+    cargs.extend([
+        "--seg",
+        execution.input_file(params.get("segmentation"))
+    ])
+    if params.get("registration") is not None:
+        cargs.extend([
+            "--reg",
+            execution.input_file(params.get("registration"))
+        ])
+    cargs.extend([
+        "--o",
+        params.get("output_directory")
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("auto_mask") is not None:
+        cargs.extend([
+            "--auto-mask",
+            str(params.get("auto_mask"))
+        ])
+    if params.get("no_reduce_fov"):
+        cargs.append("--no-reduce-fov")
+    if params.get("reduce_fov_eqodd"):
+        cargs.append("--reduce-fov-eqodd")
+    if params.get("contrast_matrix") is not None:
+        cargs.extend([
+            "--C",
+            execution.input_file(params.get("contrast_matrix"))
+        ])
+    if params.get("default_seg_merge"):
+        cargs.append("--default-seg-merge")
+    if params.get("merge_hypos"):
+        cargs.append("--merge-hypos")
+    if params.get("merge_cblum_wm_gyri"):
+        cargs.append("--merge-cblum-wm-gyri")
+    if params.get("tt_reduce"):
+        cargs.append("--tt-reduce")
+    if params.get("replace_seg") is not None:
+        cargs.extend([
+            "--replace",
+            params.get("replace_seg")
+        ])
+    if params.get("replace_file") is not None:
+        cargs.extend([
+            "--replace-file",
+            execution.input_file(params.get("replace_file"))
+        ])
+    if params.get("rescale") is not None:
+        cargs.extend([
+            "--rescale",
+            params.get("rescale")
+        ])
+    if params.get("no_rescale"):
+        cargs.append("--no-rescale")
+    if params.get("scale_refval") is not None:
+        cargs.extend([
+            "--scale-refval",
+            str(params.get("scale_refval"))
+        ])
+    if params.get("ctab") is not None:
+        cargs.extend([
+            "--ctab",
+            execution.input_file(params.get("ctab"))
+        ])
+    if params.get("ctab_default"):
+        cargs.append("--ctab-default")
+    if params.get("tt_update"):
+        cargs.append("--tt-update")
+    if params.get("lateralization"):
+        cargs.append("--lat")
+    if params.get("no_tfe"):
+        cargs.append("--no-tfe")
+    if params.get("no_pvc"):
+        cargs.append("--no-pvc")
+    if params.get("segpvfres") is not None:
+        cargs.extend([
+            "--segpvfres",
+            str(params.get("segpvfres"))
+        ])
+    if params.get("rbv"):
+        cargs.append("--rbv")
+    if params.get("rbv_res") is not None:
+        cargs.extend([
+            "--rbv-res",
+            str(params.get("rbv_res"))
+        ])
+    if params.get("mueller_pvc") is not None:
+        cargs.extend([
+            "--mg",
+            params.get("mueller_pvc")
+        ])
+    if params.get("mg_ref_cerebral_wm"):
+        cargs.append("--mg-ref-cerebral-wm")
+    if params.get("mg_ref_lobes_wm"):
+        cargs.append("--mg-ref-lobes-wm")
+    if params.get("glm_mg_pvc") is not None:
+        cargs.extend([
+            "--mgx",
+            str(params.get("glm_mg_pvc"))
+        ])
+    if params.get("km_ref") is not None:
+        cargs.extend([
+            "--km-ref",
+            params.get("km_ref")
+        ])
+    if params.get("km_hb") is not None:
+        cargs.extend([
+            "--km-hb",
+            params.get("km_hb")
+        ])
+    if params.get("steady_state") is not None:
+        cargs.extend([
+            "--ss",
+            params.get("steady_state")
+        ])
+    if params.get("save_x"):
+        cargs.append("--X")
+    if params.get("save_y"):
+        cargs.append("--y")
+    if params.get("save_beta"):
+        cargs.append("--beta")
+    if params.get("save_x0"):
+        cargs.append("--X0")
+    if params.get("save_input"):
+        cargs.append("--save-input")
+    if params.get("save_eres"):
+        cargs.append("--save-eres")
+    if params.get("save_yhat"):
+        cargs.append("--save-yhat")
+    if params.get("save_yhat_noise") is not None:
+        cargs.extend([
+            "--save-yhat-with-noise",
+            params.get("save_yhat_noise")
+        ])
+    if params.get("save_yhat_full_fov"):
+        cargs.append("--save-yhat-full-fov")
+    if params.get("save_yhat0"):
+        cargs.append("--save-yhat0")
+    if params.get("synth") is not None:
+        cargs.extend([
+            "--synth",
+            params.get("synth")
+        ])
+    if params.get("synth_only"):
+        cargs.append("--synth-only")
+    if params.get("synth_save"):
+        cargs.append("--synth-save")
+    if params.get("save_text"):
+        cargs.append("--save-text")
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("max_threads"):
+        cargs.append("--max-threads")
+    if params.get("max_threads_minus_one"):
+        cargs.append("--max-threads-minus-1")
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subjects_dir")
+        ])
+    if params.get("vg_thresh") is not None:
+        cargs.extend([
+            "--vg-thresh",
+            str(params.get("vg_thresh"))
+        ])
+    if params.get("gdiag") is not None:
+        cargs.extend([
+            "--gdiag",
+            str(params.get("gdiag"))
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("checkopts"):
+        cargs.append("--checkopts")
+    if params.get("help"):
+        cargs.append("--help")
+    if params.get("version"):
+        cargs.append("--version")
+    return cargs
+
+
+def mri_gtmpvc_outputs(
+    params: MriGtmpvcParameters,
+    execution: Execution,
+) -> MriGtmpvcOutputs:
+    """
+    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 = MriGtmpvcOutputs(
+        root=execution.output_file("."),
+        synthesized_volume=execution.output_file(params.get("output_directory") + "/synth.nii.gz"),
+        rescaled_input=execution.output_file(params.get("output_directory") + "/input.rescaled.nii.gz"),
+        eresiduals=execution.output_file(params.get("output_directory") + "/eresiduals.nii.gz"),
+        yhat=execution.output_file(params.get("output_directory") + "/yhat.nii.gz"),
+        yhat_with_noise=execution.output_file(params.get("output_directory") + "/yhat_with_noise.nii.gz"),
+        yhat_full_fov=execution.output_file(params.get("output_directory") + "/yhat_full_fov.nii.gz"),
+        yhat_prior=execution.output_file(params.get("output_directory") + "/yhat_prior.nii.gz"),
+        x_matrix=execution.output_file(params.get("output_directory") + "/X.mat"),
+        y_matrix=execution.output_file(params.get("output_directory") + "/y.mat"),
+        beta_matrix=execution.output_file(params.get("output_directory") + "/beta.mat"),
+        x0_matrix=execution.output_file(params.get("output_directory") + "/X0.mat"),
+        gtm_values_text=execution.output_file(params.get("output_directory") + "/gtm_values.txt"),
+    )
+    return ret
+
+
+def mri_gtmpvc_execute(
+    params: MriGtmpvcParameters,
+    execution: Execution,
+) -> MriGtmpvcOutputs:
+    """
+    mri_gtmpvc performs partial volume correction on PET data using anatomical
+    segmentation.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriGtmpvcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_gtmpvc_cargs(params, execution)
+    ret = mri_gtmpvc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_gtmpvc(
+    input_volume: InputPathType,
+    psf: float,
+    segmentation: InputPathType,
+    output_directory: str,
+    frame: float | None = None,
+    registration: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    auto_mask: int | None = None,
+    no_reduce_fov: bool = False,
+    reduce_fov_eqodd: bool = False,
+    contrast_matrix: InputPathType | None = None,
+    default_seg_merge: bool = False,
+    merge_hypos: bool = False,
+    merge_cblum_wm_gyri: bool = False,
+    tt_reduce: bool = False,
+    replace_seg: str | None = None,
+    replace_file: InputPathType | None = None,
+    rescale: str | None = None,
+    no_rescale: bool = False,
+    scale_refval: float | None = None,
+    ctab: InputPathType | None = None,
+    ctab_default: bool = False,
+    tt_update: bool = False,
+    lateralization: bool = False,
+    no_tfe: bool = False,
+    no_pvc: bool = False,
+    segpvfres: float | None = None,
+    rbv: bool = False,
+    rbv_res: float | None = None,
+    mueller_pvc: str | None = None,
+    mg_ref_cerebral_wm: bool = False,
+    mg_ref_lobes_wm: bool = False,
+    glm_mg_pvc: float | None = None,
+    km_ref: str | None = None,
+    km_hb: str | None = None,
+    steady_state: str | None = None,
+    save_x: bool = False,
+    save_y: bool = False,
+    save_beta: bool = False,
+    save_x0: bool = False,
+    save_input: bool = False,
+    save_eres: bool = False,
+    save_yhat: bool = False,
+    save_yhat_noise: str | None = None,
+    save_yhat_full_fov: bool = False,
+    save_yhat0: bool = False,
+    synth: str | None = None,
+    synth_only: bool = False,
+    synth_save: bool = False,
+    save_text: bool = False,
+    threads: float | None = None,
+    max_threads: bool = False,
+    max_threads_minus_one: bool = False,
+    subjects_dir: str | None = None,
+    vg_thresh: float | None = None,
+    gdiag: float | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MriGtmpvcOutputs:
+    """
+    mri_gtmpvc performs partial volume correction on PET data using anatomical
+    segmentation.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volume: Input volume: source data to PVC.
+        psf: Scanner PSF FWHM in mm.
+        segmentation: Anatomical segmentation to define regions for GTM.
+        output_directory: Output directory.
+        frame: Only process 0-based frame F from input volume.
+        registration: LTA registration file that maps PET to anatomical.
+        mask: Ignore areas outside of the mask (in input vol space).
+        auto_mask: Automatically compute mask with FWHM and threshold.
+        no_reduce_fov: Do not reduce FoV to encompass mask.
+        reduce_fov_eqodd: Reduce FoV to encompass mask but force nc=nr and ns\
+            to be odd.
+        contrast_matrix: Univariate contrast to test.
+        default_seg_merge: Default schema for merging ROIs.
+        merge_hypos: Merge left and right hypointensites into ROI.
+        merge_cblum_wm_gyri: Cerebellum WM gyri back into cerebellum WM.
+        tt_reduce: Reduce segmentation to that of a tissue type.
+        replace_seg: Replace seg Id1 with seg Id2.
+        replace_file: File with a list of Ids to replace.
+        rescale: Specify reference region(s) used to rescale (default is pons).
+        no_rescale: Do not global rescale such that mean of reference region is\
+            scaleref.
+        scale_refval: Scale such that mean in reference region is refval.
+        ctab: Specify color table explicitly.
+        ctab_default: Use default color table.
+        tt_update: Changes tissue type of VentralDC, BrainStem, and Pons to be\
+            SubcortGM.
+        lateralization: Lateralize tissue types.
+        no_tfe: Do not correct for tissue fraction effect.
+        no_pvc: Turns off PVC entirely.
+        segpvfres: Set the tissue fraction resolution parameter (default is\
+            0.5).
+        rbv: Perform RBV PVC.
+        rbv_res: Set RBV voxel resolution.
+        mueller_pvc: Perform Mueller-Gaertner PVC.
+        mg_ref_cerebral_wm: Set MG RefIds to 2 and 41.
+        mg_ref_lobes_wm: Set MG RefIds to those for lobes when using wm subseg.
+        glm_mg_pvc: GLM-based Mueller-Gaertner PVC.
+        km_ref: Compute reference TAC for KM as mean of given RefIds.
+        km_hb: Compute HiBinding TAC for KM as mean of given RefIds.
+        steady_state: Steady-state analysis spec blood plasma concentration,\
+            unit scale, and decay correction factor.
+        save_x: Save X matrix in matlab4 format as X.mat.
+        save_y: Save y matrix in matlab4 format as y.mat.
+        save_beta: Save beta matrix in matlab4 format as beta.mat.
+        save_x0: Save X0 matrix in matlab4 format as X0.mat.
+        save_input: Saves rescaled input as input.rescaled.nii.gz.
+        save_eres: Saves residual error.
+        save_yhat: Saves yhat.
+        save_yhat_noise: Saves yhat with noise, seed < 0 for TOD.
+        save_yhat_full_fov: Saves yhat in full FoV (if FoV was reduced).
+        save_yhat0: Saves yhat prior to smoothing.
+        synth: Synthesize volume with gtmbeta as input.
+        synth_only: Exit after doing synthesis (implies --synth-save).
+        synth_save: With --synth saves synthesized volume to\
+            outdir/synth.nii.gz.
+        save_text: Save demeaned GTM values out to text files named after the\
+            seg.
+        threads: Use N threads (with Open MP).
+        max_threads: Use the maximum allowable number of threads for this\
+            computer.
+        max_threads_minus_one: Use one less than the maximum allowable number\
+            of threads for this computer.
+        subjects_dir: Specify SUBJECTS_DIR.
+        vg_thresh: Threshold for LTAconcat error.
+        gdiag: Set diagnostic level.
+        debug: Turn on debugging.
+        checkopts: Don't run anything, just check options and exit.
+        help_: Print out information on how to use this program.
+        version: Print out version and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriGtmpvcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GTMPVC_METADATA)
+    params = mri_gtmpvc_params(
+        input_volume=input_volume,
+        frame=frame,
+        psf=psf,
+        segmentation=segmentation,
+        registration=registration,
+        output_directory=output_directory,
+        mask=mask,
+        auto_mask=auto_mask,
+        no_reduce_fov=no_reduce_fov,
+        reduce_fov_eqodd=reduce_fov_eqodd,
+        contrast_matrix=contrast_matrix,
+        default_seg_merge=default_seg_merge,
+        merge_hypos=merge_hypos,
+        merge_cblum_wm_gyri=merge_cblum_wm_gyri,
+        tt_reduce=tt_reduce,
+        replace_seg=replace_seg,
+        replace_file=replace_file,
+        rescale=rescale,
+        no_rescale=no_rescale,
+        scale_refval=scale_refval,
+        ctab=ctab,
+        ctab_default=ctab_default,
+        tt_update=tt_update,
+        lateralization=lateralization,
+        no_tfe=no_tfe,
+        no_pvc=no_pvc,
+        segpvfres=segpvfres,
+        rbv=rbv,
+        rbv_res=rbv_res,
+        mueller_pvc=mueller_pvc,
+        mg_ref_cerebral_wm=mg_ref_cerebral_wm,
+        mg_ref_lobes_wm=mg_ref_lobes_wm,
+        glm_mg_pvc=glm_mg_pvc,
+        km_ref=km_ref,
+        km_hb=km_hb,
+        steady_state=steady_state,
+        save_x=save_x,
+        save_y=save_y,
+        save_beta=save_beta,
+        save_x0=save_x0,
+        save_input=save_input,
+        save_eres=save_eres,
+        save_yhat=save_yhat,
+        save_yhat_noise=save_yhat_noise,
+        save_yhat_full_fov=save_yhat_full_fov,
+        save_yhat0=save_yhat0,
+        synth=synth,
+        synth_only=synth_only,
+        synth_save=synth_save,
+        save_text=save_text,
+        threads=threads,
+        max_threads=max_threads,
+        max_threads_minus_one=max_threads_minus_one,
+        subjects_dir=subjects_dir,
+        vg_thresh=vg_thresh,
+        gdiag=gdiag,
+        debug=debug,
+        checkopts=checkopts,
+        help_=help_,
+        version=version,
+    )
+    return mri_gtmpvc_execute(params, execution)
+
+
+__all__ = [
+    "MRI_GTMPVC_METADATA",
+    "MriGtmpvcOutputs",
+    "MriGtmpvcParameters",
+    "mri_gtmpvc",
+    "mri_gtmpvc_params",
+]