niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_coreg.py

@@ -0,0 +1,813 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_COREG_METADATA = Metadata(
+    id="057f6d3fb653672744b9e6411c4faf5cf046f03e.boutiques",
+    name="mri_coreg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriCoregParameters = typing.TypedDict('MriCoregParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_coreg"],
+    "movvol": InputPathType,
+    "refvol": InputPathType,
+    "reg": str,
+    "subject": typing.NotRequired[str | None],
+    "dof": typing.NotRequired[int | None],
+    "zscale": bool,
+    "xztrans_yrot": bool,
+    "xytrans_zrot": bool,
+    "xytrans_zrot_xyscale_xyshear": bool,
+    "ref_maskvol": typing.NotRequired[InputPathType | None],
+    "no_ref_mask": bool,
+    "mov_maskvol": typing.NotRequired[InputPathType | None],
+    "threads": typing.NotRequired[int | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "regdat": typing.NotRequired[str | None],
+    "no_coord_dither": bool,
+    "no_intensity_dither": bool,
+    "spatial_scales": typing.NotRequired[list[str] | None],
+    "trans": typing.NotRequired[list[float] | None],
+    "rot": typing.NotRequired[list[float] | None],
+    "scale": typing.NotRequired[list[float] | None],
+    "shear": typing.NotRequired[list[float] | None],
+    "init_reg": typing.NotRequired[InputPathType | None],
+    "out_param_file": typing.NotRequired[str | None],
+    "out_cost_file": typing.NotRequired[str | None],
+    "no_cras0": bool,
+    "centroid": bool,
+    "ras2ras": bool,
+    "nitersmax": typing.NotRequired[int | None],
+    "ftol": typing.NotRequired[float | None],
+    "linmintol": typing.NotRequired[float | None],
+    "seed": typing.NotRequired[int | None],
+    "sat": typing.NotRequired[float | None],
+    "conf_ref": bool,
+    "no_bf": bool,
+    "bf_lim": typing.NotRequired[float | None],
+    "bf_nsamp": typing.NotRequired[int | None],
+    "no_smooth": bool,
+    "ref_fwhm": typing.NotRequired[float | None],
+    "mov_oob": bool,
+    "init_reg_save": typing.NotRequired[InputPathType | None],
+    "init_reg_save_only": typing.NotRequired[InputPathType | None],
+    "mat2par": typing.NotRequired[InputPathType | None],
+    "mat2rot": typing.NotRequired[InputPathType | None],
+    "par2mat": typing.NotRequired[str | None],
+    "lrrev": typing.NotRequired[InputPathType | None],
+    "landmarks": typing.NotRequired[list[str] | None],
+    "rms": typing.NotRequired[list[str] | None],
+    "movout": typing.NotRequired[InputPathType | None],
+    "mov_idither": typing.NotRequired[InputPathType | None],
+    "debug": bool,
+    "checkopts": 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_coreg": mri_coreg_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_coreg": mri_coreg_outputs,
+    }.get(t)
+
+
+class MriCoregOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_coreg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_registration: OutputPathType
+    """Output registration (LTA format)"""
+    out_params: OutputPathType | None
+    """File with output parameters"""
+    out_cost: OutputPathType | None
+    """Final cost value file"""
+    saved_init_reg: OutputPathType | None
+    """Saved initial registration"""
+    saved_init_reg_only: OutputPathType | None
+    """Saved initial registration (exit after save)"""
+    movout_volume: OutputPathType | None
+    """Preprocessed moving volume"""
+    mov_idither_volume: OutputPathType | None
+    """Moving intensity dither volume"""
+
+
+def mri_coreg_params(
+    movvol: InputPathType,
+    refvol: InputPathType,
+    reg: str,
+    subject: str | None = None,
+    dof: int | None = None,
+    zscale: bool = False,
+    xztrans_yrot: bool = False,
+    xytrans_zrot: bool = False,
+    xytrans_zrot_xyscale_xyshear: bool = False,
+    ref_maskvol: InputPathType | None = None,
+    no_ref_mask: bool = False,
+    mov_maskvol: InputPathType | None = None,
+    threads: int | None = None,
+    subjects_dir: str | None = None,
+    regdat: str | None = None,
+    no_coord_dither: bool = False,
+    no_intensity_dither: bool = False,
+    spatial_scales: list[str] | None = None,
+    trans: list[float] | None = None,
+    rot: list[float] | None = None,
+    scale: list[float] | None = None,
+    shear: list[float] | None = None,
+    init_reg: InputPathType | None = None,
+    out_param_file: str | None = None,
+    out_cost_file: str | None = None,
+    no_cras0: bool = False,
+    centroid: bool = False,
+    ras2ras: bool = False,
+    nitersmax: int | None = None,
+    ftol: float | None = None,
+    linmintol: float | None = None,
+    seed: int | None = None,
+    sat: float | None = None,
+    conf_ref: bool = False,
+    no_bf: bool = False,
+    bf_lim: float | None = None,
+    bf_nsamp: int | None = None,
+    no_smooth: bool = False,
+    ref_fwhm: float | None = None,
+    mov_oob: bool = False,
+    init_reg_save: InputPathType | None = None,
+    init_reg_save_only: InputPathType | None = None,
+    mat2par: InputPathType | None = None,
+    mat2rot: InputPathType | None = None,
+    par2mat: str | None = None,
+    lrrev: InputPathType | None = None,
+    landmarks: list[str] | None = None,
+    rms: list[str] | None = None,
+    movout: InputPathType | None = None,
+    mov_idither: InputPathType | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    version: bool = False,
+) -> MriCoregParameters:
+    """
+    Build parameters.
+    
+    Args:
+        movvol: Source volume (mov).
+        refvol: Target volume (ref or targ).
+        reg: Output registration file.
+        subject: Subject ID, forces --ref-mask aparc+aseg.mgz.
+        dof: Degrees of freedom. Default is 6.
+        zscale: Enable 7 dof registration with scaling in Z.
+        xztrans_yrot: For 2D images: uses shifts in x and z and rotation about\
+            y (no scale).
+        xytrans_zrot: For 2D images: uses shifts in x and y and rotation about\
+            z (no scale).
+        xytrans_zrot_xyscale_xyshear: For 2D images: uses shifts in x and y,\
+            rotation about z, scale in xy, and xy shear.
+        ref_maskvol: Mask reference volume with specified mask volume.
+        no_ref_mask: Do not mask reference volume.
+        mov_maskvol: Mask moving volume with specified mask volume.
+        threads: Number of threads to use.
+        subjects_dir: Freesurfer SUBJECTS_DIR.
+        regdat: Specify registration data file.
+        no_coord_dither: Turn off coordinate dithering.
+        no_intensity_dither: Turn off intensity dithering.
+        spatial_scales: Set spatial scales.
+        trans: Initial translation in mm.
+        rot: Initial rotation in degrees.
+        scale: Initial scale.
+        shear: Initial shear.
+        init_reg: Initialize with given registration file.
+        out_param_file: Save parameters in specified file.
+        out_cost_file: Save final cost value in specified file.
+        no_cras0: Do not set translation parameters to align centers of mov and\
+            ref.
+        centroid: Initialize by aligning centroids of mov and ref.
+        ras2ras: Save output LTA as RAS2RAS.
+        nitersmax: Set maximum number of iterations.
+        ftol: Set function tolerance.
+        linmintol: Set line minimum tolerance.
+        seed: Set random seed for dithering.
+        sat: Set saturation threshold.
+        conf_ref: Conform the reference without rescaling.
+        no_bf: Do not perform brute force search.
+        bf_lim: Set constraint limits for brute force search.
+        bf_nsamp: Set number of samples for brute force search.
+        no_smooth: Do not apply smoothing to either ref or mov.
+        ref_fwhm: Apply smoothing to ref with specified FWHM.
+        mov_oob: Count mov voxels that are out-of-bounds as 0.
+        init_reg_save: Save initial registration.
+        init_reg_save_only: Save initial registration and exit.
+        mat2par: Extract parameters out of registration.
+        mat2rot: Convert registration to a pure rotation.
+        par2mat: Convert parameters to a registration.
+        lrrev: Approximate registration if you were to left-right reverse the\
+            pixels of the input image.
+        landmarks: Convert landmarks to a registration.
+        rms: Compute RMS difference between two registrations.
+        movout: Save the mov after all preprocessing steps.
+        mov_idither: Save the mov intensity dither volume.
+        debug: Enable debugging mode.
+        checkopts: Check options and exit without running.
+        version: Print out version and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_coreg",
+        "movvol": movvol,
+        "refvol": refvol,
+        "reg": reg,
+        "zscale": zscale,
+        "xztrans_yrot": xztrans_yrot,
+        "xytrans_zrot": xytrans_zrot,
+        "xytrans_zrot_xyscale_xyshear": xytrans_zrot_xyscale_xyshear,
+        "no_ref_mask": no_ref_mask,
+        "no_coord_dither": no_coord_dither,
+        "no_intensity_dither": no_intensity_dither,
+        "no_cras0": no_cras0,
+        "centroid": centroid,
+        "ras2ras": ras2ras,
+        "conf_ref": conf_ref,
+        "no_bf": no_bf,
+        "no_smooth": no_smooth,
+        "mov_oob": mov_oob,
+        "debug": debug,
+        "checkopts": checkopts,
+        "version": version,
+    }
+    if subject is not None:
+        params["subject"] = subject
+    if dof is not None:
+        params["dof"] = dof
+    if ref_maskvol is not None:
+        params["ref_maskvol"] = ref_maskvol
+    if mov_maskvol is not None:
+        params["mov_maskvol"] = mov_maskvol
+    if threads is not None:
+        params["threads"] = threads
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if regdat is not None:
+        params["regdat"] = regdat
+    if spatial_scales is not None:
+        params["spatial_scales"] = spatial_scales
+    if trans is not None:
+        params["trans"] = trans
+    if rot is not None:
+        params["rot"] = rot
+    if scale is not None:
+        params["scale"] = scale
+    if shear is not None:
+        params["shear"] = shear
+    if init_reg is not None:
+        params["init_reg"] = init_reg
+    if out_param_file is not None:
+        params["out_param_file"] = out_param_file
+    if out_cost_file is not None:
+        params["out_cost_file"] = out_cost_file
+    if nitersmax is not None:
+        params["nitersmax"] = nitersmax
+    if ftol is not None:
+        params["ftol"] = ftol
+    if linmintol is not None:
+        params["linmintol"] = linmintol
+    if seed is not None:
+        params["seed"] = seed
+    if sat is not None:
+        params["sat"] = sat
+    if bf_lim is not None:
+        params["bf_lim"] = bf_lim
+    if bf_nsamp is not None:
+        params["bf_nsamp"] = bf_nsamp
+    if ref_fwhm is not None:
+        params["ref_fwhm"] = ref_fwhm
+    if init_reg_save is not None:
+        params["init_reg_save"] = init_reg_save
+    if init_reg_save_only is not None:
+        params["init_reg_save_only"] = init_reg_save_only
+    if mat2par is not None:
+        params["mat2par"] = mat2par
+    if mat2rot is not None:
+        params["mat2rot"] = mat2rot
+    if par2mat is not None:
+        params["par2mat"] = par2mat
+    if lrrev is not None:
+        params["lrrev"] = lrrev
+    if landmarks is not None:
+        params["landmarks"] = landmarks
+    if rms is not None:
+        params["rms"] = rms
+    if movout is not None:
+        params["movout"] = movout
+    if mov_idither is not None:
+        params["mov_idither"] = mov_idither
+    return params
+
+
+def mri_coreg_cargs(
+    params: MriCoregParameters,
+    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_coreg")
+    cargs.extend([
+        "-mov",
+        execution.input_file(params.get("movvol"))
+    ])
+    cargs.extend([
+        "-ref",
+        execution.input_file(params.get("refvol"))
+    ])
+    cargs.extend([
+        "-reg",
+        params.get("reg")
+    ])
+    if params.get("subject") is not None:
+        cargs.extend([
+            "--s",
+            params.get("subject")
+        ])
+    if params.get("dof") is not None:
+        cargs.extend([
+            "--dof",
+            str(params.get("dof"))
+        ])
+    if params.get("zscale"):
+        cargs.append("--zscale")
+    if params.get("xztrans_yrot"):
+        cargs.append("--xztrans+yrot")
+    if params.get("xytrans_zrot"):
+        cargs.append("--xytrans+zrot")
+    if params.get("xytrans_zrot_xyscale_xyshear"):
+        cargs.append("--xytrans+zrot+xyscale+xyshear")
+    if params.get("ref_maskvol") is not None:
+        cargs.extend([
+            "--ref-mask",
+            execution.input_file(params.get("ref_maskvol"))
+        ])
+    if params.get("no_ref_mask"):
+        cargs.append("--no-ref-mask")
+    if params.get("mov_maskvol") is not None:
+        cargs.extend([
+            "--mov-mask",
+            execution.input_file(params.get("mov_maskvol"))
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subjects_dir")
+        ])
+    if params.get("regdat") is not None:
+        cargs.extend([
+            "--regdat",
+            params.get("regdat")
+        ])
+    if params.get("no_coord_dither"):
+        cargs.append("--no-coord-dither")
+    if params.get("no_intensity_dither"):
+        cargs.append("--no-intensity-dither")
+    if params.get("spatial_scales") is not None:
+        cargs.extend([
+            "--sep",
+            *params.get("spatial_scales")
+        ])
+    if params.get("trans") is not None:
+        cargs.extend([
+            "--trans",
+            *map(str, params.get("trans"))
+        ])
+    if params.get("rot") is not None:
+        cargs.extend([
+            "--rot",
+            *map(str, params.get("rot"))
+        ])
+    if params.get("scale") is not None:
+        cargs.extend([
+            "--scale",
+            *map(str, params.get("scale"))
+        ])
+    if params.get("shear") is not None:
+        cargs.extend([
+            "--shear",
+            *map(str, params.get("shear"))
+        ])
+    if params.get("init_reg") is not None:
+        cargs.extend([
+            "--init-reg",
+            execution.input_file(params.get("init_reg"))
+        ])
+    if params.get("out_param_file") is not None:
+        cargs.extend([
+            "--params",
+            params.get("out_param_file")
+        ])
+    if params.get("out_cost_file") is not None:
+        cargs.extend([
+            "--final-cost",
+            params.get("out_cost_file")
+        ])
+    if params.get("no_cras0"):
+        cargs.append("--no-cras0")
+    if params.get("centroid"):
+        cargs.append("--centroid")
+    if params.get("ras2ras"):
+        cargs.append("--ras2ras")
+    if params.get("nitersmax") is not None:
+        cargs.extend([
+            "--nitersmax",
+            str(params.get("nitersmax"))
+        ])
+    if params.get("ftol") is not None:
+        cargs.extend([
+            "--ftol",
+            str(params.get("ftol"))
+        ])
+    if params.get("linmintol") is not None:
+        cargs.extend([
+            "--linmintol",
+            str(params.get("linmintol"))
+        ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "--seed",
+            str(params.get("seed"))
+        ])
+    if params.get("sat") is not None:
+        cargs.extend([
+            "--sat",
+            str(params.get("sat"))
+        ])
+    if params.get("conf_ref"):
+        cargs.append("--conf-ref")
+    if params.get("no_bf"):
+        cargs.append("--no-bf")
+    if params.get("bf_lim") is not None:
+        cargs.extend([
+            "--bf-lim",
+            str(params.get("bf_lim"))
+        ])
+    if params.get("bf_nsamp") is not None:
+        cargs.extend([
+            "--bf-nsamp",
+            str(params.get("bf_nsamp"))
+        ])
+    if params.get("no_smooth"):
+        cargs.append("--no-smooth")
+    if params.get("ref_fwhm") is not None:
+        cargs.extend([
+            "--ref-fwhm",
+            str(params.get("ref_fwhm"))
+        ])
+    if params.get("mov_oob"):
+        cargs.append("--mov-oob")
+    if params.get("init_reg_save") is not None:
+        cargs.extend([
+            "--init-reg-save",
+            execution.input_file(params.get("init_reg_save"))
+        ])
+    if params.get("init_reg_save_only") is not None:
+        cargs.extend([
+            "--init-reg-save-only",
+            execution.input_file(params.get("init_reg_save_only"))
+        ])
+    if params.get("mat2par") is not None:
+        cargs.extend([
+            "--mat2par",
+            execution.input_file(params.get("mat2par"))
+        ])
+    if params.get("mat2rot") is not None:
+        cargs.extend([
+            "--mat2rot",
+            execution.input_file(params.get("mat2rot"))
+        ])
+    if params.get("par2mat") is not None:
+        cargs.extend([
+            "--par2mat",
+            params.get("par2mat")
+        ])
+    if params.get("lrrev") is not None:
+        cargs.extend([
+            "--lrrev",
+            execution.input_file(params.get("lrrev"))
+        ])
+    if params.get("landmarks") is not None:
+        cargs.extend([
+            "--landmarks",
+            *params.get("landmarks")
+        ])
+    if params.get("rms") is not None:
+        cargs.extend([
+            "--rms",
+            *params.get("rms")
+        ])
+    if params.get("movout") is not None:
+        cargs.extend([
+            "--movout",
+            execution.input_file(params.get("movout"))
+        ])
+    if params.get("mov_idither") is not None:
+        cargs.extend([
+            "--mov-idither",
+            execution.input_file(params.get("mov_idither"))
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("checkopts"):
+        cargs.append("--checkopts")
+    if params.get("version"):
+        cargs.append("--version")
+    return cargs
+
+
+def mri_coreg_outputs(
+    params: MriCoregParameters,
+    execution: Execution,
+) -> MriCoregOutputs:
+    """
+    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 = MriCoregOutputs(
+        root=execution.output_file("."),
+        out_registration=execution.output_file(params.get("reg")),
+        out_params=execution.output_file(params.get("out_param_file")) if (params.get("out_param_file") is not None) else None,
+        out_cost=execution.output_file(params.get("out_cost_file")) if (params.get("out_cost_file") is not None) else None,
+        saved_init_reg=execution.output_file(pathlib.Path(params.get("init_reg_save")).name) if (params.get("init_reg_save") is not None) else None,
+        saved_init_reg_only=execution.output_file(pathlib.Path(params.get("init_reg_save_only")).name) if (params.get("init_reg_save_only") is not None) else None,
+        movout_volume=execution.output_file(pathlib.Path(params.get("movout")).name) if (params.get("movout") is not None) else None,
+        mov_idither_volume=execution.output_file(pathlib.Path(params.get("mov_idither")).name) if (params.get("mov_idither") is not None) else None,
+    )
+    return ret
+
+
+def mri_coreg_execute(
+    params: MriCoregParameters,
+    execution: Execution,
+) -> MriCoregOutputs:
+    """
+    mri_coreg performs a linear registration between two volumes using the method
+    compatible with spm_coreg.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriCoregOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_coreg_cargs(params, execution)
+    ret = mri_coreg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_coreg(
+    movvol: InputPathType,
+    refvol: InputPathType,
+    reg: str,
+    subject: str | None = None,
+    dof: int | None = None,
+    zscale: bool = False,
+    xztrans_yrot: bool = False,
+    xytrans_zrot: bool = False,
+    xytrans_zrot_xyscale_xyshear: bool = False,
+    ref_maskvol: InputPathType | None = None,
+    no_ref_mask: bool = False,
+    mov_maskvol: InputPathType | None = None,
+    threads: int | None = None,
+    subjects_dir: str | None = None,
+    regdat: str | None = None,
+    no_coord_dither: bool = False,
+    no_intensity_dither: bool = False,
+    spatial_scales: list[str] | None = None,
+    trans: list[float] | None = None,
+    rot: list[float] | None = None,
+    scale: list[float] | None = None,
+    shear: list[float] | None = None,
+    init_reg: InputPathType | None = None,
+    out_param_file: str | None = None,
+    out_cost_file: str | None = None,
+    no_cras0: bool = False,
+    centroid: bool = False,
+    ras2ras: bool = False,
+    nitersmax: int | None = None,
+    ftol: float | None = None,
+    linmintol: float | None = None,
+    seed: int | None = None,
+    sat: float | None = None,
+    conf_ref: bool = False,
+    no_bf: bool = False,
+    bf_lim: float | None = None,
+    bf_nsamp: int | None = None,
+    no_smooth: bool = False,
+    ref_fwhm: float | None = None,
+    mov_oob: bool = False,
+    init_reg_save: InputPathType | None = None,
+    init_reg_save_only: InputPathType | None = None,
+    mat2par: InputPathType | None = None,
+    mat2rot: InputPathType | None = None,
+    par2mat: str | None = None,
+    lrrev: InputPathType | None = None,
+    landmarks: list[str] | None = None,
+    rms: list[str] | None = None,
+    movout: InputPathType | None = None,
+    mov_idither: InputPathType | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MriCoregOutputs:
+    """
+    mri_coreg performs a linear registration between two volumes using the method
+    compatible with spm_coreg.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        movvol: Source volume (mov).
+        refvol: Target volume (ref or targ).
+        reg: Output registration file.
+        subject: Subject ID, forces --ref-mask aparc+aseg.mgz.
+        dof: Degrees of freedom. Default is 6.
+        zscale: Enable 7 dof registration with scaling in Z.
+        xztrans_yrot: For 2D images: uses shifts in x and z and rotation about\
+            y (no scale).
+        xytrans_zrot: For 2D images: uses shifts in x and y and rotation about\
+            z (no scale).
+        xytrans_zrot_xyscale_xyshear: For 2D images: uses shifts in x and y,\
+            rotation about z, scale in xy, and xy shear.
+        ref_maskvol: Mask reference volume with specified mask volume.
+        no_ref_mask: Do not mask reference volume.
+        mov_maskvol: Mask moving volume with specified mask volume.
+        threads: Number of threads to use.
+        subjects_dir: Freesurfer SUBJECTS_DIR.
+        regdat: Specify registration data file.
+        no_coord_dither: Turn off coordinate dithering.
+        no_intensity_dither: Turn off intensity dithering.
+        spatial_scales: Set spatial scales.
+        trans: Initial translation in mm.
+        rot: Initial rotation in degrees.
+        scale: Initial scale.
+        shear: Initial shear.
+        init_reg: Initialize with given registration file.
+        out_param_file: Save parameters in specified file.
+        out_cost_file: Save final cost value in specified file.
+        no_cras0: Do not set translation parameters to align centers of mov and\
+            ref.
+        centroid: Initialize by aligning centroids of mov and ref.
+        ras2ras: Save output LTA as RAS2RAS.
+        nitersmax: Set maximum number of iterations.
+        ftol: Set function tolerance.
+        linmintol: Set line minimum tolerance.
+        seed: Set random seed for dithering.
+        sat: Set saturation threshold.
+        conf_ref: Conform the reference without rescaling.
+        no_bf: Do not perform brute force search.
+        bf_lim: Set constraint limits for brute force search.
+        bf_nsamp: Set number of samples for brute force search.
+        no_smooth: Do not apply smoothing to either ref or mov.
+        ref_fwhm: Apply smoothing to ref with specified FWHM.
+        mov_oob: Count mov voxels that are out-of-bounds as 0.
+        init_reg_save: Save initial registration.
+        init_reg_save_only: Save initial registration and exit.
+        mat2par: Extract parameters out of registration.
+        mat2rot: Convert registration to a pure rotation.
+        par2mat: Convert parameters to a registration.
+        lrrev: Approximate registration if you were to left-right reverse the\
+            pixels of the input image.
+        landmarks: Convert landmarks to a registration.
+        rms: Compute RMS difference between two registrations.
+        movout: Save the mov after all preprocessing steps.
+        mov_idither: Save the mov intensity dither volume.
+        debug: Enable debugging mode.
+        checkopts: Check options and exit without running.
+        version: Print out version and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriCoregOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COREG_METADATA)
+    params = mri_coreg_params(
+        movvol=movvol,
+        refvol=refvol,
+        reg=reg,
+        subject=subject,
+        dof=dof,
+        zscale=zscale,
+        xztrans_yrot=xztrans_yrot,
+        xytrans_zrot=xytrans_zrot,
+        xytrans_zrot_xyscale_xyshear=xytrans_zrot_xyscale_xyshear,
+        ref_maskvol=ref_maskvol,
+        no_ref_mask=no_ref_mask,
+        mov_maskvol=mov_maskvol,
+        threads=threads,
+        subjects_dir=subjects_dir,
+        regdat=regdat,
+        no_coord_dither=no_coord_dither,
+        no_intensity_dither=no_intensity_dither,
+        spatial_scales=spatial_scales,
+        trans=trans,
+        rot=rot,
+        scale=scale,
+        shear=shear,
+        init_reg=init_reg,
+        out_param_file=out_param_file,
+        out_cost_file=out_cost_file,
+        no_cras0=no_cras0,
+        centroid=centroid,
+        ras2ras=ras2ras,
+        nitersmax=nitersmax,
+        ftol=ftol,
+        linmintol=linmintol,
+        seed=seed,
+        sat=sat,
+        conf_ref=conf_ref,
+        no_bf=no_bf,
+        bf_lim=bf_lim,
+        bf_nsamp=bf_nsamp,
+        no_smooth=no_smooth,
+        ref_fwhm=ref_fwhm,
+        mov_oob=mov_oob,
+        init_reg_save=init_reg_save,
+        init_reg_save_only=init_reg_save_only,
+        mat2par=mat2par,
+        mat2rot=mat2rot,
+        par2mat=par2mat,
+        lrrev=lrrev,
+        landmarks=landmarks,
+        rms=rms,
+        movout=movout,
+        mov_idither=mov_idither,
+        debug=debug,
+        checkopts=checkopts,
+        version=version,
+    )
+    return mri_coreg_execute(params, execution)
+
+
+__all__ = [
+    "MRI_COREG_METADATA",
+    "MriCoregOutputs",
+    "MriCoregParameters",
+    "mri_coreg",
+    "mri_coreg_params",
+]