niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/tkregister2_cmdl.py

@@ -0,0 +1,864 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TKREGISTER2_CMDL_METADATA = Metadata(
+    id="a084019981b8c19c88bf65a10695c9febf690ada.boutiques",
+    name="tkregister2_cmdl",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+Tkregister2CmdlParameters = typing.TypedDict('Tkregister2CmdlParameters', {
+    "__STYX_TYPE__": typing.Literal["tkregister2_cmdl"],
+    "movable_volume": InputPathType,
+    "target_volume": InputPathType,
+    "fstarg_flag": bool,
+    "reg_file": typing.NotRequired[InputPathType | None],
+    "check_reg_flag": bool,
+    "regheader_flag": bool,
+    "regheader_center_flag": bool,
+    "fsl_targ_flag": bool,
+    "fsl_targ_lr_flag": bool,
+    "gca_subject": typing.NotRequired[str | None],
+    "gca_skull_subject": typing.NotRequired[str | None],
+    "no_zero_cras_flag": bool,
+    "movbright": typing.NotRequired[float | None],
+    "no_inorm_flag": bool,
+    "fmov": typing.NotRequired[float | None],
+    "fmov_targ_flag": bool,
+    "plane": typing.NotRequired[str | None],
+    "slice": typing.NotRequired[float | None],
+    "volview": typing.NotRequired[str | None],
+    "fov": typing.NotRequired[float | None],
+    "movscale": typing.NotRequired[float | None],
+    "surf": typing.NotRequired[str | None],
+    "surf_rgb": typing.NotRequired[list[float] | None],
+    "lh_only_flag": bool,
+    "rh_only_flag": bool,
+    "fstal_flag": bool,
+    "talxfmname": typing.NotRequired[str | None],
+    "ixfm": typing.NotRequired[InputPathType | None],
+    "xfm": typing.NotRequired[InputPathType | None],
+    "xfmout": typing.NotRequired[InputPathType | None],
+    "fsl": typing.NotRequired[InputPathType | None],
+    "fslregout": typing.NotRequired[InputPathType | None],
+    "freeview": typing.NotRequired[InputPathType | None],
+    "vox2vox": typing.NotRequired[InputPathType | None],
+    "lta": typing.NotRequired[InputPathType | None],
+    "lta_inv": typing.NotRequired[InputPathType | None],
+    "ltaout": typing.NotRequired[InputPathType | None],
+    "ltaout_inv_flag": bool,
+    "feat": typing.NotRequired[str | None],
+    "fsfeat": typing.NotRequired[str | None],
+    "identity_flag": bool,
+    "subject_id": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "nofix_flag": bool,
+    "float2int": typing.NotRequired[str | None],
+    "title": typing.NotRequired[str | None],
+    "tag_flag": bool,
+    "mov_orientation": typing.NotRequired[str | None],
+    "targ_orientation": typing.NotRequired[str | None],
+    "int": typing.NotRequired[list[str] | None],
+    "double_window_size_flag": bool,
+    "window_scale": typing.NotRequired[float | None],
+    "det": typing.NotRequired[InputPathType | None],
+    "aseg_flag": bool,
+    "aparc_flag": bool,
+    "wmparc_flag": bool,
+    "gdiagno": typing.NotRequired[float | None],
+    "trans": typing.NotRequired[list[float] | None],
+    "rot": typing.NotRequired[list[float] | None],
+    "conf_targ_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "tkregister2_cmdl": tkregister2_cmdl_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class Tkregister2CmdlOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tkregister2_cmdl(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def tkregister2_cmdl_params(
+    movable_volume: InputPathType,
+    target_volume: InputPathType,
+    fstarg_flag: bool = False,
+    reg_file: InputPathType | None = None,
+    check_reg_flag: bool = False,
+    regheader_flag: bool = False,
+    regheader_center_flag: bool = False,
+    fsl_targ_flag: bool = False,
+    fsl_targ_lr_flag: bool = False,
+    gca_subject: str | None = None,
+    gca_skull_subject: str | None = None,
+    no_zero_cras_flag: bool = False,
+    movbright: float | None = None,
+    no_inorm_flag: bool = False,
+    fmov: float | None = None,
+    fmov_targ_flag: bool = False,
+    plane: str | None = None,
+    slice_: float | None = None,
+    volview: str | None = None,
+    fov: float | None = None,
+    movscale: float | None = None,
+    surf: str | None = None,
+    surf_rgb: list[float] | None = None,
+    lh_only_flag: bool = False,
+    rh_only_flag: bool = False,
+    fstal_flag: bool = False,
+    talxfmname: str | None = None,
+    ixfm: InputPathType | None = None,
+    xfm: InputPathType | None = None,
+    xfmout: InputPathType | None = None,
+    fsl: InputPathType | None = None,
+    fslregout: InputPathType | None = None,
+    freeview: InputPathType | None = None,
+    vox2vox: InputPathType | None = None,
+    lta: InputPathType | None = None,
+    lta_inv: InputPathType | None = None,
+    ltaout: InputPathType | None = None,
+    ltaout_inv_flag: bool = False,
+    feat: str | None = None,
+    fsfeat: str | None = None,
+    identity_flag: bool = False,
+    subject_id: str | None = None,
+    subjects_dir: str | None = None,
+    nofix_flag: bool = False,
+    float2int: str | None = None,
+    title: str | None = None,
+    tag_flag: bool = False,
+    mov_orientation: str | None = None,
+    targ_orientation: str | None = None,
+    int_: list[str] | None = None,
+    double_window_size_flag: bool = False,
+    window_scale: float | None = None,
+    det: InputPathType | None = None,
+    aseg_flag: bool = False,
+    aparc_flag: bool = False,
+    wmparc_flag: bool = False,
+    gdiagno: float | None = None,
+    trans: list[float] | None = None,
+    rot: list[float] | None = None,
+    conf_targ_flag: bool = False,
+) -> Tkregister2CmdlParameters:
+    """
+    Build parameters.
+    
+    Args:
+        movable_volume: Path to the movable volume.
+        target_volume: Path to the target volume.
+        fstarg_flag: Target is relative to subjectid/mri.
+        reg_file: Path to input/output registration file.
+        check_reg_flag: Only check, no --reg needed.
+        regheader_flag: Compute registration from headers.
+        regheader_center_flag: Same as --regheader but aligns volume centers.
+        fsl_targ_flag: Use FSLDIR/data/standard/avg152T1.nii.gz.
+        fsl_targ_lr_flag: Use FSLDIR/data/standard/avg152T1_LR-marked.nii.gz.
+        gca_subject: Subject ID for linear GCA registration check.
+        gca_skull_subject: Subject ID for linear 'with skull' GCA registration\
+            check.
+        no_zero_cras_flag: Do not zero target cras (done with --fstal).
+        movbright: Brightness of movable volume.
+        no_inorm_flag: Turn off intensity normalization.
+        fmov: Set movable volume brightness.
+        fmov_targ_flag: Apply movable brightness to the target.
+        plane: Startup view plane: cor, sag, ax.
+        slice_: Startup slice number.
+        volview: Startup with targ or mov.
+        fov: Window FOV in mm (default is 256).
+        movscale: Scale size of movable volume by scale.
+        surf: Display surface as an overlay.
+        surf_rgb: Set surface color (0-255) for R G B.
+        lh_only_flag: Only load/display left hemisphere.
+        rh_only_flag: Only load/display right hemisphere.
+        fstal_flag: Set movable to be tal and reg to be taliarach.xfm.
+        talxfmname: Set movable to be tal and reg to be talxfmname.
+        ixfm: MNI-style inverse registration input matrix.
+        xfm: MNI-style registration input matrix.
+        xfmout: MNI-style registration output matrix.
+        fsl: FSL-style registration input matrix.
+        fslregout: FSL-Style registration output matrix.
+        freeview: FreeView registration output matrix.
+        vox2vox: Vox2vox matrix in ascii.
+        lta: Linear Transform Array file.
+        lta_inv: Read in LTA and invert.
+        ltaout: Output a Linear Transform Array.
+        ltaout_inv_flag: Invert transform in ltaoutfile.
+        feat: Check example_func2standard registration.
+        fsfeat: Check reg/freesurfer/register.dat registration.
+        identity_flag: Use identity as registration matrix.
+        subject_id: Set subject id.
+        subjects_dir: Use specified directory as SUBJECTS_DIR.
+        nofix_flag: Don't fix old tkregister matrices.
+        float2int: Specify old tkregister float2int.
+        title: Set window title.
+        tag_flag: Tag movable volume near the col/row origin.
+        mov_orientation: Supply orientation string for movable volume.
+        targ_orientation: Supply orientation string for target volume.
+        int_: Use registration from intermediate volume.
+        double_window_size_flag: Double window size.
+        window_scale: Scale window by specified scale.
+        det: Save determinant of registration matrix to specified file.
+        aseg_flag: Load aseg and hit 'd' to toggle.
+        aparc_flag: Load aparc+aseg and hit 'c' to toggle.
+        wmparc_flag: Load wmparc and hit 'c' to toggle.
+        gdiagno: Set debug level.
+        trans: Translation (mm) to apply to registration matrix.
+        rot: Rotation angles (deg) to apply to registration matrix.
+        conf_targ_flag: Conform target (assumes reg computed to conform target,\
+            eg, GCA).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "tkregister2_cmdl",
+        "movable_volume": movable_volume,
+        "target_volume": target_volume,
+        "fstarg_flag": fstarg_flag,
+        "check_reg_flag": check_reg_flag,
+        "regheader_flag": regheader_flag,
+        "regheader_center_flag": regheader_center_flag,
+        "fsl_targ_flag": fsl_targ_flag,
+        "fsl_targ_lr_flag": fsl_targ_lr_flag,
+        "no_zero_cras_flag": no_zero_cras_flag,
+        "no_inorm_flag": no_inorm_flag,
+        "fmov_targ_flag": fmov_targ_flag,
+        "lh_only_flag": lh_only_flag,
+        "rh_only_flag": rh_only_flag,
+        "fstal_flag": fstal_flag,
+        "ltaout_inv_flag": ltaout_inv_flag,
+        "identity_flag": identity_flag,
+        "nofix_flag": nofix_flag,
+        "tag_flag": tag_flag,
+        "double_window_size_flag": double_window_size_flag,
+        "aseg_flag": aseg_flag,
+        "aparc_flag": aparc_flag,
+        "wmparc_flag": wmparc_flag,
+        "conf_targ_flag": conf_targ_flag,
+    }
+    if reg_file is not None:
+        params["reg_file"] = reg_file
+    if gca_subject is not None:
+        params["gca_subject"] = gca_subject
+    if gca_skull_subject is not None:
+        params["gca_skull_subject"] = gca_skull_subject
+    if movbright is not None:
+        params["movbright"] = movbright
+    if fmov is not None:
+        params["fmov"] = fmov
+    if plane is not None:
+        params["plane"] = plane
+    if slice_ is not None:
+        params["slice"] = slice_
+    if volview is not None:
+        params["volview"] = volview
+    if fov is not None:
+        params["fov"] = fov
+    if movscale is not None:
+        params["movscale"] = movscale
+    if surf is not None:
+        params["surf"] = surf
+    if surf_rgb is not None:
+        params["surf_rgb"] = surf_rgb
+    if talxfmname is not None:
+        params["talxfmname"] = talxfmname
+    if ixfm is not None:
+        params["ixfm"] = ixfm
+    if xfm is not None:
+        params["xfm"] = xfm
+    if xfmout is not None:
+        params["xfmout"] = xfmout
+    if fsl is not None:
+        params["fsl"] = fsl
+    if fslregout is not None:
+        params["fslregout"] = fslregout
+    if freeview is not None:
+        params["freeview"] = freeview
+    if vox2vox is not None:
+        params["vox2vox"] = vox2vox
+    if lta is not None:
+        params["lta"] = lta
+    if lta_inv is not None:
+        params["lta_inv"] = lta_inv
+    if ltaout is not None:
+        params["ltaout"] = ltaout
+    if feat is not None:
+        params["feat"] = feat
+    if fsfeat is not None:
+        params["fsfeat"] = fsfeat
+    if subject_id is not None:
+        params["subject_id"] = subject_id
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if float2int is not None:
+        params["float2int"] = float2int
+    if title is not None:
+        params["title"] = title
+    if mov_orientation is not None:
+        params["mov_orientation"] = mov_orientation
+    if targ_orientation is not None:
+        params["targ_orientation"] = targ_orientation
+    if int_ is not None:
+        params["int"] = int_
+    if window_scale is not None:
+        params["window_scale"] = window_scale
+    if det is not None:
+        params["det"] = det
+    if gdiagno is not None:
+        params["gdiagno"] = gdiagno
+    if trans is not None:
+        params["trans"] = trans
+    if rot is not None:
+        params["rot"] = rot
+    return params
+
+
+def tkregister2_cmdl_cargs(
+    params: Tkregister2CmdlParameters,
+    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("tkregister2_cmdl")
+    cargs.extend([
+        "--mov",
+        execution.input_file(params.get("movable_volume"))
+    ])
+    cargs.extend([
+        "--targ",
+        execution.input_file(params.get("target_volume"))
+    ])
+    if params.get("fstarg_flag"):
+        cargs.append("--fstarg")
+    if params.get("reg_file") is not None:
+        cargs.extend([
+            "--reg",
+            execution.input_file(params.get("reg_file"))
+        ])
+    if params.get("check_reg_flag"):
+        cargs.append("--check-reg")
+    if params.get("regheader_flag"):
+        cargs.append("--regheader")
+    if params.get("regheader_center_flag"):
+        cargs.append("--regheader-center")
+    if params.get("fsl_targ_flag"):
+        cargs.append("--fsl-targ")
+    if params.get("fsl_targ_lr_flag"):
+        cargs.append("--fsl-targ-lr")
+    if params.get("gca_subject") is not None:
+        cargs.extend([
+            "--gca",
+            params.get("gca_subject")
+        ])
+    if params.get("gca_skull_subject") is not None:
+        cargs.extend([
+            "--gca-skull",
+            params.get("gca_skull_subject")
+        ])
+    if params.get("no_zero_cras_flag"):
+        cargs.append("--no-zero-cras")
+    if params.get("movbright") is not None:
+        cargs.extend([
+            "--movbright",
+            str(params.get("movbright"))
+        ])
+    if params.get("no_inorm_flag"):
+        cargs.append("--no-inorm")
+    if params.get("fmov") is not None:
+        cargs.extend([
+            "--fmov",
+            str(params.get("fmov"))
+        ])
+    if params.get("fmov_targ_flag"):
+        cargs.append("--fmov-targ")
+    if params.get("plane") is not None:
+        cargs.extend([
+            "--plane",
+            params.get("plane")
+        ])
+    if params.get("slice") is not None:
+        cargs.extend([
+            "--slice",
+            str(params.get("slice"))
+        ])
+    if params.get("volview") is not None:
+        cargs.extend([
+            "--volview",
+            params.get("volview")
+        ])
+    if params.get("fov") is not None:
+        cargs.extend([
+            "--fov",
+            str(params.get("fov"))
+        ])
+    if params.get("movscale") is not None:
+        cargs.extend([
+            "--movscale",
+            str(params.get("movscale"))
+        ])
+    if params.get("surf") is not None:
+        cargs.extend([
+            "--surf",
+            params.get("surf")
+        ])
+    if params.get("surf_rgb") is not None:
+        cargs.extend([
+            "--surf-rgb",
+            *map(str, params.get("surf_rgb"))
+        ])
+    if params.get("lh_only_flag"):
+        cargs.append("--lh-only")
+    if params.get("rh_only_flag"):
+        cargs.append("--rh-only")
+    if params.get("fstal_flag"):
+        cargs.append("--fstal")
+    if params.get("talxfmname") is not None:
+        cargs.extend([
+            "--talxfmname",
+            params.get("talxfmname")
+        ])
+    if params.get("ixfm") is not None:
+        cargs.extend([
+            "--ixfm",
+            execution.input_file(params.get("ixfm"))
+        ])
+    if params.get("xfm") is not None:
+        cargs.extend([
+            "--xfm",
+            execution.input_file(params.get("xfm"))
+        ])
+    if params.get("xfmout") is not None:
+        cargs.extend([
+            "--xfmout",
+            execution.input_file(params.get("xfmout"))
+        ])
+    if params.get("fsl") is not None:
+        cargs.extend([
+            "--fsl",
+            execution.input_file(params.get("fsl"))
+        ])
+    if params.get("fslregout") is not None:
+        cargs.extend([
+            "--fslregout",
+            execution.input_file(params.get("fslregout"))
+        ])
+    if params.get("freeview") is not None:
+        cargs.extend([
+            "--freeview",
+            execution.input_file(params.get("freeview"))
+        ])
+    if params.get("vox2vox") is not None:
+        cargs.extend([
+            "--vox2vox",
+            execution.input_file(params.get("vox2vox"))
+        ])
+    if params.get("lta") is not None:
+        cargs.extend([
+            "--lta",
+            execution.input_file(params.get("lta"))
+        ])
+    if params.get("lta_inv") is not None:
+        cargs.extend([
+            "--lta-inv",
+            execution.input_file(params.get("lta_inv"))
+        ])
+    if params.get("ltaout") is not None:
+        cargs.extend([
+            "--ltaout",
+            execution.input_file(params.get("ltaout"))
+        ])
+    if params.get("ltaout_inv_flag"):
+        cargs.append("--ltaout-inv")
+    if params.get("feat") is not None:
+        cargs.extend([
+            "--feat",
+            params.get("feat")
+        ])
+    if params.get("fsfeat") is not None:
+        cargs.extend([
+            "--fsfeat",
+            params.get("fsfeat")
+        ])
+    if params.get("identity_flag"):
+        cargs.append("--identity")
+    if params.get("subject_id") is not None:
+        cargs.extend([
+            "--s",
+            params.get("subject_id")
+        ])
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subjects_dir")
+        ])
+    if params.get("nofix_flag"):
+        cargs.append("--nofix")
+    if params.get("float2int") is not None:
+        cargs.extend([
+            "--float2int",
+            params.get("float2int")
+        ])
+    if params.get("title") is not None:
+        cargs.extend([
+            "--title",
+            params.get("title")
+        ])
+    if params.get("tag_flag"):
+        cargs.append("--tag")
+    if params.get("mov_orientation") is not None:
+        cargs.extend([
+            "--mov-orientation",
+            params.get("mov_orientation")
+        ])
+    if params.get("targ_orientation") is not None:
+        cargs.extend([
+            "--targ-orientation",
+            params.get("targ_orientation")
+        ])
+    if params.get("int") is not None:
+        cargs.extend([
+            "--int",
+            *params.get("int")
+        ])
+    if params.get("double_window_size_flag"):
+        cargs.append("--2")
+    if params.get("window_scale") is not None:
+        cargs.extend([
+            "--size",
+            str(params.get("window_scale"))
+        ])
+    if params.get("det") is not None:
+        cargs.extend([
+            "--det",
+            execution.input_file(params.get("det"))
+        ])
+    if params.get("aseg_flag"):
+        cargs.append("--aseg")
+    if params.get("aparc_flag"):
+        cargs.append("--aparc+aseg")
+    if params.get("wmparc_flag"):
+        cargs.append("--wmparc")
+    if params.get("gdiagno") is not None:
+        cargs.extend([
+            "--gdiagno",
+            str(params.get("gdiagno"))
+        ])
+    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("conf_targ_flag"):
+        cargs.append("--conf-targ")
+    return cargs
+
+
+def tkregister2_cmdl_outputs(
+    params: Tkregister2CmdlParameters,
+    execution: Execution,
+) -> Tkregister2CmdlOutputs:
+    """
+    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 = Tkregister2CmdlOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def tkregister2_cmdl_execute(
+    params: Tkregister2CmdlParameters,
+    execution: Execution,
+) -> Tkregister2CmdlOutputs:
+    """
+    tkregister2 is a tool to assist in the manual tuning of the linear registration
+    between two volumes, mainly for the purpose of interacting with the FreeSurfer
+    anatomical stream.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Tkregister2CmdlOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tkregister2_cmdl_cargs(params, execution)
+    ret = tkregister2_cmdl_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tkregister2_cmdl(
+    movable_volume: InputPathType,
+    target_volume: InputPathType,
+    fstarg_flag: bool = False,
+    reg_file: InputPathType | None = None,
+    check_reg_flag: bool = False,
+    regheader_flag: bool = False,
+    regheader_center_flag: bool = False,
+    fsl_targ_flag: bool = False,
+    fsl_targ_lr_flag: bool = False,
+    gca_subject: str | None = None,
+    gca_skull_subject: str | None = None,
+    no_zero_cras_flag: bool = False,
+    movbright: float | None = None,
+    no_inorm_flag: bool = False,
+    fmov: float | None = None,
+    fmov_targ_flag: bool = False,
+    plane: str | None = None,
+    slice_: float | None = None,
+    volview: str | None = None,
+    fov: float | None = None,
+    movscale: float | None = None,
+    surf: str | None = None,
+    surf_rgb: list[float] | None = None,
+    lh_only_flag: bool = False,
+    rh_only_flag: bool = False,
+    fstal_flag: bool = False,
+    talxfmname: str | None = None,
+    ixfm: InputPathType | None = None,
+    xfm: InputPathType | None = None,
+    xfmout: InputPathType | None = None,
+    fsl: InputPathType | None = None,
+    fslregout: InputPathType | None = None,
+    freeview: InputPathType | None = None,
+    vox2vox: InputPathType | None = None,
+    lta: InputPathType | None = None,
+    lta_inv: InputPathType | None = None,
+    ltaout: InputPathType | None = None,
+    ltaout_inv_flag: bool = False,
+    feat: str | None = None,
+    fsfeat: str | None = None,
+    identity_flag: bool = False,
+    subject_id: str | None = None,
+    subjects_dir: str | None = None,
+    nofix_flag: bool = False,
+    float2int: str | None = None,
+    title: str | None = None,
+    tag_flag: bool = False,
+    mov_orientation: str | None = None,
+    targ_orientation: str | None = None,
+    int_: list[str] | None = None,
+    double_window_size_flag: bool = False,
+    window_scale: float | None = None,
+    det: InputPathType | None = None,
+    aseg_flag: bool = False,
+    aparc_flag: bool = False,
+    wmparc_flag: bool = False,
+    gdiagno: float | None = None,
+    trans: list[float] | None = None,
+    rot: list[float] | None = None,
+    conf_targ_flag: bool = False,
+    runner: Runner | None = None,
+) -> Tkregister2CmdlOutputs:
+    """
+    tkregister2 is a tool to assist in the manual tuning of the linear registration
+    between two volumes, mainly for the purpose of interacting with the FreeSurfer
+    anatomical stream.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        movable_volume: Path to the movable volume.
+        target_volume: Path to the target volume.
+        fstarg_flag: Target is relative to subjectid/mri.
+        reg_file: Path to input/output registration file.
+        check_reg_flag: Only check, no --reg needed.
+        regheader_flag: Compute registration from headers.
+        regheader_center_flag: Same as --regheader but aligns volume centers.
+        fsl_targ_flag: Use FSLDIR/data/standard/avg152T1.nii.gz.
+        fsl_targ_lr_flag: Use FSLDIR/data/standard/avg152T1_LR-marked.nii.gz.
+        gca_subject: Subject ID for linear GCA registration check.
+        gca_skull_subject: Subject ID for linear 'with skull' GCA registration\
+            check.
+        no_zero_cras_flag: Do not zero target cras (done with --fstal).
+        movbright: Brightness of movable volume.
+        no_inorm_flag: Turn off intensity normalization.
+        fmov: Set movable volume brightness.
+        fmov_targ_flag: Apply movable brightness to the target.
+        plane: Startup view plane: cor, sag, ax.
+        slice_: Startup slice number.
+        volview: Startup with targ or mov.
+        fov: Window FOV in mm (default is 256).
+        movscale: Scale size of movable volume by scale.
+        surf: Display surface as an overlay.
+        surf_rgb: Set surface color (0-255) for R G B.
+        lh_only_flag: Only load/display left hemisphere.
+        rh_only_flag: Only load/display right hemisphere.
+        fstal_flag: Set movable to be tal and reg to be taliarach.xfm.
+        talxfmname: Set movable to be tal and reg to be talxfmname.
+        ixfm: MNI-style inverse registration input matrix.
+        xfm: MNI-style registration input matrix.
+        xfmout: MNI-style registration output matrix.
+        fsl: FSL-style registration input matrix.
+        fslregout: FSL-Style registration output matrix.
+        freeview: FreeView registration output matrix.
+        vox2vox: Vox2vox matrix in ascii.
+        lta: Linear Transform Array file.
+        lta_inv: Read in LTA and invert.
+        ltaout: Output a Linear Transform Array.
+        ltaout_inv_flag: Invert transform in ltaoutfile.
+        feat: Check example_func2standard registration.
+        fsfeat: Check reg/freesurfer/register.dat registration.
+        identity_flag: Use identity as registration matrix.
+        subject_id: Set subject id.
+        subjects_dir: Use specified directory as SUBJECTS_DIR.
+        nofix_flag: Don't fix old tkregister matrices.
+        float2int: Specify old tkregister float2int.
+        title: Set window title.
+        tag_flag: Tag movable volume near the col/row origin.
+        mov_orientation: Supply orientation string for movable volume.
+        targ_orientation: Supply orientation string for target volume.
+        int_: Use registration from intermediate volume.
+        double_window_size_flag: Double window size.
+        window_scale: Scale window by specified scale.
+        det: Save determinant of registration matrix to specified file.
+        aseg_flag: Load aseg and hit 'd' to toggle.
+        aparc_flag: Load aparc+aseg and hit 'c' to toggle.
+        wmparc_flag: Load wmparc and hit 'c' to toggle.
+        gdiagno: Set debug level.
+        trans: Translation (mm) to apply to registration matrix.
+        rot: Rotation angles (deg) to apply to registration matrix.
+        conf_targ_flag: Conform target (assumes reg computed to conform target,\
+            eg, GCA).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Tkregister2CmdlOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TKREGISTER2_CMDL_METADATA)
+    params = tkregister2_cmdl_params(
+        movable_volume=movable_volume,
+        target_volume=target_volume,
+        fstarg_flag=fstarg_flag,
+        reg_file=reg_file,
+        check_reg_flag=check_reg_flag,
+        regheader_flag=regheader_flag,
+        regheader_center_flag=regheader_center_flag,
+        fsl_targ_flag=fsl_targ_flag,
+        fsl_targ_lr_flag=fsl_targ_lr_flag,
+        gca_subject=gca_subject,
+        gca_skull_subject=gca_skull_subject,
+        no_zero_cras_flag=no_zero_cras_flag,
+        movbright=movbright,
+        no_inorm_flag=no_inorm_flag,
+        fmov=fmov,
+        fmov_targ_flag=fmov_targ_flag,
+        plane=plane,
+        slice_=slice_,
+        volview=volview,
+        fov=fov,
+        movscale=movscale,
+        surf=surf,
+        surf_rgb=surf_rgb,
+        lh_only_flag=lh_only_flag,
+        rh_only_flag=rh_only_flag,
+        fstal_flag=fstal_flag,
+        talxfmname=talxfmname,
+        ixfm=ixfm,
+        xfm=xfm,
+        xfmout=xfmout,
+        fsl=fsl,
+        fslregout=fslregout,
+        freeview=freeview,
+        vox2vox=vox2vox,
+        lta=lta,
+        lta_inv=lta_inv,
+        ltaout=ltaout,
+        ltaout_inv_flag=ltaout_inv_flag,
+        feat=feat,
+        fsfeat=fsfeat,
+        identity_flag=identity_flag,
+        subject_id=subject_id,
+        subjects_dir=subjects_dir,
+        nofix_flag=nofix_flag,
+        float2int=float2int,
+        title=title,
+        tag_flag=tag_flag,
+        mov_orientation=mov_orientation,
+        targ_orientation=targ_orientation,
+        int_=int_,
+        double_window_size_flag=double_window_size_flag,
+        window_scale=window_scale,
+        det=det,
+        aseg_flag=aseg_flag,
+        aparc_flag=aparc_flag,
+        wmparc_flag=wmparc_flag,
+        gdiagno=gdiagno,
+        trans=trans,
+        rot=rot,
+        conf_targ_flag=conf_targ_flag,
+    )
+    return tkregister2_cmdl_execute(params, execution)
+
+
+__all__ = [
+    "TKREGISTER2_CMDL_METADATA",
+    "Tkregister2CmdlOutputs",
+    "Tkregister2CmdlParameters",
+    "tkregister2_cmdl",
+    "tkregister2_cmdl_params",
+]