niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/recon_all.py

@@ -0,0 +1,856 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+RECON_ALL_METADATA = Metadata(
+    id="de72948bacd270ce7d872b3cb30e555b07de540c.boutiques",
+    name="recon-all",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+ReconAllParameters = typing.TypedDict('ReconAllParameters', {
+    "__STYX_TYPE__": typing.Literal["recon-all"],
+    "subjid": str,
+    "autorecon3_flag": bool,
+    "hemi": typing.NotRequired[str | None],
+    "pons_crs": typing.NotRequired[list[float] | None],
+    "cc_crs": typing.NotRequired[list[float] | None],
+    "lh_crs": typing.NotRequired[list[float] | None],
+    "rh_crs": typing.NotRequired[list[float] | None],
+    "nofill": bool,
+    "watershed": typing.NotRequired[str | None],
+    "external_brain_mask": typing.NotRequired[InputPathType | None],
+    "wsless": bool,
+    "wsmore": bool,
+    "wsatlas": bool,
+    "no_wsatlas": bool,
+    "no_wsgcaatlas": bool,
+    "wsthresh": typing.NotRequired[float | None],
+    "wsseed": typing.NotRequired[list[float] | None],
+    "norm_3d_iters": typing.NotRequired[float | None],
+    "norm_max_grad": typing.NotRequired[float | None],
+    "norm1_b": typing.NotRequired[float | None],
+    "norm2_b": typing.NotRequired[float | None],
+    "norm1_n": typing.NotRequired[float | None],
+    "norm2_n": typing.NotRequired[float | None],
+    "cm": bool,
+    "no_fix_with_ga": bool,
+    "fix_diag_only": bool,
+    "seg_wlo": typing.NotRequired[float | None],
+    "seg_ghi": typing.NotRequired[float | None],
+    "nothicken": bool,
+    "no_ca_align_after": bool,
+    "no_ca_align": bool,
+    "deface": bool,
+    "expert_file": typing.NotRequired[InputPathType | None],
+    "xopts_use": bool,
+    "xopts_clean": bool,
+    "xopts_overwrite": bool,
+    "termscript_file": typing.NotRequired[InputPathType | None],
+    "mprage": bool,
+    "washu_mprage": bool,
+    "schwartzya3t_atlas": bool,
+    "threads": typing.NotRequired[float | None],
+    "waitfor_file": typing.NotRequired[InputPathType | None],
+    "notify_file": typing.NotRequired[InputPathType | None],
+    "log_file": typing.NotRequired[InputPathType | None],
+    "status_file": typing.NotRequired[InputPathType | None],
+    "noappend": bool,
+    "no_isrunning": bool,
+    "hippocampal_subfields_t1": bool,
+    "hippocampal_subfields_t2": typing.NotRequired[str | None],
+    "hippocampal_subfields_t1t2": typing.NotRequired[str | None],
+    "brainstem_structures": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+    "mail_user": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[str | None],
+    "group_id": typing.NotRequired[str | None],
+    "only_versions": bool,
+    "debug": bool,
+    "allow_coredump": bool,
+    "dontrun": bool,
+    "version": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "recon-all": recon_all_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 {
+        "recon-all": recon_all_outputs,
+    }.get(t)
+
+
+class ReconAllOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `recon_all(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    logfile: OutputPathType
+    """Log file of the recon-all process"""
+    statusfile: OutputPathType
+    """Status file of the recon-all process"""
+
+
+def recon_all_params(
+    subjid: str,
+    autorecon3_flag: bool = False,
+    hemi: str | None = None,
+    pons_crs: list[float] | None = None,
+    cc_crs: list[float] | None = None,
+    lh_crs: list[float] | None = None,
+    rh_crs: list[float] | None = None,
+    nofill: bool = False,
+    watershed: str | None = None,
+    external_brain_mask: InputPathType | None = None,
+    wsless: bool = False,
+    wsmore: bool = False,
+    wsatlas: bool = False,
+    no_wsatlas: bool = False,
+    no_wsgcaatlas: bool = False,
+    wsthresh: float | None = None,
+    wsseed: list[float] | None = None,
+    norm_3d_iters: float | None = None,
+    norm_max_grad: float | None = None,
+    norm1_b: float | None = None,
+    norm2_b: float | None = None,
+    norm1_n: float | None = None,
+    norm2_n: float | None = None,
+    cm: bool = False,
+    no_fix_with_ga: bool = False,
+    fix_diag_only: bool = False,
+    seg_wlo: float | None = None,
+    seg_ghi: float | None = None,
+    nothicken: bool = False,
+    no_ca_align_after: bool = False,
+    no_ca_align: bool = False,
+    deface: bool = False,
+    expert_file: InputPathType | None = None,
+    xopts_use: bool = False,
+    xopts_clean: bool = False,
+    xopts_overwrite: bool = False,
+    termscript_file: InputPathType | None = None,
+    mprage: bool = False,
+    washu_mprage: bool = False,
+    schwartzya3t_atlas: bool = False,
+    threads: float | None = None,
+    waitfor_file: InputPathType | None = None,
+    notify_file: InputPathType | None = None,
+    log_file: InputPathType | None = None,
+    status_file: InputPathType | None = None,
+    noappend: bool = False,
+    no_isrunning: bool = False,
+    hippocampal_subfields_t1: bool = False,
+    hippocampal_subfields_t2: str | None = None,
+    hippocampal_subfields_t1t2: str | None = None,
+    brainstem_structures: bool = False,
+    subjects_dir: str | None = None,
+    mail_user: str | None = None,
+    umask: str | None = None,
+    group_id: str | None = None,
+    only_versions: bool = False,
+    debug: bool = False,
+    allow_coredump: bool = False,
+    dontrun: bool = False,
+    version: bool = False,
+    help_: bool = False,
+) -> ReconAllParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjid: Subject ID for the FreeSurfer analysis.
+        autorecon3_flag: Process stages 24-34.
+        hemi: Specify hemisphere ('lh' or 'rh').
+        pons_crs: Specify CRS for pons during fill operation.
+        cc_crs: Specify CRS for corpus callosum during fill operation.
+        lh_crs: Specify CRS for left hemisphere during fill operation.
+        rh_crs: Specify CRS for right hemisphere during fill operation.
+        nofill: Do not use automatic subcortical seg to fill.
+        watershed: Control skull stripping/watershed program.
+        external_brain_mask: Custom external brain mask file.
+        wsless: Decrease watershed threshold.
+        wsmore: Increase watershed threshold.
+        wsatlas: Use atlas when skull stripping.
+        no_wsatlas: Do not use atlas when skull stripping.
+        no_wsgcaatlas: Do not use GCA atlas when skull stripping.
+        wsthresh: Explicitly set watershed threshold.
+        wsseed: Identify an index (C, R, S) point in the skull.
+        norm_3d_iters: Number of 3D iterations for mri_normalize.
+        norm_max_grad: Max grad for mri_normalize.
+        norm1_b: First usage of mri_normalize with control point intensity N\
+            below target.
+        norm2_b: Second usage of mri_normalize with control point intensity N\
+            below target.
+        norm1_n: First usage of mri_normalize, number of iterations.
+        norm2_n: Second usage of mri_normalize, number of iterations.
+        cm: Conform volumes to the min voxel size.
+        no_fix_with_ga: Do not use genetic algorithm when fixing topology.
+        fix_diag_only: Topology fixer runs until ?h.defect_labels files are\
+            created.
+        seg_wlo: Set WLO value for mri_segment and mris_make_surfaces.
+        seg_ghi: Set GHI value for mri_segment and mris_make_surfaces.
+        nothicken: Pass '-thicken 0' to mri_segment.
+        no_ca_align_after: Turn off '-align-after' with mri_ca_register.
+        no_ca_align: Turn off '-align' with mri_ca_label.
+        deface: Deface subject, written to orig_defaced.mgz.
+        expert_file: Read-in expert options file.
+        xopts_use: Use pre-existing expert options file.
+        xopts_clean: Delete pre-existing expert options file.
+        xopts_overwrite: Overwrite pre-existing expert options file.
+        termscript_file: Run script before exiting.
+        mprage: Assume scan parameters are MGH MP-RAGE protocol.
+        washu_mprage: Assume scan parameters are Wash.U. MP-RAGE protocol.
+        schwartzya3t_atlas: Use special young adult 3T atlas for tal reg.
+        threads: Set number of threads to use.
+        waitfor_file: Wait for file to appear before beginning.
+        notify_file: Create this file after finishing.
+        log_file: Specify log file.
+        status_file: Specify status file.
+        noappend: Start new log and status files instead of appending.
+        no_isrunning: Do not check whether this subject is currently being\
+            processed.
+        hippocampal_subfields_t1: Segmentation of hippocampal subfields using\
+            input T1 scan.
+        hippocampal_subfields_t2: Segmentation using an additional scan and\
+            input T2 scan.
+        hippocampal_subfields_t1t2: Segmentation using additional scan and\
+            input T1.
+        brainstem_structures: Segmentation of brainstem structures.
+        subjects_dir: Specify subjects directory.
+        mail_user: Mail user when done.
+        umask: Set unix file permission mask.
+        group_id: Check that current group is alpha group.
+        only_versions: Print version of each binary and exit.
+        debug: Print out lots of info.
+        allow_coredump: Set coredump limit to unlimited.
+        dontrun: Do everything but execute each command.
+        version: Print version of this script and exit.
+        help_: Display help message and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "recon-all",
+        "subjid": subjid,
+        "autorecon3_flag": autorecon3_flag,
+        "nofill": nofill,
+        "wsless": wsless,
+        "wsmore": wsmore,
+        "wsatlas": wsatlas,
+        "no_wsatlas": no_wsatlas,
+        "no_wsgcaatlas": no_wsgcaatlas,
+        "cm": cm,
+        "no_fix_with_ga": no_fix_with_ga,
+        "fix_diag_only": fix_diag_only,
+        "nothicken": nothicken,
+        "no_ca_align_after": no_ca_align_after,
+        "no_ca_align": no_ca_align,
+        "deface": deface,
+        "xopts_use": xopts_use,
+        "xopts_clean": xopts_clean,
+        "xopts_overwrite": xopts_overwrite,
+        "mprage": mprage,
+        "washu_mprage": washu_mprage,
+        "schwartzya3t_atlas": schwartzya3t_atlas,
+        "noappend": noappend,
+        "no_isrunning": no_isrunning,
+        "hippocampal_subfields_t1": hippocampal_subfields_t1,
+        "brainstem_structures": brainstem_structures,
+        "only_versions": only_versions,
+        "debug": debug,
+        "allow_coredump": allow_coredump,
+        "dontrun": dontrun,
+        "version": version,
+        "help": help_,
+    }
+    if hemi is not None:
+        params["hemi"] = hemi
+    if pons_crs is not None:
+        params["pons_crs"] = pons_crs
+    if cc_crs is not None:
+        params["cc_crs"] = cc_crs
+    if lh_crs is not None:
+        params["lh_crs"] = lh_crs
+    if rh_crs is not None:
+        params["rh_crs"] = rh_crs
+    if watershed is not None:
+        params["watershed"] = watershed
+    if external_brain_mask is not None:
+        params["external_brain_mask"] = external_brain_mask
+    if wsthresh is not None:
+        params["wsthresh"] = wsthresh
+    if wsseed is not None:
+        params["wsseed"] = wsseed
+    if norm_3d_iters is not None:
+        params["norm_3d_iters"] = norm_3d_iters
+    if norm_max_grad is not None:
+        params["norm_max_grad"] = norm_max_grad
+    if norm1_b is not None:
+        params["norm1_b"] = norm1_b
+    if norm2_b is not None:
+        params["norm2_b"] = norm2_b
+    if norm1_n is not None:
+        params["norm1_n"] = norm1_n
+    if norm2_n is not None:
+        params["norm2_n"] = norm2_n
+    if seg_wlo is not None:
+        params["seg_wlo"] = seg_wlo
+    if seg_ghi is not None:
+        params["seg_ghi"] = seg_ghi
+    if expert_file is not None:
+        params["expert_file"] = expert_file
+    if termscript_file is not None:
+        params["termscript_file"] = termscript_file
+    if threads is not None:
+        params["threads"] = threads
+    if waitfor_file is not None:
+        params["waitfor_file"] = waitfor_file
+    if notify_file is not None:
+        params["notify_file"] = notify_file
+    if log_file is not None:
+        params["log_file"] = log_file
+    if status_file is not None:
+        params["status_file"] = status_file
+    if hippocampal_subfields_t2 is not None:
+        params["hippocampal_subfields_t2"] = hippocampal_subfields_t2
+    if hippocampal_subfields_t1t2 is not None:
+        params["hippocampal_subfields_t1t2"] = hippocampal_subfields_t1t2
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if mail_user is not None:
+        params["mail_user"] = mail_user
+    if umask is not None:
+        params["umask"] = umask
+    if group_id is not None:
+        params["group_id"] = group_id
+    return params
+
+
+def recon_all_cargs(
+    params: ReconAllParameters,
+    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("recon-all")
+    cargs.extend([
+        "-subjid",
+        params.get("subjid")
+    ])
+    if params.get("autorecon3_flag"):
+        cargs.append("-autorecon3")
+    if params.get("hemi") is not None:
+        cargs.extend([
+            "-hemi",
+            params.get("hemi")
+        ])
+    if params.get("pons_crs") is not None:
+        cargs.extend([
+            "-pons-crs",
+            *map(str, params.get("pons_crs"))
+        ])
+    if params.get("cc_crs") is not None:
+        cargs.extend([
+            "-cc-crs",
+            *map(str, params.get("cc_crs"))
+        ])
+    if params.get("lh_crs") is not None:
+        cargs.extend([
+            "-lh-crs",
+            *map(str, params.get("lh_crs"))
+        ])
+    if params.get("rh_crs") is not None:
+        cargs.extend([
+            "-rh-crs",
+            *map(str, params.get("rh_crs"))
+        ])
+    if params.get("nofill"):
+        cargs.append("-nofill")
+    if params.get("watershed") is not None:
+        cargs.extend([
+            "-watershed",
+            params.get("watershed")
+        ])
+    if params.get("external_brain_mask") is not None:
+        cargs.extend([
+            "-xmask",
+            execution.input_file(params.get("external_brain_mask"))
+        ])
+    if params.get("wsless"):
+        cargs.append("-wsless")
+    if params.get("wsmore"):
+        cargs.append("-wsmore")
+    if params.get("wsatlas"):
+        cargs.append("-wsatlas")
+    if params.get("no_wsatlas"):
+        cargs.append("-no-wsatlas")
+    if params.get("no_wsgcaatlas"):
+        cargs.append("-no-wsgcaatlas")
+    if params.get("wsthresh") is not None:
+        cargs.extend([
+            "-wsthresh",
+            str(params.get("wsthresh"))
+        ])
+    if params.get("wsseed") is not None:
+        cargs.extend([
+            "-wsseed",
+            *map(str, params.get("wsseed"))
+        ])
+    if params.get("norm_3d_iters") is not None:
+        cargs.extend([
+            "-norm3diters",
+            str(params.get("norm_3d_iters"))
+        ])
+    if params.get("norm_max_grad") is not None:
+        cargs.extend([
+            "-normmaxgrad",
+            str(params.get("norm_max_grad"))
+        ])
+    if params.get("norm1_b") is not None:
+        cargs.extend([
+            "-norm1-b",
+            str(params.get("norm1_b"))
+        ])
+    if params.get("norm2_b") is not None:
+        cargs.extend([
+            "-norm2-b",
+            str(params.get("norm2_b"))
+        ])
+    if params.get("norm1_n") is not None:
+        cargs.extend([
+            "-norm1-n",
+            str(params.get("norm1_n"))
+        ])
+    if params.get("norm2_n") is not None:
+        cargs.extend([
+            "-norm2-n",
+            str(params.get("norm2_n"))
+        ])
+    if params.get("cm"):
+        cargs.append("-cm")
+    if params.get("no_fix_with_ga"):
+        cargs.append("-no-fix-with-ga")
+    if params.get("fix_diag_only"):
+        cargs.append("-fix-diag-only")
+    if params.get("seg_wlo") is not None:
+        cargs.extend([
+            "-seg-wlo",
+            str(params.get("seg_wlo"))
+        ])
+    if params.get("seg_ghi") is not None:
+        cargs.extend([
+            "-seg-ghi",
+            str(params.get("seg_ghi"))
+        ])
+    if params.get("nothicken"):
+        cargs.append("-nothicken")
+    if params.get("no_ca_align_after"):
+        cargs.append("-no-ca-align-after")
+    if params.get("no_ca_align"):
+        cargs.append("-no-ca-align")
+    if params.get("deface"):
+        cargs.append("-deface")
+    if params.get("expert_file") is not None:
+        cargs.extend([
+            "-expert",
+            execution.input_file(params.get("expert_file"))
+        ])
+    if params.get("xopts_use"):
+        cargs.append("-xopts-use")
+    if params.get("xopts_clean"):
+        cargs.append("-xopts-clean")
+    if params.get("xopts_overwrite"):
+        cargs.append("-xopts-overwrite")
+    if params.get("termscript_file") is not None:
+        cargs.extend([
+            "-termscript",
+            execution.input_file(params.get("termscript_file"))
+        ])
+    if params.get("mprage"):
+        cargs.append("-mprage")
+    if params.get("washu_mprage"):
+        cargs.append("-washu_mprage")
+    if params.get("schwartzya3t_atlas"):
+        cargs.append("-schwartzya3t-atlas")
+    if params.get("threads") is not None:
+        cargs.extend([
+            "-threads",
+            str(params.get("threads"))
+        ])
+    if params.get("waitfor_file") is not None:
+        cargs.extend([
+            "-waitfor",
+            execution.input_file(params.get("waitfor_file"))
+        ])
+    if params.get("notify_file") is not None:
+        cargs.extend([
+            "-notify",
+            execution.input_file(params.get("notify_file"))
+        ])
+    if params.get("log_file") is not None:
+        cargs.extend([
+            "-log",
+            execution.input_file(params.get("log_file"))
+        ])
+    if params.get("status_file") is not None:
+        cargs.extend([
+            "-status",
+            execution.input_file(params.get("status_file"))
+        ])
+    if params.get("noappend"):
+        cargs.append("-noappend")
+    if params.get("no_isrunning"):
+        cargs.append("-no-isrunning")
+    if params.get("hippocampal_subfields_t1"):
+        cargs.append("-hippocampal-subfields-T1")
+    if params.get("hippocampal_subfields_t2") is not None:
+        cargs.extend([
+            "-hippocampal-subfields-T2",
+            params.get("hippocampal_subfields_t2")
+        ])
+    if params.get("hippocampal_subfields_t1t2") is not None:
+        cargs.extend([
+            "-hippocampal-subfields-T1T2",
+            params.get("hippocampal_subfields_t1t2")
+        ])
+    if params.get("brainstem_structures"):
+        cargs.append("-brainstem-structures")
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "-sd",
+            params.get("subjects_dir")
+        ])
+    if params.get("mail_user") is not None:
+        cargs.extend([
+            "-mail",
+            params.get("mail_user")
+        ])
+    if params.get("umask") is not None:
+        cargs.extend([
+            "-umask",
+            params.get("umask")
+        ])
+    if params.get("group_id") is not None:
+        cargs.extend([
+            "-grp",
+            params.get("group_id")
+        ])
+    if params.get("only_versions"):
+        cargs.append("-onlyversions")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("allow_coredump"):
+        cargs.append("-allowcoredump")
+    if params.get("dontrun"):
+        cargs.append("-dontrun")
+    if params.get("version"):
+        cargs.append("-version")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def recon_all_outputs(
+    params: ReconAllParameters,
+    execution: Execution,
+) -> ReconAllOutputs:
+    """
+    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 = ReconAllOutputs(
+        root=execution.output_file("."),
+        logfile=execution.output_file(params.get("subjid") + "/scripts/recon-all.log"),
+        statusfile=execution.output_file(params.get("subjid") + "/scripts/recon-all-status.log"),
+    )
+    return ret
+
+
+def recon_all_execute(
+    params: ReconAllParameters,
+    execution: Execution,
+) -> ReconAllOutputs:
+    """
+    Performs all, or any part of, the FreeSurfer cortical reconstruction process.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ReconAllOutputs`).
+    """
+    params = execution.params(params)
+    cargs = recon_all_cargs(params, execution)
+    ret = recon_all_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def recon_all(
+    subjid: str,
+    autorecon3_flag: bool = False,
+    hemi: str | None = None,
+    pons_crs: list[float] | None = None,
+    cc_crs: list[float] | None = None,
+    lh_crs: list[float] | None = None,
+    rh_crs: list[float] | None = None,
+    nofill: bool = False,
+    watershed: str | None = None,
+    external_brain_mask: InputPathType | None = None,
+    wsless: bool = False,
+    wsmore: bool = False,
+    wsatlas: bool = False,
+    no_wsatlas: bool = False,
+    no_wsgcaatlas: bool = False,
+    wsthresh: float | None = None,
+    wsseed: list[float] | None = None,
+    norm_3d_iters: float | None = None,
+    norm_max_grad: float | None = None,
+    norm1_b: float | None = None,
+    norm2_b: float | None = None,
+    norm1_n: float | None = None,
+    norm2_n: float | None = None,
+    cm: bool = False,
+    no_fix_with_ga: bool = False,
+    fix_diag_only: bool = False,
+    seg_wlo: float | None = None,
+    seg_ghi: float | None = None,
+    nothicken: bool = False,
+    no_ca_align_after: bool = False,
+    no_ca_align: bool = False,
+    deface: bool = False,
+    expert_file: InputPathType | None = None,
+    xopts_use: bool = False,
+    xopts_clean: bool = False,
+    xopts_overwrite: bool = False,
+    termscript_file: InputPathType | None = None,
+    mprage: bool = False,
+    washu_mprage: bool = False,
+    schwartzya3t_atlas: bool = False,
+    threads: float | None = None,
+    waitfor_file: InputPathType | None = None,
+    notify_file: InputPathType | None = None,
+    log_file: InputPathType | None = None,
+    status_file: InputPathType | None = None,
+    noappend: bool = False,
+    no_isrunning: bool = False,
+    hippocampal_subfields_t1: bool = False,
+    hippocampal_subfields_t2: str | None = None,
+    hippocampal_subfields_t1t2: str | None = None,
+    brainstem_structures: bool = False,
+    subjects_dir: str | None = None,
+    mail_user: str | None = None,
+    umask: str | None = None,
+    group_id: str | None = None,
+    only_versions: bool = False,
+    debug: bool = False,
+    allow_coredump: bool = False,
+    dontrun: bool = False,
+    version: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> ReconAllOutputs:
+    """
+    Performs all, or any part of, the FreeSurfer cortical reconstruction process.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjid: Subject ID for the FreeSurfer analysis.
+        autorecon3_flag: Process stages 24-34.
+        hemi: Specify hemisphere ('lh' or 'rh').
+        pons_crs: Specify CRS for pons during fill operation.
+        cc_crs: Specify CRS for corpus callosum during fill operation.
+        lh_crs: Specify CRS for left hemisphere during fill operation.
+        rh_crs: Specify CRS for right hemisphere during fill operation.
+        nofill: Do not use automatic subcortical seg to fill.
+        watershed: Control skull stripping/watershed program.
+        external_brain_mask: Custom external brain mask file.
+        wsless: Decrease watershed threshold.
+        wsmore: Increase watershed threshold.
+        wsatlas: Use atlas when skull stripping.
+        no_wsatlas: Do not use atlas when skull stripping.
+        no_wsgcaatlas: Do not use GCA atlas when skull stripping.
+        wsthresh: Explicitly set watershed threshold.
+        wsseed: Identify an index (C, R, S) point in the skull.
+        norm_3d_iters: Number of 3D iterations for mri_normalize.
+        norm_max_grad: Max grad for mri_normalize.
+        norm1_b: First usage of mri_normalize with control point intensity N\
+            below target.
+        norm2_b: Second usage of mri_normalize with control point intensity N\
+            below target.
+        norm1_n: First usage of mri_normalize, number of iterations.
+        norm2_n: Second usage of mri_normalize, number of iterations.
+        cm: Conform volumes to the min voxel size.
+        no_fix_with_ga: Do not use genetic algorithm when fixing topology.
+        fix_diag_only: Topology fixer runs until ?h.defect_labels files are\
+            created.
+        seg_wlo: Set WLO value for mri_segment and mris_make_surfaces.
+        seg_ghi: Set GHI value for mri_segment and mris_make_surfaces.
+        nothicken: Pass '-thicken 0' to mri_segment.
+        no_ca_align_after: Turn off '-align-after' with mri_ca_register.
+        no_ca_align: Turn off '-align' with mri_ca_label.
+        deface: Deface subject, written to orig_defaced.mgz.
+        expert_file: Read-in expert options file.
+        xopts_use: Use pre-existing expert options file.
+        xopts_clean: Delete pre-existing expert options file.
+        xopts_overwrite: Overwrite pre-existing expert options file.
+        termscript_file: Run script before exiting.
+        mprage: Assume scan parameters are MGH MP-RAGE protocol.
+        washu_mprage: Assume scan parameters are Wash.U. MP-RAGE protocol.
+        schwartzya3t_atlas: Use special young adult 3T atlas for tal reg.
+        threads: Set number of threads to use.
+        waitfor_file: Wait for file to appear before beginning.
+        notify_file: Create this file after finishing.
+        log_file: Specify log file.
+        status_file: Specify status file.
+        noappend: Start new log and status files instead of appending.
+        no_isrunning: Do not check whether this subject is currently being\
+            processed.
+        hippocampal_subfields_t1: Segmentation of hippocampal subfields using\
+            input T1 scan.
+        hippocampal_subfields_t2: Segmentation using an additional scan and\
+            input T2 scan.
+        hippocampal_subfields_t1t2: Segmentation using additional scan and\
+            input T1.
+        brainstem_structures: Segmentation of brainstem structures.
+        subjects_dir: Specify subjects directory.
+        mail_user: Mail user when done.
+        umask: Set unix file permission mask.
+        group_id: Check that current group is alpha group.
+        only_versions: Print version of each binary and exit.
+        debug: Print out lots of info.
+        allow_coredump: Set coredump limit to unlimited.
+        dontrun: Do everything but execute each command.
+        version: Print version of this script and exit.
+        help_: Display help message and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ReconAllOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RECON_ALL_METADATA)
+    params = recon_all_params(
+        subjid=subjid,
+        autorecon3_flag=autorecon3_flag,
+        hemi=hemi,
+        pons_crs=pons_crs,
+        cc_crs=cc_crs,
+        lh_crs=lh_crs,
+        rh_crs=rh_crs,
+        nofill=nofill,
+        watershed=watershed,
+        external_brain_mask=external_brain_mask,
+        wsless=wsless,
+        wsmore=wsmore,
+        wsatlas=wsatlas,
+        no_wsatlas=no_wsatlas,
+        no_wsgcaatlas=no_wsgcaatlas,
+        wsthresh=wsthresh,
+        wsseed=wsseed,
+        norm_3d_iters=norm_3d_iters,
+        norm_max_grad=norm_max_grad,
+        norm1_b=norm1_b,
+        norm2_b=norm2_b,
+        norm1_n=norm1_n,
+        norm2_n=norm2_n,
+        cm=cm,
+        no_fix_with_ga=no_fix_with_ga,
+        fix_diag_only=fix_diag_only,
+        seg_wlo=seg_wlo,
+        seg_ghi=seg_ghi,
+        nothicken=nothicken,
+        no_ca_align_after=no_ca_align_after,
+        no_ca_align=no_ca_align,
+        deface=deface,
+        expert_file=expert_file,
+        xopts_use=xopts_use,
+        xopts_clean=xopts_clean,
+        xopts_overwrite=xopts_overwrite,
+        termscript_file=termscript_file,
+        mprage=mprage,
+        washu_mprage=washu_mprage,
+        schwartzya3t_atlas=schwartzya3t_atlas,
+        threads=threads,
+        waitfor_file=waitfor_file,
+        notify_file=notify_file,
+        log_file=log_file,
+        status_file=status_file,
+        noappend=noappend,
+        no_isrunning=no_isrunning,
+        hippocampal_subfields_t1=hippocampal_subfields_t1,
+        hippocampal_subfields_t2=hippocampal_subfields_t2,
+        hippocampal_subfields_t1t2=hippocampal_subfields_t1t2,
+        brainstem_structures=brainstem_structures,
+        subjects_dir=subjects_dir,
+        mail_user=mail_user,
+        umask=umask,
+        group_id=group_id,
+        only_versions=only_versions,
+        debug=debug,
+        allow_coredump=allow_coredump,
+        dontrun=dontrun,
+        version=version,
+        help_=help_,
+    )
+    return recon_all_execute(params, execution)
+
+
+__all__ = [
+    "RECON_ALL_METADATA",
+    "ReconAllOutputs",
+    "ReconAllParameters",
+    "recon_all",
+    "recon_all_params",
+]