niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_preproc.py

@@ -0,0 +1,739 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_PREPROC_METADATA = Metadata(
+    id="dd5edb4541571b929ce3905d2cb09807c8f4d850.boutiques",
+    name="mris_preproc",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisPreprocParameters = typing.TypedDict('MrisPreprocParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_preproc"],
+    "outfile": str,
+    "target_subject": str,
+    "hemi": str,
+    "meas": typing.NotRequired[str | None],
+    "label": typing.NotRequired[str | None],
+    "measdir": typing.NotRequired[str | None],
+    "subjects": typing.NotRequired[list[str] | None],
+    "fsgd": typing.NotRequired[InputPathType | None],
+    "subjectlist": typing.NotRequired[InputPathType | None],
+    "qdec": typing.NotRequired[InputPathType | None],
+    "qdec_long": typing.NotRequired[InputPathType | None],
+    "surfmeasfile": typing.NotRequired[list[InputPathType] | None],
+    "projfrac": typing.NotRequired[float | None],
+    "projfrac_max": typing.NotRequired[list[float] | None],
+    "projfrac_avg": typing.NotRequired[list[float] | None],
+    "no_mask_non_cortex": bool,
+    "session_file": typing.NotRequired[InputPathType | None],
+    "dir_file": typing.NotRequired[InputPathType | None],
+    "analysis": typing.NotRequired[str | None],
+    "contrast": typing.NotRequired[str | None],
+    "cvar_flag": bool,
+    "offset_flag": bool,
+    "map": typing.NotRequired[str | None],
+    "etiv_flag": bool,
+    "fwhm": typing.NotRequired[float | None],
+    "fwhm_src": typing.NotRequired[float | None],
+    "niters": typing.NotRequired[float | None],
+    "niters_src": typing.NotRequired[float | None],
+    "cortex_only": bool,
+    "mgz_flag": bool,
+    "no_jac_flag": bool,
+    "paired_diff_flag": bool,
+    "cache_out": typing.NotRequired[str | None],
+    "cache_in": typing.NotRequired[str | None],
+    "cache_out_only": typing.NotRequired[str | None],
+    "no_prune_flag": bool,
+    "mean_flag": bool,
+    "std_flag": bool,
+    "reshape_flag": bool,
+    "surfreg": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "synth_flag": bool,
+    "tmpdir": typing.NotRequired[str | None],
+    "nocleanup_flag": bool,
+    "cleanup_flag": bool,
+    "log": typing.NotRequired[str | None],
+    "nolog_flag": bool,
+    "debug_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 {
+        "mris_preproc": mris_preproc_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 MrisPreprocOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_preproc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_preproc_params(
+    outfile: str,
+    target_subject: str,
+    hemi: str,
+    meas: str | None = None,
+    label: str | None = None,
+    measdir: str | None = None,
+    subjects: list[str] | None = None,
+    fsgd: InputPathType | None = None,
+    subjectlist: InputPathType | None = None,
+    qdec: InputPathType | None = None,
+    qdec_long: InputPathType | None = None,
+    surfmeasfile: list[InputPathType] | None = None,
+    projfrac: float | None = None,
+    projfrac_max: list[float] | None = None,
+    projfrac_avg: list[float] | None = None,
+    no_mask_non_cortex: bool = False,
+    session_file: InputPathType | None = None,
+    dir_file: InputPathType | None = None,
+    analysis: str | None = None,
+    contrast: str | None = None,
+    cvar_flag: bool = False,
+    offset_flag: bool = False,
+    map_: str | None = None,
+    etiv_flag: bool = False,
+    fwhm: float | None = None,
+    fwhm_src: float | None = None,
+    niters: float | None = None,
+    niters_src: float | None = None,
+    cortex_only: bool = False,
+    mgz_flag: bool = False,
+    no_jac_flag: bool = False,
+    paired_diff_flag: bool = False,
+    cache_out: str | None = None,
+    cache_in: str | None = None,
+    cache_out_only: str | None = None,
+    no_prune_flag: bool = False,
+    mean_flag: bool = False,
+    std_flag: bool = False,
+    reshape_flag: bool = False,
+    surfreg: str | None = None,
+    subjects_dir: str | None = None,
+    synth_flag: bool = False,
+    tmpdir: str | None = None,
+    nocleanup_flag: bool = False,
+    cleanup_flag: bool = False,
+    log: str | None = None,
+    nolog_flag: bool = False,
+    debug_flag: bool = False,
+) -> MrisPreprocParameters:
+    """
+    Build parameters.
+    
+    Args:
+        outfile: Save output here.
+        target_subject: Subject to use as the common-space. All input data will\
+            be resampled to the surface of this subject.
+        hemi: Use hemisphere for source and target surfaces. Can be lh or rh.
+        meas: Use subject/surf/hemi.surfmeasure as input. Implies --srcfmt\
+            curv.
+        label: Look in label/hemi.annotname.(annot,mgz) and use mapmethod nnf.
+        measdir: Look in subdir instead of surf.
+        subjects: Specify an input subject on the command-line. All subjects\
+            must be specified in this way.
+        fsgd: Specify the list of input subjects from the fsgd file.
+        subjectlist: List all subjects separated by white space in\
+            subjlistfile.
+        qdec: Specify list of subjects via qdec table file. Assumes the first\
+            column is the "fsid".
+        qdec_long: Specify list of subjects via longitudinal qdec table file.
+        surfmeasfile: Specify full path to input surface measure file.
+        projfrac: When sampling a volume onto the surface, sample a fraction of\
+            the thickness along the surface normal.
+        projfrac_max: When sampling a volume onto the surface, find max along\
+            projection for vol2surf.
+        projfrac_avg: Compute average along projection for vol2surf.
+        no_mask_non_cortex: Do not mask out non-cortex in vol2surf.
+        session_file: FS-FAST session file.
+        dir_file: FS-FAST session directory file.
+        analysis: FS-FAST analysis.
+        contrast: FS-FAST contrast.
+        cvar_flag: Use fsfast contrast variance (cesvar).
+        offset_flag: Use fsfast mean offset (h-offset).
+        map_: Use fsfast contrast/map.
+        etiv_flag: Divide each subject's value by the Estimated Total Intra\
+            Cranial Volume as found in aseg.stats.
+        fwhm: Smooth by fwhm mm on the target surface.
+        fwhm_src: Smooth by fwhm mm on the source surface.
+        niters: Smooth by niters on the target surface.
+        niters_src: Smooth by niters on the source surface.
+        cortex_only: Exclude medial wall.
+        mgz_flag: Use mgz format internally.
+        no_jac_flag: Turn off jacobian correction.
+        paired_diff_flag: Compute paired differences after concatenating all\
+            inputs together.
+        cache_out: Cache the output in the specified cache file.
+        cache_in: Use the pre-computed cached data from the specified cache\
+            file.
+        cache_out_only: Cache data without actually creating an output.
+        no_prune_flag: Do not prune the inputs.
+        mean_flag: Compute the mean of all inputs.
+        std_flag: Compute the standard deviation of all inputs.
+        reshape_flag: Reshape spatial dimensions.
+        surfreg: Use specified surface registration to the common space.
+        subjects_dir: Set SUBJECTS_DIR environment variable.
+        synth_flag: Synthesize the input data with white gaussian noise.
+        tmpdir: Use specified temporary directory.
+        nocleanup_flag: Do not delete temporary files.
+        cleanup_flag: Delete temporary files (default).
+        log: Specify log file.
+        nolog_flag: Do not create a log file.
+        debug_flag: Enable debug mode.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_preproc",
+        "outfile": outfile,
+        "target_subject": target_subject,
+        "hemi": hemi,
+        "no_mask_non_cortex": no_mask_non_cortex,
+        "cvar_flag": cvar_flag,
+        "offset_flag": offset_flag,
+        "etiv_flag": etiv_flag,
+        "cortex_only": cortex_only,
+        "mgz_flag": mgz_flag,
+        "no_jac_flag": no_jac_flag,
+        "paired_diff_flag": paired_diff_flag,
+        "no_prune_flag": no_prune_flag,
+        "mean_flag": mean_flag,
+        "std_flag": std_flag,
+        "reshape_flag": reshape_flag,
+        "synth_flag": synth_flag,
+        "nocleanup_flag": nocleanup_flag,
+        "cleanup_flag": cleanup_flag,
+        "nolog_flag": nolog_flag,
+        "debug_flag": debug_flag,
+    }
+    if meas is not None:
+        params["meas"] = meas
+    if label is not None:
+        params["label"] = label
+    if measdir is not None:
+        params["measdir"] = measdir
+    if subjects is not None:
+        params["subjects"] = subjects
+    if fsgd is not None:
+        params["fsgd"] = fsgd
+    if subjectlist is not None:
+        params["subjectlist"] = subjectlist
+    if qdec is not None:
+        params["qdec"] = qdec
+    if qdec_long is not None:
+        params["qdec_long"] = qdec_long
+    if surfmeasfile is not None:
+        params["surfmeasfile"] = surfmeasfile
+    if projfrac is not None:
+        params["projfrac"] = projfrac
+    if projfrac_max is not None:
+        params["projfrac_max"] = projfrac_max
+    if projfrac_avg is not None:
+        params["projfrac_avg"] = projfrac_avg
+    if session_file is not None:
+        params["session_file"] = session_file
+    if dir_file is not None:
+        params["dir_file"] = dir_file
+    if analysis is not None:
+        params["analysis"] = analysis
+    if contrast is not None:
+        params["contrast"] = contrast
+    if map_ is not None:
+        params["map"] = map_
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if fwhm_src is not None:
+        params["fwhm_src"] = fwhm_src
+    if niters is not None:
+        params["niters"] = niters
+    if niters_src is not None:
+        params["niters_src"] = niters_src
+    if cache_out is not None:
+        params["cache_out"] = cache_out
+    if cache_in is not None:
+        params["cache_in"] = cache_in
+    if cache_out_only is not None:
+        params["cache_out_only"] = cache_out_only
+    if surfreg is not None:
+        params["surfreg"] = surfreg
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if tmpdir is not None:
+        params["tmpdir"] = tmpdir
+    if log is not None:
+        params["log"] = log
+    return params
+
+
+def mris_preproc_cargs(
+    params: MrisPreprocParameters,
+    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("mris_preproc")
+    cargs.extend([
+        "--out",
+        params.get("outfile")
+    ])
+    cargs.extend([
+        "--target",
+        params.get("target_subject")
+    ])
+    cargs.extend([
+        "--hemi",
+        params.get("hemi")
+    ])
+    if params.get("meas") is not None:
+        cargs.extend([
+            "--meas",
+            params.get("meas")
+        ])
+    if params.get("label") is not None:
+        cargs.extend([
+            "--label",
+            params.get("label")
+        ])
+    if params.get("measdir") is not None:
+        cargs.extend([
+            "--measdir",
+            params.get("measdir")
+        ])
+    if params.get("subjects") is not None:
+        cargs.extend([
+            "--s",
+            *params.get("subjects")
+        ])
+    if params.get("fsgd") is not None:
+        cargs.extend([
+            "--fsgd",
+            execution.input_file(params.get("fsgd"))
+        ])
+    if params.get("subjectlist") is not None:
+        cargs.extend([
+            "--f",
+            execution.input_file(params.get("subjectlist"))
+        ])
+    if params.get("qdec") is not None:
+        cargs.extend([
+            "--qdec",
+            execution.input_file(params.get("qdec"))
+        ])
+    if params.get("qdec_long") is not None:
+        cargs.extend([
+            "--qdec-long",
+            execution.input_file(params.get("qdec_long"))
+        ])
+    if params.get("surfmeasfile") is not None:
+        cargs.extend([
+            "--is",
+            *[execution.input_file(f) for f in params.get("surfmeasfile")]
+        ])
+    cargs.append("[VOLMEASFILE]")
+    if params.get("projfrac") is not None:
+        cargs.extend([
+            "--projfrac",
+            str(params.get("projfrac"))
+        ])
+    if params.get("projfrac_max") is not None:
+        cargs.extend([
+            "--projfrac-max",
+            *map(str, params.get("projfrac_max"))
+        ])
+    if params.get("projfrac_avg") is not None:
+        cargs.extend([
+            "--projfrac-avg",
+            *map(str, params.get("projfrac_avg"))
+        ])
+    if params.get("no_mask_non_cortex"):
+        cargs.append("--no-mask-non-cortex")
+    if params.get("session_file") is not None:
+        cargs.extend([
+            "--sf",
+            execution.input_file(params.get("session_file"))
+        ])
+    if params.get("dir_file") is not None:
+        cargs.extend([
+            "--df",
+            execution.input_file(params.get("dir_file"))
+        ])
+    if params.get("analysis") is not None:
+        cargs.extend([
+            "--analysis",
+            params.get("analysis")
+        ])
+    if params.get("contrast") is not None:
+        cargs.extend([
+            "--contrast",
+            params.get("contrast")
+        ])
+    if params.get("cvar_flag"):
+        cargs.append("--cvar")
+    if params.get("offset_flag"):
+        cargs.append("--offset")
+    if params.get("map") is not None:
+        cargs.extend([
+            "--map",
+            params.get("map")
+        ])
+    if params.get("etiv_flag"):
+        cargs.append("--etiv")
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "--fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("fwhm_src") is not None:
+        cargs.extend([
+            "--fwhm-src",
+            str(params.get("fwhm_src"))
+        ])
+    if params.get("niters") is not None:
+        cargs.extend([
+            "--niters",
+            str(params.get("niters"))
+        ])
+    if params.get("niters_src") is not None:
+        cargs.extend([
+            "--niters-src",
+            str(params.get("niters_src"))
+        ])
+    if params.get("cortex_only"):
+        cargs.append("--cortex-only")
+    if params.get("mgz_flag"):
+        cargs.append("--mgz")
+    if params.get("no_jac_flag"):
+        cargs.append("--no-jac")
+    if params.get("paired_diff_flag"):
+        cargs.append("--paired-diff")
+    if params.get("cache_out") is not None:
+        cargs.extend([
+            "--cache-out",
+            params.get("cache_out")
+        ])
+    if params.get("cache_in") is not None:
+        cargs.extend([
+            "--cache-in",
+            params.get("cache_in")
+        ])
+    if params.get("cache_out_only") is not None:
+        cargs.extend([
+            "--cache-out-only",
+            params.get("cache_out_only")
+        ])
+    if params.get("no_prune_flag"):
+        cargs.append("--no-prune")
+    if params.get("mean_flag"):
+        cargs.append("--mean")
+    if params.get("std_flag"):
+        cargs.append("--std")
+    if params.get("reshape_flag"):
+        cargs.append("--reshape")
+    if params.get("surfreg") is not None:
+        cargs.extend([
+            "--surfreg",
+            params.get("surfreg")
+        ])
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--SUBJECTS_DIR",
+            params.get("subjects_dir")
+        ])
+    if params.get("synth_flag"):
+        cargs.append("--synth")
+    if params.get("tmpdir") is not None:
+        cargs.extend([
+            "--tmpdir",
+            params.get("tmpdir")
+        ])
+    if params.get("nocleanup_flag"):
+        cargs.append("--nocleanup")
+    if params.get("cleanup_flag"):
+        cargs.append("--cleanup")
+    if params.get("log") is not None:
+        cargs.extend([
+            "--log",
+            params.get("log")
+        ])
+    if params.get("nolog_flag"):
+        cargs.append("--nolog")
+    if params.get("debug_flag"):
+        cargs.append("--debug")
+    return cargs
+
+
+def mris_preproc_outputs(
+    params: MrisPreprocParameters,
+    execution: Execution,
+) -> MrisPreprocOutputs:
+    """
+    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 = MrisPreprocOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_preproc_execute(
+    params: MrisPreprocParameters,
+    execution: Execution,
+) -> MrisPreprocOutputs:
+    """
+    Script to prepare surface-based data for high-level analysis by resampling
+    surface or volume source data to a common subject and concatenating them into
+    one file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisPreprocOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_preproc_cargs(params, execution)
+    ret = mris_preproc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_preproc(
+    outfile: str,
+    target_subject: str,
+    hemi: str,
+    meas: str | None = None,
+    label: str | None = None,
+    measdir: str | None = None,
+    subjects: list[str] | None = None,
+    fsgd: InputPathType | None = None,
+    subjectlist: InputPathType | None = None,
+    qdec: InputPathType | None = None,
+    qdec_long: InputPathType | None = None,
+    surfmeasfile: list[InputPathType] | None = None,
+    projfrac: float | None = None,
+    projfrac_max: list[float] | None = None,
+    projfrac_avg: list[float] | None = None,
+    no_mask_non_cortex: bool = False,
+    session_file: InputPathType | None = None,
+    dir_file: InputPathType | None = None,
+    analysis: str | None = None,
+    contrast: str | None = None,
+    cvar_flag: bool = False,
+    offset_flag: bool = False,
+    map_: str | None = None,
+    etiv_flag: bool = False,
+    fwhm: float | None = None,
+    fwhm_src: float | None = None,
+    niters: float | None = None,
+    niters_src: float | None = None,
+    cortex_only: bool = False,
+    mgz_flag: bool = False,
+    no_jac_flag: bool = False,
+    paired_diff_flag: bool = False,
+    cache_out: str | None = None,
+    cache_in: str | None = None,
+    cache_out_only: str | None = None,
+    no_prune_flag: bool = False,
+    mean_flag: bool = False,
+    std_flag: bool = False,
+    reshape_flag: bool = False,
+    surfreg: str | None = None,
+    subjects_dir: str | None = None,
+    synth_flag: bool = False,
+    tmpdir: str | None = None,
+    nocleanup_flag: bool = False,
+    cleanup_flag: bool = False,
+    log: str | None = None,
+    nolog_flag: bool = False,
+    debug_flag: bool = False,
+    runner: Runner | None = None,
+) -> MrisPreprocOutputs:
+    """
+    Script to prepare surface-based data for high-level analysis by resampling
+    surface or volume source data to a common subject and concatenating them into
+    one file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        outfile: Save output here.
+        target_subject: Subject to use as the common-space. All input data will\
+            be resampled to the surface of this subject.
+        hemi: Use hemisphere for source and target surfaces. Can be lh or rh.
+        meas: Use subject/surf/hemi.surfmeasure as input. Implies --srcfmt\
+            curv.
+        label: Look in label/hemi.annotname.(annot,mgz) and use mapmethod nnf.
+        measdir: Look in subdir instead of surf.
+        subjects: Specify an input subject on the command-line. All subjects\
+            must be specified in this way.
+        fsgd: Specify the list of input subjects from the fsgd file.
+        subjectlist: List all subjects separated by white space in\
+            subjlistfile.
+        qdec: Specify list of subjects via qdec table file. Assumes the first\
+            column is the "fsid".
+        qdec_long: Specify list of subjects via longitudinal qdec table file.
+        surfmeasfile: Specify full path to input surface measure file.
+        projfrac: When sampling a volume onto the surface, sample a fraction of\
+            the thickness along the surface normal.
+        projfrac_max: When sampling a volume onto the surface, find max along\
+            projection for vol2surf.
+        projfrac_avg: Compute average along projection for vol2surf.
+        no_mask_non_cortex: Do not mask out non-cortex in vol2surf.
+        session_file: FS-FAST session file.
+        dir_file: FS-FAST session directory file.
+        analysis: FS-FAST analysis.
+        contrast: FS-FAST contrast.
+        cvar_flag: Use fsfast contrast variance (cesvar).
+        offset_flag: Use fsfast mean offset (h-offset).
+        map_: Use fsfast contrast/map.
+        etiv_flag: Divide each subject's value by the Estimated Total Intra\
+            Cranial Volume as found in aseg.stats.
+        fwhm: Smooth by fwhm mm on the target surface.
+        fwhm_src: Smooth by fwhm mm on the source surface.
+        niters: Smooth by niters on the target surface.
+        niters_src: Smooth by niters on the source surface.
+        cortex_only: Exclude medial wall.
+        mgz_flag: Use mgz format internally.
+        no_jac_flag: Turn off jacobian correction.
+        paired_diff_flag: Compute paired differences after concatenating all\
+            inputs together.
+        cache_out: Cache the output in the specified cache file.
+        cache_in: Use the pre-computed cached data from the specified cache\
+            file.
+        cache_out_only: Cache data without actually creating an output.
+        no_prune_flag: Do not prune the inputs.
+        mean_flag: Compute the mean of all inputs.
+        std_flag: Compute the standard deviation of all inputs.
+        reshape_flag: Reshape spatial dimensions.
+        surfreg: Use specified surface registration to the common space.
+        subjects_dir: Set SUBJECTS_DIR environment variable.
+        synth_flag: Synthesize the input data with white gaussian noise.
+        tmpdir: Use specified temporary directory.
+        nocleanup_flag: Do not delete temporary files.
+        cleanup_flag: Delete temporary files (default).
+        log: Specify log file.
+        nolog_flag: Do not create a log file.
+        debug_flag: Enable debug mode.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisPreprocOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_PREPROC_METADATA)
+    params = mris_preproc_params(
+        outfile=outfile,
+        target_subject=target_subject,
+        hemi=hemi,
+        meas=meas,
+        label=label,
+        measdir=measdir,
+        subjects=subjects,
+        fsgd=fsgd,
+        subjectlist=subjectlist,
+        qdec=qdec,
+        qdec_long=qdec_long,
+        surfmeasfile=surfmeasfile,
+        projfrac=projfrac,
+        projfrac_max=projfrac_max,
+        projfrac_avg=projfrac_avg,
+        no_mask_non_cortex=no_mask_non_cortex,
+        session_file=session_file,
+        dir_file=dir_file,
+        analysis=analysis,
+        contrast=contrast,
+        cvar_flag=cvar_flag,
+        offset_flag=offset_flag,
+        map_=map_,
+        etiv_flag=etiv_flag,
+        fwhm=fwhm,
+        fwhm_src=fwhm_src,
+        niters=niters,
+        niters_src=niters_src,
+        cortex_only=cortex_only,
+        mgz_flag=mgz_flag,
+        no_jac_flag=no_jac_flag,
+        paired_diff_flag=paired_diff_flag,
+        cache_out=cache_out,
+        cache_in=cache_in,
+        cache_out_only=cache_out_only,
+        no_prune_flag=no_prune_flag,
+        mean_flag=mean_flag,
+        std_flag=std_flag,
+        reshape_flag=reshape_flag,
+        surfreg=surfreg,
+        subjects_dir=subjects_dir,
+        synth_flag=synth_flag,
+        tmpdir=tmpdir,
+        nocleanup_flag=nocleanup_flag,
+        cleanup_flag=cleanup_flag,
+        log=log,
+        nolog_flag=nolog_flag,
+        debug_flag=debug_flag,
+    )
+    return mris_preproc_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_PREPROC_METADATA",
+    "MrisPreprocOutputs",
+    "MrisPreprocParameters",
+    "mris_preproc",
+    "mris_preproc_params",
+]