niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/map_central_sulcus.py

@@ -0,0 +1,584 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAP_CENTRAL_SULCUS_METADATA = Metadata(
+    id="13b958f09713b9767ab00695cb856a93c2ef9725.boutiques",
+    name="map_central_sulcus",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MapCentralSulcusParameters = typing.TypedDict('MapCentralSulcusParameters', {
+    "__STYX_TYPE__": typing.Literal["map_central_sulcus"],
+    "subjid": str,
+    "process_directive": str,
+    "hemi_flag": typing.NotRequired[str | None],
+    "expert_prefs_file": typing.NotRequired[InputPathType | None],
+    "xopts_use": bool,
+    "xopts_clean": bool,
+    "xopts_overwrite": bool,
+    "watershed_cmd": typing.NotRequired[str | None],
+    "xmask_file": typing.NotRequired[InputPathType | None],
+    "wsless": bool,
+    "wsmore": bool,
+    "wsatlas": bool,
+    "no_wsatlas": bool,
+    "no_wsgcaatlas": bool,
+    "wsthresh": typing.NotRequired[float | None],
+    "wsseed": typing.NotRequired[str | None],
+    "norm3diters": typing.NotRequired[float | None],
+    "normmaxgrad": 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_flag": 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,
+    "mprage": bool,
+    "washu_mprage": bool,
+    "schwartzya3t_atlas": bool,
+    "mail_username": typing.NotRequired[str | None],
+    "threads": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "map_central_sulcus": map_central_sulcus_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 {
+        "map_central_sulcus": map_central_sulcus_outputs,
+    }.get(t)
+
+
+class MapCentralSulcusOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `map_central_sulcus(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    log_file: OutputPathType
+    """Log file from recon-all process."""
+    status_log_file: OutputPathType
+    """Status log file from recon-all process."""
+
+
+def map_central_sulcus_params(
+    subjid: str,
+    process_directive: str,
+    hemi_flag: str | None = None,
+    expert_prefs_file: InputPathType | None = None,
+    xopts_use: bool = False,
+    xopts_clean: bool = False,
+    xopts_overwrite: bool = False,
+    watershed_cmd: str | None = None,
+    xmask_file: 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: str | None = None,
+    norm3diters: float | None = None,
+    normmaxgrad: float | None = None,
+    norm1_b: float | None = None,
+    norm2_b: float | None = None,
+    norm1_n: float | None = None,
+    norm2_n: float | None = None,
+    cm_flag: 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,
+    mprage: bool = False,
+    washu_mprage: bool = False,
+    schwartzya3t_atlas: bool = False,
+    mail_username: str | None = None,
+    threads: float | None = None,
+) -> MapCentralSulcusParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjid: FreeSurfer subject identification string which doubles as the\
+            name of the reconstruction root directory for the subject.
+        process_directive: Process directive for recon-all (e.g. -all,\
+            -autorecon-all, -autorecon1).
+        hemi_flag: Specify hemisphere processing (e.g., lh for left hemisphere\
+            or rh for right hemisphere).
+        expert_prefs_file: Read-in expert options file for processing.\
+            Overrides default options.
+        xopts_use: Use pre-existing expert options file.
+        xopts_clean: Delete pre-existing expert options file.
+        xopts_overwrite: Overwrite pre-existing expert options file.
+        watershed_cmd: Controls how the skull stripping will be performed.
+        xmask_file: Custom external brain mask to replace automated\
+            skullstripping.
+        wsless: Decrease watershed threshold (leaves less skull, but can strip\
+            more brain).
+        wsmore: Increase watershed threshold (leaves more skull, but can strip\
+            less brain).
+        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: Specify an index (C, R, S) point in the skull.
+        norm3diters: Number of 3d iterations for mri_normalize.
+        normmaxgrad: Max grad (-g) for mri_normalize. Default is 1.
+        norm1_b: In the first usage of mri_normalize, use control point with\
+            intensity N below target (default=10.0).
+        norm2_b: In the second usage of mri_normalize, use control point with\
+            intensity N below target (default=10.0).
+        norm1_n: In the first usage of mri_normalize, do N number of\
+            iterations.
+        norm2_n: In the second usage of mri_normalize, do N number of\
+            iterations.
+        cm_flag: 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, then stops.
+        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.
+        mprage: Assume scan parameters are MGH MP-RAGE protocol.
+        washu_mprage: Assume scan parameters are Wash.U. MP-RAGE protocol.
+        schwartzya3t_atlas: For tal reg, use special young adult 3T atlas.
+        mail_username: Mail user when done.
+        threads: Set number of threads to use.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "map_central_sulcus",
+        "subjid": subjid,
+        "process_directive": process_directive,
+        "xopts_use": xopts_use,
+        "xopts_clean": xopts_clean,
+        "xopts_overwrite": xopts_overwrite,
+        "wsless": wsless,
+        "wsmore": wsmore,
+        "wsatlas": wsatlas,
+        "no_wsatlas": no_wsatlas,
+        "no_wsgcaatlas": no_wsgcaatlas,
+        "cm_flag": cm_flag,
+        "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,
+        "mprage": mprage,
+        "washu_mprage": washu_mprage,
+        "schwartzya3t_atlas": schwartzya3t_atlas,
+    }
+    if hemi_flag is not None:
+        params["hemi_flag"] = hemi_flag
+    if expert_prefs_file is not None:
+        params["expert_prefs_file"] = expert_prefs_file
+    if watershed_cmd is not None:
+        params["watershed_cmd"] = watershed_cmd
+    if xmask_file is not None:
+        params["xmask_file"] = xmask_file
+    if wsthresh is not None:
+        params["wsthresh"] = wsthresh
+    if wsseed is not None:
+        params["wsseed"] = wsseed
+    if norm3diters is not None:
+        params["norm3diters"] = norm3diters
+    if normmaxgrad is not None:
+        params["normmaxgrad"] = normmaxgrad
+    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 mail_username is not None:
+        params["mail_username"] = mail_username
+    if threads is not None:
+        params["threads"] = threads
+    return params
+
+
+def map_central_sulcus_cargs(
+    params: MapCentralSulcusParameters,
+    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")
+    ])
+    cargs.append(params.get("process_directive"))
+    if params.get("hemi_flag") is not None:
+        cargs.extend([
+            "-hemi",
+            params.get("hemi_flag")
+        ])
+    if params.get("expert_prefs_file") is not None:
+        cargs.extend([
+            "-expert",
+            execution.input_file(params.get("expert_prefs_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("watershed_cmd") is not None:
+        cargs.extend([
+            "-watershed",
+            params.get("watershed_cmd")
+        ])
+    if params.get("xmask_file") is not None:
+        cargs.extend([
+            "-xmask",
+            execution.input_file(params.get("xmask_file"))
+        ])
+    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",
+            params.get("wsseed")
+        ])
+    if params.get("norm3diters") is not None:
+        cargs.extend([
+            "-norm3diters",
+            str(params.get("norm3diters"))
+        ])
+    if params.get("normmaxgrad") is not None:
+        cargs.extend([
+            "-normmaxgrad",
+            str(params.get("normmaxgrad"))
+        ])
+    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_flag"):
+        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("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("mail_username") is not None:
+        cargs.extend([
+            "-mail",
+            params.get("mail_username")
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "-threads",
+            str(params.get("threads"))
+        ])
+    return cargs
+
+
+def map_central_sulcus_outputs(
+    params: MapCentralSulcusParameters,
+    execution: Execution,
+) -> MapCentralSulcusOutputs:
+    """
+    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 = MapCentralSulcusOutputs(
+        root=execution.output_file("."),
+        log_file=execution.output_file(params.get("subjid") + "/scripts/recon-all.log"),
+        status_log_file=execution.output_file(params.get("subjid") + "/scripts/recon-all-status.log"),
+    )
+    return ret
+
+
+def map_central_sulcus_execute(
+    params: MapCentralSulcusParameters,
+    execution: Execution,
+) -> MapCentralSulcusOutputs:
+    """
+    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 `MapCentralSulcusOutputs`).
+    """
+    params = execution.params(params)
+    cargs = map_central_sulcus_cargs(params, execution)
+    ret = map_central_sulcus_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def map_central_sulcus(
+    subjid: str,
+    process_directive: str,
+    hemi_flag: str | None = None,
+    expert_prefs_file: InputPathType | None = None,
+    xopts_use: bool = False,
+    xopts_clean: bool = False,
+    xopts_overwrite: bool = False,
+    watershed_cmd: str | None = None,
+    xmask_file: 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: str | None = None,
+    norm3diters: float | None = None,
+    normmaxgrad: float | None = None,
+    norm1_b: float | None = None,
+    norm2_b: float | None = None,
+    norm1_n: float | None = None,
+    norm2_n: float | None = None,
+    cm_flag: 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,
+    mprage: bool = False,
+    washu_mprage: bool = False,
+    schwartzya3t_atlas: bool = False,
+    mail_username: str | None = None,
+    threads: float | None = None,
+    runner: Runner | None = None,
+) -> MapCentralSulcusOutputs:
+    """
+    Performs all, or any part of, the FreeSurfer cortical reconstruction process.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjid: FreeSurfer subject identification string which doubles as the\
+            name of the reconstruction root directory for the subject.
+        process_directive: Process directive for recon-all (e.g. -all,\
+            -autorecon-all, -autorecon1).
+        hemi_flag: Specify hemisphere processing (e.g., lh for left hemisphere\
+            or rh for right hemisphere).
+        expert_prefs_file: Read-in expert options file for processing.\
+            Overrides default options.
+        xopts_use: Use pre-existing expert options file.
+        xopts_clean: Delete pre-existing expert options file.
+        xopts_overwrite: Overwrite pre-existing expert options file.
+        watershed_cmd: Controls how the skull stripping will be performed.
+        xmask_file: Custom external brain mask to replace automated\
+            skullstripping.
+        wsless: Decrease watershed threshold (leaves less skull, but can strip\
+            more brain).
+        wsmore: Increase watershed threshold (leaves more skull, but can strip\
+            less brain).
+        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: Specify an index (C, R, S) point in the skull.
+        norm3diters: Number of 3d iterations for mri_normalize.
+        normmaxgrad: Max grad (-g) for mri_normalize. Default is 1.
+        norm1_b: In the first usage of mri_normalize, use control point with\
+            intensity N below target (default=10.0).
+        norm2_b: In the second usage of mri_normalize, use control point with\
+            intensity N below target (default=10.0).
+        norm1_n: In the first usage of mri_normalize, do N number of\
+            iterations.
+        norm2_n: In the second usage of mri_normalize, do N number of\
+            iterations.
+        cm_flag: 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, then stops.
+        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.
+        mprage: Assume scan parameters are MGH MP-RAGE protocol.
+        washu_mprage: Assume scan parameters are Wash.U. MP-RAGE protocol.
+        schwartzya3t_atlas: For tal reg, use special young adult 3T atlas.
+        mail_username: Mail user when done.
+        threads: Set number of threads to use.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MapCentralSulcusOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAP_CENTRAL_SULCUS_METADATA)
+    params = map_central_sulcus_params(
+        subjid=subjid,
+        process_directive=process_directive,
+        hemi_flag=hemi_flag,
+        expert_prefs_file=expert_prefs_file,
+        xopts_use=xopts_use,
+        xopts_clean=xopts_clean,
+        xopts_overwrite=xopts_overwrite,
+        watershed_cmd=watershed_cmd,
+        xmask_file=xmask_file,
+        wsless=wsless,
+        wsmore=wsmore,
+        wsatlas=wsatlas,
+        no_wsatlas=no_wsatlas,
+        no_wsgcaatlas=no_wsgcaatlas,
+        wsthresh=wsthresh,
+        wsseed=wsseed,
+        norm3diters=norm3diters,
+        normmaxgrad=normmaxgrad,
+        norm1_b=norm1_b,
+        norm2_b=norm2_b,
+        norm1_n=norm1_n,
+        norm2_n=norm2_n,
+        cm_flag=cm_flag,
+        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,
+        mprage=mprage,
+        washu_mprage=washu_mprage,
+        schwartzya3t_atlas=schwartzya3t_atlas,
+        mail_username=mail_username,
+        threads=threads,
+    )
+    return map_central_sulcus_execute(params, execution)
+
+
+__all__ = [
+    "MAP_CENTRAL_SULCUS_METADATA",
+    "MapCentralSulcusOutputs",
+    "MapCentralSulcusParameters",
+    "map_central_sulcus",
+    "map_central_sulcus_params",
+]