niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/gtmseg.py

@@ -0,0 +1,373 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+GTMSEG_METADATA = Metadata(
+    id="29e1c1370e446a18137bbf4e9561c7972ac57725.boutiques",
+    name="gtmseg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+GtmsegParameters = typing.TypedDict('GtmsegParameters', {
+    "__STYX_TYPE__": typing.Literal["gtmseg"],
+    "subject": str,
+    "outvol": typing.NotRequired[str | None],
+    "usf": typing.NotRequired[float | None],
+    "subsegwm": bool,
+    "keep_hypo": bool,
+    "keep_cc": bool,
+    "dmax": typing.NotRequired[float | None],
+    "ctx_annot": typing.NotRequired[str | None],
+    "wm_annot": typing.NotRequired[str | None],
+    "output_usf": typing.NotRequired[float | None],
+    "head": typing.NotRequired[str | None],
+    "subseg_cbwm": bool,
+    "no_pons": bool,
+    "no_vermis": bool,
+    "ctab": typing.NotRequired[InputPathType | None],
+    "no_seg_stats": bool,
+    "xcerseg": bool,
+    "debug": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "gtmseg": gtmseg_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 {
+        "gtmseg": gtmseg_outputs,
+    }.get(t)
+
+
+class GtmsegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `gtmseg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume: OutputPathType | None
+    """Output segmentation volume"""
+    output_ctab: OutputPathType
+    """Generated color table for the output segmentation"""
+
+
+def gtmseg_params(
+    subject: str,
+    outvol: str | None = "gtmseg.mgz",
+    usf: float | None = 2,
+    subsegwm: bool = False,
+    keep_hypo: bool = False,
+    keep_cc: bool = False,
+    dmax: float | None = 5,
+    ctx_annot: str | None = "aparc 1000 2000",
+    wm_annot: str | None = "lobes 3200 4200",
+    output_usf: float | None = None,
+    head: str | None = None,
+    subseg_cbwm: bool = False,
+    no_pons: bool = False,
+    no_vermis: bool = False,
+    ctab: InputPathType | None = None,
+    no_seg_stats: bool = False,
+    xcerseg: bool = False,
+    debug: bool = False,
+) -> GtmsegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject: Subject to analyze.
+        outvol: Output volume relative to subject/mri.
+        usf: Upsampling factor for segmentation resolution.
+        subsegwm: Subsegment white matter into lobes.
+        keep_hypo: Do not relabel hypointensities as white matter when\
+            subsegmenting WM.
+        keep_cc: Do not relabel corpus callosum as white matter.
+        dmax: Distance threshold for subsegmenting WM.
+        ctx_annot: Annotation for cortical segmentation.
+        wm_annot: Annotation for WM segmentation with --subsegwm.
+        output_usf: Set output upsampling factor different from input USF for\
+            debugging.
+        head: Use alternative head segmentation file.
+        subseg_cbwm: Subsegment cerebellum WM into core and gyri.
+        no_pons: Do not add pons segmentation when running xcerebralseg.
+        no_vermis: Do not add vermis segmentation when running xcerebralseg.
+        ctab: Color table for custom segmentation.
+        no_seg_stats: Do not compute segmentation statistics.
+        xcerseg: Run xcerebralseg to create apas+head.mgz.
+        debug: Enable debugging mode.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "gtmseg",
+        "subject": subject,
+        "subsegwm": subsegwm,
+        "keep_hypo": keep_hypo,
+        "keep_cc": keep_cc,
+        "subseg_cbwm": subseg_cbwm,
+        "no_pons": no_pons,
+        "no_vermis": no_vermis,
+        "no_seg_stats": no_seg_stats,
+        "xcerseg": xcerseg,
+        "debug": debug,
+    }
+    if outvol is not None:
+        params["outvol"] = outvol
+    if usf is not None:
+        params["usf"] = usf
+    if dmax is not None:
+        params["dmax"] = dmax
+    if ctx_annot is not None:
+        params["ctx_annot"] = ctx_annot
+    if wm_annot is not None:
+        params["wm_annot"] = wm_annot
+    if output_usf is not None:
+        params["output_usf"] = output_usf
+    if head is not None:
+        params["head"] = head
+    if ctab is not None:
+        params["ctab"] = ctab
+    return params
+
+
+def gtmseg_cargs(
+    params: GtmsegParameters,
+    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("gtmseg")
+    cargs.extend([
+        "--s",
+        params.get("subject")
+    ])
+    if params.get("outvol") is not None:
+        cargs.extend([
+            "--o",
+            params.get("outvol")
+        ])
+    if params.get("usf") is not None:
+        cargs.extend([
+            "--usf",
+            str(params.get("usf"))
+        ])
+    if params.get("subsegwm"):
+        cargs.append("--subsegwm")
+    if params.get("keep_hypo"):
+        cargs.append("--keep-hypo")
+    if params.get("keep_cc"):
+        cargs.append("--keep-cc")
+    if params.get("dmax") is not None:
+        cargs.extend([
+            "--dmax",
+            str(params.get("dmax"))
+        ])
+    if params.get("ctx_annot") is not None:
+        cargs.extend([
+            "--ctx-annot",
+            params.get("ctx_annot")
+        ])
+    if params.get("wm_annot") is not None:
+        cargs.extend([
+            "--wm-annot",
+            params.get("wm_annot")
+        ])
+    if params.get("output_usf") is not None:
+        cargs.extend([
+            "--output-usf",
+            str(params.get("output_usf"))
+        ])
+    if params.get("head") is not None:
+        cargs.extend([
+            "--head",
+            params.get("head")
+        ])
+    if params.get("subseg_cbwm"):
+        cargs.append("--subseg-cblum-wm")
+    if params.get("no_pons"):
+        cargs.append("--no-pons")
+    if params.get("no_vermis"):
+        cargs.append("--no-vermis")
+    if params.get("ctab") is not None:
+        cargs.extend([
+            "--ctab",
+            execution.input_file(params.get("ctab"))
+        ])
+    if params.get("no_seg_stats"):
+        cargs.append("--no-seg-stats")
+    if params.get("xcerseg"):
+        cargs.append("--xcerseg")
+    if params.get("debug"):
+        cargs.append("--debug")
+    return cargs
+
+
+def gtmseg_outputs(
+    params: GtmsegParameters,
+    execution: Execution,
+) -> GtmsegOutputs:
+    """
+    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 = GtmsegOutputs(
+        root=execution.output_file("."),
+        output_volume=execution.output_file("$SUBJECTS_DIR/" + params.get("subject") + "/mri/" + params.get("outvol")) if (params.get("outvol") is not None) else None,
+        output_ctab=execution.output_file("$SUBJECTS_DIR/" + params.get("subject") + "/mri/gtmseg+myseg.ctab"),
+    )
+    return ret
+
+
+def gtmseg_execute(
+    params: GtmsegParameters,
+    execution: Execution,
+) -> GtmsegOutputs:
+    """
+    Creates an anatomical segmentation for the geometric transfer matrix (GTM) used
+    in PET partial volume correction.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `GtmsegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = gtmseg_cargs(params, execution)
+    ret = gtmseg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def gtmseg(
+    subject: str,
+    outvol: str | None = "gtmseg.mgz",
+    usf: float | None = 2,
+    subsegwm: bool = False,
+    keep_hypo: bool = False,
+    keep_cc: bool = False,
+    dmax: float | None = 5,
+    ctx_annot: str | None = "aparc 1000 2000",
+    wm_annot: str | None = "lobes 3200 4200",
+    output_usf: float | None = None,
+    head: str | None = None,
+    subseg_cbwm: bool = False,
+    no_pons: bool = False,
+    no_vermis: bool = False,
+    ctab: InputPathType | None = None,
+    no_seg_stats: bool = False,
+    xcerseg: bool = False,
+    debug: bool = False,
+    runner: Runner | None = None,
+) -> GtmsegOutputs:
+    """
+    Creates an anatomical segmentation for the geometric transfer matrix (GTM) used
+    in PET partial volume correction.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject: Subject to analyze.
+        outvol: Output volume relative to subject/mri.
+        usf: Upsampling factor for segmentation resolution.
+        subsegwm: Subsegment white matter into lobes.
+        keep_hypo: Do not relabel hypointensities as white matter when\
+            subsegmenting WM.
+        keep_cc: Do not relabel corpus callosum as white matter.
+        dmax: Distance threshold for subsegmenting WM.
+        ctx_annot: Annotation for cortical segmentation.
+        wm_annot: Annotation for WM segmentation with --subsegwm.
+        output_usf: Set output upsampling factor different from input USF for\
+            debugging.
+        head: Use alternative head segmentation file.
+        subseg_cbwm: Subsegment cerebellum WM into core and gyri.
+        no_pons: Do not add pons segmentation when running xcerebralseg.
+        no_vermis: Do not add vermis segmentation when running xcerebralseg.
+        ctab: Color table for custom segmentation.
+        no_seg_stats: Do not compute segmentation statistics.
+        xcerseg: Run xcerebralseg to create apas+head.mgz.
+        debug: Enable debugging mode.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `GtmsegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GTMSEG_METADATA)
+    params = gtmseg_params(
+        subject=subject,
+        outvol=outvol,
+        usf=usf,
+        subsegwm=subsegwm,
+        keep_hypo=keep_hypo,
+        keep_cc=keep_cc,
+        dmax=dmax,
+        ctx_annot=ctx_annot,
+        wm_annot=wm_annot,
+        output_usf=output_usf,
+        head=head,
+        subseg_cbwm=subseg_cbwm,
+        no_pons=no_pons,
+        no_vermis=no_vermis,
+        ctab=ctab,
+        no_seg_stats=no_seg_stats,
+        xcerseg=xcerseg,
+        debug=debug,
+    )
+    return gtmseg_execute(params, execution)
+
+
+__all__ = [
+    "GTMSEG_METADATA",
+    "GtmsegOutputs",
+    "GtmsegParameters",
+    "gtmseg",
+    "gtmseg_params",
+]

niwrap_freesurfer/freesurfer/hiam_make_surfaces.py

@@ -0,0 +1,183 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+HIAM_MAKE_SURFACES_METADATA = Metadata(
+    id="eedce2967ed9d851c796ec7ce683d74d056d3684.boutiques",
+    name="hiam_make_surfaces",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+HiamMakeSurfacesParameters = typing.TypedDict('HiamMakeSurfacesParameters', {
+    "__STYX_TYPE__": typing.Literal["hiam_make_surfaces"],
+    "subject_name": str,
+    "structure": typing.Literal["RA", "LA", "RH", "LH"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "hiam_make_surfaces": hiam_make_surfaces_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 HiamMakeSurfacesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `hiam_make_surfaces(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def hiam_make_surfaces_params(
+    subject_name: str,
+    structure: typing.Literal["RA", "LA", "RH", "LH"],
+) -> HiamMakeSurfacesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_name: Subject name for which surfaces are to be created.
+        structure: Structure for which surfaces will be created. Valid values\
+            are RA, LA, RH, and LH.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "hiam_make_surfaces",
+        "subject_name": subject_name,
+        "structure": structure,
+    }
+    return params
+
+
+def hiam_make_surfaces_cargs(
+    params: HiamMakeSurfacesParameters,
+    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("hiam_make_surfaces")
+    cargs.append("[OPTIONS]")
+    cargs.append(params.get("subject_name"))
+    cargs.append(params.get("structure"))
+    return cargs
+
+
+def hiam_make_surfaces_outputs(
+    params: HiamMakeSurfacesParameters,
+    execution: Execution,
+) -> HiamMakeSurfacesOutputs:
+    """
+    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 = HiamMakeSurfacesOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def hiam_make_surfaces_execute(
+    params: HiamMakeSurfacesParameters,
+    execution: Execution,
+) -> HiamMakeSurfacesOutputs:
+    """
+    Surface creation tool for specified brain structures.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `HiamMakeSurfacesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = hiam_make_surfaces_cargs(params, execution)
+    ret = hiam_make_surfaces_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def hiam_make_surfaces(
+    subject_name: str,
+    structure: typing.Literal["RA", "LA", "RH", "LH"],
+    runner: Runner | None = None,
+) -> HiamMakeSurfacesOutputs:
+    """
+    Surface creation tool for specified brain structures.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_name: Subject name for which surfaces are to be created.
+        structure: Structure for which surfaces will be created. Valid values\
+            are RA, LA, RH, and LH.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `HiamMakeSurfacesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(HIAM_MAKE_SURFACES_METADATA)
+    params = hiam_make_surfaces_params(
+        subject_name=subject_name,
+        structure=structure,
+    )
+    return hiam_make_surfaces_execute(params, execution)
+
+
+__all__ = [
+    "HIAM_MAKE_SURFACES_METADATA",
+    "HiamMakeSurfacesOutputs",
+    "HiamMakeSurfacesParameters",
+    "hiam_make_surfaces",
+    "hiam_make_surfaces_params",
+]