niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_volsmooth.py

@@ -0,0 +1,339 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_VOLSMOOTH_METADATA = Metadata(
+    id="e771a27b746ea9fefc370e231755f9773a9c0720.boutiques",
+    name="mris_volsmooth",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisVolsmoothParameters = typing.TypedDict('MrisVolsmoothParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_volsmooth"],
+    "input_volume": InputPathType,
+    "output_volume": str,
+    "registration": InputPathType,
+    "projfrac": typing.NotRequired[float | None],
+    "projfrac_avg": typing.NotRequired[str | None],
+    "fill_ribbon": bool,
+    "surf_out": typing.NotRequired[str | None],
+    "fwhm": typing.NotRequired[float | None],
+    "niters": typing.NotRequired[float | None],
+    "vol_fwhm": typing.NotRequired[float | None],
+    "log": typing.NotRequired[str | None],
+    "nocleanup": 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 {
+        "mris_volsmooth": mris_volsmooth_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 {
+        "mris_volsmooth": mris_volsmooth_outputs,
+    }.get(t)
+
+
+class MrisVolsmoothOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_volsmooth(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outvol_file: OutputPathType
+    """Output volume file after surface-based smoothing."""
+    lh_surface_output: OutputPathType | None
+    """Left hemisphere smoothed surface output."""
+    rh_surface_output: OutputPathType | None
+    """Right hemisphere smoothed surface output."""
+
+
+def mris_volsmooth_params(
+    input_volume: InputPathType,
+    output_volume: str,
+    registration: InputPathType,
+    projfrac: float | None = None,
+    projfrac_avg: str | None = None,
+    fill_ribbon: bool = False,
+    surf_out: str | None = None,
+    fwhm: float | None = None,
+    niters: float | None = None,
+    vol_fwhm: float | None = None,
+    log: str | None = None,
+    nocleanup: bool = False,
+    debug: bool = False,
+) -> MrisVolsmoothParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volume: Source volume with values that will be smoothed on the\
+            surface.
+        output_volume: Output volume.
+        registration: TKRegister-style registration matrix that maps between\
+            the input/output volumes and the FreeSurfer surface anatomical.
+        projfrac: Fraction of thickness to project along surface normal.
+        projfrac_avg: Average sampling along normal, specified by min, max, and\
+            delta.
+        fill_ribbon: Fill ribbon.
+        surf_out: Save smoothed surfaces as basename.?h.mgh.
+        fwhm: Surface smoothing by full-width/half-max in mm.
+        niters: Specify surface smoothing by number of nearest neighbor\
+            smoothing iterations.
+        vol_fwhm: Volume smoothing outside of the surface. Surface voxels and\
+            non-surface voxels are smoothed separately.
+        log: Explicitly set log file.
+        nocleanup: Do not delete temporary files.
+        debug: Turn on debugging.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_volsmooth",
+        "input_volume": input_volume,
+        "output_volume": output_volume,
+        "registration": registration,
+        "fill_ribbon": fill_ribbon,
+        "nocleanup": nocleanup,
+        "debug": debug,
+    }
+    if projfrac is not None:
+        params["projfrac"] = projfrac
+    if projfrac_avg is not None:
+        params["projfrac_avg"] = projfrac_avg
+    if surf_out is not None:
+        params["surf_out"] = surf_out
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if niters is not None:
+        params["niters"] = niters
+    if vol_fwhm is not None:
+        params["vol_fwhm"] = vol_fwhm
+    if log is not None:
+        params["log"] = log
+    return params
+
+
+def mris_volsmooth_cargs(
+    params: MrisVolsmoothParameters,
+    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_volsmooth")
+    cargs.extend([
+        "-i",
+        execution.input_file(params.get("input_volume"))
+    ])
+    cargs.extend([
+        "-o",
+        params.get("output_volume")
+    ])
+    cargs.extend([
+        "-reg",
+        execution.input_file(params.get("registration"))
+    ])
+    if params.get("projfrac") is not None:
+        cargs.extend([
+            "--projfrac",
+            str(params.get("projfrac"))
+        ])
+    if params.get("projfrac_avg") is not None:
+        cargs.extend([
+            "--projfrac-avg",
+            params.get("projfrac_avg")
+        ])
+    if params.get("fill_ribbon"):
+        cargs.append("--fill-ribbon")
+    if params.get("surf_out") is not None:
+        cargs.extend([
+            "--surf-out",
+            params.get("surf_out")
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "--fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("niters") is not None:
+        cargs.extend([
+            "--niters",
+            str(params.get("niters"))
+        ])
+    if params.get("vol_fwhm") is not None:
+        cargs.extend([
+            "--vol-fwhm",
+            str(params.get("vol_fwhm"))
+        ])
+    if params.get("log") is not None:
+        cargs.extend([
+            "--log",
+            params.get("log")
+        ])
+    if params.get("nocleanup"):
+        cargs.append("--nocleanup")
+    if params.get("debug"):
+        cargs.append("--debug")
+    return cargs
+
+
+def mris_volsmooth_outputs(
+    params: MrisVolsmoothParameters,
+    execution: Execution,
+) -> MrisVolsmoothOutputs:
+    """
+    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 = MrisVolsmoothOutputs(
+        root=execution.output_file("."),
+        outvol_file=execution.output_file(params.get("output_volume") + ".mgh"),
+        lh_surface_output=execution.output_file(params.get("surf_out") + ".lh.mgh") if (params.get("surf_out") is not None) else None,
+        rh_surface_output=execution.output_file(params.get("surf_out") + ".rh.mgh") if (params.get("surf_out") is not None) else None,
+    )
+    return ret
+
+
+def mris_volsmooth_execute(
+    params: MrisVolsmoothParameters,
+    execution: Execution,
+) -> MrisVolsmoothOutputs:
+    """
+    Performs surface-based smoothing inside a volume by sampling a volume to a
+    surface, smoothing on the surface, then replacing the surface voxels in the
+    volume with values that were smoothed.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisVolsmoothOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_volsmooth_cargs(params, execution)
+    ret = mris_volsmooth_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_volsmooth(
+    input_volume: InputPathType,
+    output_volume: str,
+    registration: InputPathType,
+    projfrac: float | None = None,
+    projfrac_avg: str | None = None,
+    fill_ribbon: bool = False,
+    surf_out: str | None = None,
+    fwhm: float | None = None,
+    niters: float | None = None,
+    vol_fwhm: float | None = None,
+    log: str | None = None,
+    nocleanup: bool = False,
+    debug: bool = False,
+    runner: Runner | None = None,
+) -> MrisVolsmoothOutputs:
+    """
+    Performs surface-based smoothing inside a volume by sampling a volume to a
+    surface, smoothing on the surface, then replacing the surface voxels in the
+    volume with values that were smoothed.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volume: Source volume with values that will be smoothed on the\
+            surface.
+        output_volume: Output volume.
+        registration: TKRegister-style registration matrix that maps between\
+            the input/output volumes and the FreeSurfer surface anatomical.
+        projfrac: Fraction of thickness to project along surface normal.
+        projfrac_avg: Average sampling along normal, specified by min, max, and\
+            delta.
+        fill_ribbon: Fill ribbon.
+        surf_out: Save smoothed surfaces as basename.?h.mgh.
+        fwhm: Surface smoothing by full-width/half-max in mm.
+        niters: Specify surface smoothing by number of nearest neighbor\
+            smoothing iterations.
+        vol_fwhm: Volume smoothing outside of the surface. Surface voxels and\
+            non-surface voxels are smoothed separately.
+        log: Explicitly set log file.
+        nocleanup: Do not delete temporary files.
+        debug: Turn on debugging.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisVolsmoothOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_VOLSMOOTH_METADATA)
+    params = mris_volsmooth_params(
+        input_volume=input_volume,
+        output_volume=output_volume,
+        registration=registration,
+        projfrac=projfrac,
+        projfrac_avg=projfrac_avg,
+        fill_ribbon=fill_ribbon,
+        surf_out=surf_out,
+        fwhm=fwhm,
+        niters=niters,
+        vol_fwhm=vol_fwhm,
+        log=log,
+        nocleanup=nocleanup,
+        debug=debug,
+    )
+    return mris_volsmooth_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_VOLSMOOTH_METADATA",
+    "MrisVolsmoothOutputs",
+    "MrisVolsmoothParameters",
+    "mris_volsmooth",
+    "mris_volsmooth_params",
+]

niwrap_freesurfer/freesurfer/mris_volume.py

@@ -0,0 +1,181 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_VOLUME_METADATA = Metadata(
+    id="90a9e134e9f1f52b94a8a65439a8368906985f96.boutiques",
+    name="mris_volume",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisVolumeParameters = typing.TypedDict('MrisVolumeParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_volume"],
+    "surface_file": InputPathType,
+    "verbose_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_volume": mris_volume_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 MrisVolumeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_volume(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_volume_params(
+    surface_file: InputPathType,
+    verbose_flag: bool = False,
+) -> MrisVolumeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surface_file: The closed surface file whose volume is to be computed.
+        verbose_flag: Output more messages for verbose output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_volume",
+        "surface_file": surface_file,
+        "verbose_flag": verbose_flag,
+    }
+    return params
+
+
+def mris_volume_cargs(
+    params: MrisVolumeParameters,
+    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_volume")
+    cargs.append(execution.input_file(params.get("surface_file")))
+    if params.get("verbose_flag"):
+        cargs.append("-v")
+    return cargs
+
+
+def mris_volume_outputs(
+    params: MrisVolumeParameters,
+    execution: Execution,
+) -> MrisVolumeOutputs:
+    """
+    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 = MrisVolumeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_volume_execute(
+    params: MrisVolumeParameters,
+    execution: Execution,
+) -> MrisVolumeOutputs:
+    """
+    A tool for computing the volume of a closed surface using a divergence formula.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisVolumeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_volume_cargs(params, execution)
+    ret = mris_volume_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_volume(
+    surface_file: InputPathType,
+    verbose_flag: bool = False,
+    runner: Runner | None = None,
+) -> MrisVolumeOutputs:
+    """
+    A tool for computing the volume of a closed surface using a divergence formula.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        surface_file: The closed surface file whose volume is to be computed.
+        verbose_flag: Output more messages for verbose output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisVolumeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_VOLUME_METADATA)
+    params = mris_volume_params(
+        surface_file=surface_file,
+        verbose_flag=verbose_flag,
+    )
+    return mris_volume_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_VOLUME_METADATA",
+    "MrisVolumeOutputs",
+    "MrisVolumeParameters",
+    "mris_volume",
+    "mris_volume_params",
+]