niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_easywarp.py

@@ -0,0 +1,229 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_EASYWARP_METADATA = Metadata(
+    id="61155dbff21df2a7da1b05052571570b740944be.boutiques",
+    name="mri_easywarp",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriEasywarpParameters = typing.TypedDict('MriEasywarpParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_easywarp"],
+    "input_image": InputPathType,
+    "output_image": str,
+    "deformation_field": typing.NotRequired[InputPathType | None],
+    "nearest_neighbor": bool,
+    "num_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 {
+        "mri_easywarp": mri_easywarp_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 {
+        "mri_easywarp": mri_easywarp_outputs,
+    }.get(t)
+
+
+class MriEasywarpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_easywarp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_deformed_image: OutputPathType
+    """Output deformed image"""
+
+
+def mri_easywarp_params(
+    input_image: InputPathType,
+    output_image: str,
+    deformation_field: InputPathType | None = None,
+    nearest_neighbor: bool = False,
+    num_threads: float | None = None,
+) -> MriEasywarpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: Input image.
+        output_image: Output (deformed) image.
+        deformation_field: Deformation field.
+        nearest_neighbor: Use nearest neighbor (rather than linear)\
+            interpolation.
+        num_threads: Number of cores to be used. Default is 1. You can use -1\
+            to use all available cores.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_easywarp",
+        "input_image": input_image,
+        "output_image": output_image,
+        "nearest_neighbor": nearest_neighbor,
+    }
+    if deformation_field is not None:
+        params["deformation_field"] = deformation_field
+    if num_threads is not None:
+        params["num_threads"] = num_threads
+    return params
+
+
+def mri_easywarp_cargs(
+    params: MriEasywarpParameters,
+    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("mri_easywarp")
+    cargs.extend([
+        "--i",
+        execution.input_file(params.get("input_image"))
+    ])
+    cargs.extend([
+        "--o",
+        params.get("output_image")
+    ])
+    if params.get("deformation_field") is not None:
+        cargs.extend([
+            "--field",
+            execution.input_file(params.get("deformation_field"))
+        ])
+    if params.get("nearest_neighbor"):
+        cargs.append("--nearest")
+    if params.get("num_threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("num_threads"))
+        ])
+    return cargs
+
+
+def mri_easywarp_outputs(
+    params: MriEasywarpParameters,
+    execution: Execution,
+) -> MriEasywarpOutputs:
+    """
+    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 = MriEasywarpOutputs(
+        root=execution.output_file("."),
+        output_deformed_image=execution.output_file(params.get("output_image") + ".nii.gz"),
+    )
+    return ret
+
+
+def mri_easywarp_execute(
+    params: MriEasywarpParameters,
+    execution: Execution,
+) -> MriEasywarpOutputs:
+    """
+    EasyReg: deep learning registration simple and easy.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriEasywarpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_easywarp_cargs(params, execution)
+    ret = mri_easywarp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_easywarp(
+    input_image: InputPathType,
+    output_image: str,
+    deformation_field: InputPathType | None = None,
+    nearest_neighbor: bool = False,
+    num_threads: float | None = None,
+    runner: Runner | None = None,
+) -> MriEasywarpOutputs:
+    """
+    EasyReg: deep learning registration simple and easy.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_image: Input image.
+        output_image: Output (deformed) image.
+        deformation_field: Deformation field.
+        nearest_neighbor: Use nearest neighbor (rather than linear)\
+            interpolation.
+        num_threads: Number of cores to be used. Default is 1. You can use -1\
+            to use all available cores.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriEasywarpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EASYWARP_METADATA)
+    params = mri_easywarp_params(
+        input_image=input_image,
+        output_image=output_image,
+        deformation_field=deformation_field,
+        nearest_neighbor=nearest_neighbor,
+        num_threads=num_threads,
+    )
+    return mri_easywarp_execute(params, execution)
+
+
+__all__ = [
+    "MRI_EASYWARP_METADATA",
+    "MriEasywarpOutputs",
+    "MriEasywarpParameters",
+    "mri_easywarp",
+    "mri_easywarp_params",
+]

niwrap_freesurfer/freesurfer/mri_edit_segmentation.py

@@ -0,0 +1,192 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_EDIT_SEGMENTATION_METADATA = Metadata(
+    id="25345594af6f00c5d1125c06b5d3a088c2d5244f.boutiques",
+    name="mri_edit_segmentation",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriEditSegmentationParameters = typing.TypedDict('MriEditSegmentationParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_edit_segmentation"],
+    "input_segmentation": InputPathType,
+    "t1_volume": InputPathType,
+    "output_segmentation": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_edit_segmentation": mri_edit_segmentation_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 {
+        "mri_edit_segmentation": mri_edit_segmentation_outputs,
+    }.get(t)
+
+
+class MriEditSegmentationOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_edit_segmentation(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_segmentation_file: OutputPathType
+    """The resulting edited segmentation file."""
+
+
+def mri_edit_segmentation_params(
+    input_segmentation: InputPathType,
+    t1_volume: InputPathType,
+    output_segmentation: str,
+) -> MriEditSegmentationParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_segmentation: Input segmentation file.
+        t1_volume: T1 volume file.
+        output_segmentation: Output segmentation file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_edit_segmentation",
+        "input_segmentation": input_segmentation,
+        "t1_volume": t1_volume,
+        "output_segmentation": output_segmentation,
+    }
+    return params
+
+
+def mri_edit_segmentation_cargs(
+    params: MriEditSegmentationParameters,
+    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("mri_edit_segmentation")
+    cargs.append(execution.input_file(params.get("input_segmentation")))
+    cargs.append(execution.input_file(params.get("t1_volume")))
+    cargs.append(params.get("output_segmentation"))
+    return cargs
+
+
+def mri_edit_segmentation_outputs(
+    params: MriEditSegmentationParameters,
+    execution: Execution,
+) -> MriEditSegmentationOutputs:
+    """
+    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 = MriEditSegmentationOutputs(
+        root=execution.output_file("."),
+        output_segmentation_file=execution.output_file(params.get("output_segmentation")),
+    )
+    return ret
+
+
+def mri_edit_segmentation_execute(
+    params: MriEditSegmentationParameters,
+    execution: Execution,
+) -> MriEditSegmentationOutputs:
+    """
+    A tool used for editing segmentations.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriEditSegmentationOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_edit_segmentation_cargs(params, execution)
+    ret = mri_edit_segmentation_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_edit_segmentation(
+    input_segmentation: InputPathType,
+    t1_volume: InputPathType,
+    output_segmentation: str,
+    runner: Runner | None = None,
+) -> MriEditSegmentationOutputs:
+    """
+    A tool used for editing segmentations.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_segmentation: Input segmentation file.
+        t1_volume: T1 volume file.
+        output_segmentation: Output segmentation file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriEditSegmentationOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EDIT_SEGMENTATION_METADATA)
+    params = mri_edit_segmentation_params(
+        input_segmentation=input_segmentation,
+        t1_volume=t1_volume,
+        output_segmentation=output_segmentation,
+    )
+    return mri_edit_segmentation_execute(params, execution)
+
+
+__all__ = [
+    "MRI_EDIT_SEGMENTATION_METADATA",
+    "MriEditSegmentationOutputs",
+    "MriEditSegmentationParameters",
+    "mri_edit_segmentation",
+    "mri_edit_segmentation_params",
+]

niwrap_freesurfer/freesurfer/mri_edit_segmentation_with_surfaces.py

@@ -0,0 +1,267 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_EDIT_SEGMENTATION_WITH_SURFACES_METADATA = Metadata(
+    id="b7676f431b8610a951f255b96b0e4e26a937a332.boutiques",
+    name="mri_edit_segmentation_with_surfaces",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriEditSegmentationWithSurfacesParameters = typing.TypedDict('MriEditSegmentationWithSurfacesParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_edit_segmentation_with_surfaces"],
+    "aseg_name": InputPathType,
+    "surface_dir": str,
+    "norm_volume": InputPathType,
+    "output_volume": str,
+    "label_file": typing.NotRequired[InputPathType | None],
+    "hypo_flag": typing.NotRequired[typing.Literal["1", "0"] | None],
+    "cerebellum_flag": typing.NotRequired[typing.Literal["1", "0"] | None],
+    "cortex_flag": typing.NotRequired[typing.Literal["1", "0"] | None],
+    "annotation_file": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_edit_segmentation_with_surfaces": mri_edit_segmentation_with_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 {
+        "mri_edit_segmentation_with_surfaces": mri_edit_segmentation_with_surfaces_outputs,
+    }.get(t)
+
+
+class MriEditSegmentationWithSurfacesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_edit_segmentation_with_surfaces(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume_file: OutputPathType
+    """Edited output volume"""
+
+
+def mri_edit_segmentation_with_surfaces_params(
+    aseg_name: InputPathType,
+    surface_dir: str,
+    norm_volume: InputPathType,
+    output_volume: str,
+    label_file: InputPathType | None = None,
+    hypo_flag: typing.Literal["1", "0"] | None = None,
+    cerebellum_flag: typing.Literal["1", "0"] | None = None,
+    cortex_flag: typing.Literal["1", "0"] | None = None,
+    annotation_file: InputPathType | None = None,
+) -> MriEditSegmentationWithSurfacesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        aseg_name: The aseg file to be edited.
+        surface_dir: Directory containing surface files.
+        norm_volume: Normalized volume file.
+        output_volume: Output volume file.
+        label_file: Limit calculations to specified label.
+        hypo_flag: Turn hypointensity editing on/off (1=on, 0=off).
+        cerebellum_flag: Turn cerebellum editing on/off (1=on, 0=off).
+        cortex_flag: Turn cortex editing on/off (1=on, 0=off).
+        annotation_file: Compute properties for each label in the annotation\
+            file separately.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_edit_segmentation_with_surfaces",
+        "aseg_name": aseg_name,
+        "surface_dir": surface_dir,
+        "norm_volume": norm_volume,
+        "output_volume": output_volume,
+    }
+    if label_file is not None:
+        params["label_file"] = label_file
+    if hypo_flag is not None:
+        params["hypo_flag"] = hypo_flag
+    if cerebellum_flag is not None:
+        params["cerebellum_flag"] = cerebellum_flag
+    if cortex_flag is not None:
+        params["cortex_flag"] = cortex_flag
+    if annotation_file is not None:
+        params["annotation_file"] = annotation_file
+    return params
+
+
+def mri_edit_segmentation_with_surfaces_cargs(
+    params: MriEditSegmentationWithSurfacesParameters,
+    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("mri_edit_segmentation_with_surfaces")
+    cargs.append(execution.input_file(params.get("aseg_name")))
+    cargs.append(params.get("surface_dir"))
+    cargs.append(execution.input_file(params.get("norm_volume")))
+    cargs.append(params.get("output_volume"))
+    if params.get("label_file") is not None:
+        cargs.extend([
+            "-l",
+            execution.input_file(params.get("label_file"))
+        ])
+    if params.get("hypo_flag") is not None:
+        cargs.extend([
+            "-hypo",
+            params.get("hypo_flag")
+        ])
+    if params.get("cerebellum_flag") is not None:
+        cargs.extend([
+            "-cerebellum",
+            params.get("cerebellum_flag")
+        ])
+    if params.get("cortex_flag") is not None:
+        cargs.extend([
+            "-cortex",
+            params.get("cortex_flag")
+        ])
+    if params.get("annotation_file") is not None:
+        cargs.extend([
+            "-a",
+            execution.input_file(params.get("annotation_file"))
+        ])
+    return cargs
+
+
+def mri_edit_segmentation_with_surfaces_outputs(
+    params: MriEditSegmentationWithSurfacesParameters,
+    execution: Execution,
+) -> MriEditSegmentationWithSurfacesOutputs:
+    """
+    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 = MriEditSegmentationWithSurfacesOutputs(
+        root=execution.output_file("."),
+        output_volume_file=execution.output_file(params.get("output_volume")),
+    )
+    return ret
+
+
+def mri_edit_segmentation_with_surfaces_execute(
+    params: MriEditSegmentationWithSurfacesParameters,
+    execution: Execution,
+) -> MriEditSegmentationWithSurfacesOutputs:
+    """
+    This program edits an aseg with the surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriEditSegmentationWithSurfacesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_edit_segmentation_with_surfaces_cargs(params, execution)
+    ret = mri_edit_segmentation_with_surfaces_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_edit_segmentation_with_surfaces(
+    aseg_name: InputPathType,
+    surface_dir: str,
+    norm_volume: InputPathType,
+    output_volume: str,
+    label_file: InputPathType | None = None,
+    hypo_flag: typing.Literal["1", "0"] | None = None,
+    cerebellum_flag: typing.Literal["1", "0"] | None = None,
+    cortex_flag: typing.Literal["1", "0"] | None = None,
+    annotation_file: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> MriEditSegmentationWithSurfacesOutputs:
+    """
+    This program edits an aseg with the surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        aseg_name: The aseg file to be edited.
+        surface_dir: Directory containing surface files.
+        norm_volume: Normalized volume file.
+        output_volume: Output volume file.
+        label_file: Limit calculations to specified label.
+        hypo_flag: Turn hypointensity editing on/off (1=on, 0=off).
+        cerebellum_flag: Turn cerebellum editing on/off (1=on, 0=off).
+        cortex_flag: Turn cortex editing on/off (1=on, 0=off).
+        annotation_file: Compute properties for each label in the annotation\
+            file separately.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriEditSegmentationWithSurfacesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EDIT_SEGMENTATION_WITH_SURFACES_METADATA)
+    params = mri_edit_segmentation_with_surfaces_params(
+        aseg_name=aseg_name,
+        surface_dir=surface_dir,
+        norm_volume=norm_volume,
+        output_volume=output_volume,
+        label_file=label_file,
+        hypo_flag=hypo_flag,
+        cerebellum_flag=cerebellum_flag,
+        cortex_flag=cortex_flag,
+        annotation_file=annotation_file,
+    )
+    return mri_edit_segmentation_with_surfaces_execute(params, execution)
+
+
+__all__ = [
+    "MRI_EDIT_SEGMENTATION_WITH_SURFACES_METADATA",
+    "MriEditSegmentationWithSurfacesOutputs",
+    "MriEditSegmentationWithSurfacesParameters",
+    "mri_edit_segmentation_with_surfaces",
+    "mri_edit_segmentation_with_surfaces_params",
+]