niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_annot_to_segmentation.py

@@ -0,0 +1,216 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_ANNOT_TO_SEGMENTATION_METADATA = Metadata(
+    id="a6fe77811c128028277a69a99f1e7f945cb0ac57.boutiques",
+    name="mris_annot_to_segmentation",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisAnnotToSegmentationParameters = typing.TypedDict('MrisAnnotToSegmentationParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_annot_to_segmentation"],
+    "subject_name": str,
+    "hemi": str,
+    "surface": str,
+    "annot_file": InputPathType,
+    "color_table": InputPathType,
+    "output_volume": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_annot_to_segmentation": mris_annot_to_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 {
+        "mris_annot_to_segmentation": mris_annot_to_segmentation_outputs,
+    }.get(t)
+
+
+class MrisAnnotToSegmentationOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_annot_to_segmentation(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume_file: OutputPathType
+    """Generated segmentation volume."""
+
+
+def mris_annot_to_segmentation_params(
+    subject_name: str,
+    hemi: str,
+    surface: str,
+    annot_file: InputPathType,
+    color_table: InputPathType,
+    output_volume: str,
+) -> MrisAnnotToSegmentationParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_name: Subject name.
+        hemi: Hemisphere (e.g., lh or rh).
+        surface: Surface file.
+        annot_file: Annotation file.
+        color_table: Color table file.
+        output_volume: Output volume file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_annot_to_segmentation",
+        "subject_name": subject_name,
+        "hemi": hemi,
+        "surface": surface,
+        "annot_file": annot_file,
+        "color_table": color_table,
+        "output_volume": output_volume,
+    }
+    return params
+
+
+def mris_annot_to_segmentation_cargs(
+    params: MrisAnnotToSegmentationParameters,
+    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_annot_to_segmentation")
+    cargs.append(params.get("subject_name"))
+    cargs.append(params.get("hemi"))
+    cargs.append(params.get("surface"))
+    cargs.append(execution.input_file(params.get("annot_file")))
+    cargs.append(execution.input_file(params.get("color_table")))
+    cargs.append(params.get("output_volume"))
+    return cargs
+
+
+def mris_annot_to_segmentation_outputs(
+    params: MrisAnnotToSegmentationParameters,
+    execution: Execution,
+) -> MrisAnnotToSegmentationOutputs:
+    """
+    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 = MrisAnnotToSegmentationOutputs(
+        root=execution.output_file("."),
+        output_volume_file=execution.output_file(params.get("output_volume")),
+    )
+    return ret
+
+
+def mris_annot_to_segmentation_execute(
+    params: MrisAnnotToSegmentationParameters,
+    execution: Execution,
+) -> MrisAnnotToSegmentationOutputs:
+    """
+    Converts annotation files to segmentation volumes in FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisAnnotToSegmentationOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_annot_to_segmentation_cargs(params, execution)
+    ret = mris_annot_to_segmentation_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_annot_to_segmentation(
+    subject_name: str,
+    hemi: str,
+    surface: str,
+    annot_file: InputPathType,
+    color_table: InputPathType,
+    output_volume: str,
+    runner: Runner | None = None,
+) -> MrisAnnotToSegmentationOutputs:
+    """
+    Converts annotation files to segmentation volumes in FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_name: Subject name.
+        hemi: Hemisphere (e.g., lh or rh).
+        surface: Surface file.
+        annot_file: Annotation file.
+        color_table: Color table file.
+        output_volume: Output volume file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisAnnotToSegmentationOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ANNOT_TO_SEGMENTATION_METADATA)
+    params = mris_annot_to_segmentation_params(
+        subject_name=subject_name,
+        hemi=hemi,
+        surface=surface,
+        annot_file=annot_file,
+        color_table=color_table,
+        output_volume=output_volume,
+    )
+    return mris_annot_to_segmentation_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_ANNOT_TO_SEGMENTATION_METADATA",
+    "MrisAnnotToSegmentationOutputs",
+    "MrisAnnotToSegmentationParameters",
+    "mris_annot_to_segmentation",
+    "mris_annot_to_segmentation_params",
+]

niwrap_freesurfer/freesurfer/mris_apply_reg.py

@@ -0,0 +1,430 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_APPLY_REG_METADATA = Metadata(
+    id="cba2fa7ec9ece7dd7da7631135e083c0bc5bc503.boutiques",
+    name="mris_apply_reg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisApplyRegParameters = typing.TypedDict('MrisApplyRegParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_apply_reg"],
+    "src_input": InputPathType,
+    "trg_output": str,
+    "streg_pair": str,
+    "src_label": typing.NotRequired[InputPathType | None],
+    "src_annotation": typing.NotRequired[InputPathType | None],
+    "src_xyz": typing.NotRequired[InputPathType | None],
+    "jacobian": bool,
+    "no_reverse": bool,
+    "rand_noise": bool,
+    "replace_ones": bool,
+    "center_output": bool,
+    "curv_format": bool,
+    "lta_transform": typing.NotRequired[str | None],
+    "lta_patch_transform": typing.NotRequired[str | None],
+    "reverse_surface": typing.NotRequired[str | None],
+    "patch_apply": typing.NotRequired[str | None],
+    "save_vertex_pair": typing.NotRequired[InputPathType | None],
+    "m3z_transform": typing.NotRequired[str | None],
+    "inv_m3z_transform": typing.NotRequired[str | None],
+    "src_reg_scale": typing.NotRequired[float | None],
+    "trg_reg_scale": typing.NotRequired[float | None],
+    "debug_mode": bool,
+    "check_options": 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_apply_reg": mris_apply_reg_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_apply_reg": mris_apply_reg_outputs,
+    }.get(t)
+
+
+class MrisApplyRegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_apply_reg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_result: OutputPathType
+    """The output file resulting from registration"""
+
+
+def mris_apply_reg_params(
+    src_input: InputPathType,
+    trg_output: str,
+    streg_pair: str,
+    src_label: InputPathType | None = None,
+    src_annotation: InputPathType | None = None,
+    src_xyz: InputPathType | None = None,
+    jacobian: bool = False,
+    no_reverse: bool = False,
+    rand_noise: bool = False,
+    replace_ones: bool = False,
+    center_output: bool = False,
+    curv_format: bool = False,
+    lta_transform: str | None = None,
+    lta_patch_transform: str | None = None,
+    reverse_surface: str | None = None,
+    patch_apply: str | None = None,
+    save_vertex_pair: InputPathType | None = None,
+    m3z_transform: str | None = None,
+    inv_m3z_transform: str | None = None,
+    src_reg_scale: float | None = None,
+    trg_reg_scale: float | None = None,
+    debug_mode: bool = False,
+    check_options: bool = False,
+) -> MrisApplyRegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        src_input: Source values (surface overlay).
+        trg_output: Target output file.
+        streg_pair: Source and target registration file pair.
+        src_label: Source label file (implies --no-rev).
+        src_annotation: Source annotation file (implies --no-rev).
+        src_xyz: XYZ coordinates from the given surface file as input.
+        jacobian: Use jacobian correction.
+        no_reverse: Do not do reverse mapping.
+        rand_noise: Replace input with white Gaussian noise.
+        replace_ones: Replace input with ones.
+        center_output: Place the center of the output surface at (0,0,0).
+        curv_format: Save output in curvature file format.
+        lta_transform: Apply LTA transform to the surface.
+        lta_patch_transform: Apply LTA transform to surface patch.
+        reverse_surface: LR reverse surface with optional patch.
+        patch_apply: Apply patch for each --streg.
+        save_vertex_pair: Save vertex pairs from source and target surfaces.
+        m3z_transform: Apply M3Z transform.
+        inv_m3z_transform: Apply inverse M3Z transform.
+        src_reg_scale: Scale the coordinates of the first surface.
+        trg_reg_scale: Scale the coordinates of the last surface.
+        debug_mode: Turn on debugging.
+        check_options: Check options without executing anything.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_apply_reg",
+        "src_input": src_input,
+        "trg_output": trg_output,
+        "streg_pair": streg_pair,
+        "jacobian": jacobian,
+        "no_reverse": no_reverse,
+        "rand_noise": rand_noise,
+        "replace_ones": replace_ones,
+        "center_output": center_output,
+        "curv_format": curv_format,
+        "debug_mode": debug_mode,
+        "check_options": check_options,
+    }
+    if src_label is not None:
+        params["src_label"] = src_label
+    if src_annotation is not None:
+        params["src_annotation"] = src_annotation
+    if src_xyz is not None:
+        params["src_xyz"] = src_xyz
+    if lta_transform is not None:
+        params["lta_transform"] = lta_transform
+    if lta_patch_transform is not None:
+        params["lta_patch_transform"] = lta_patch_transform
+    if reverse_surface is not None:
+        params["reverse_surface"] = reverse_surface
+    if patch_apply is not None:
+        params["patch_apply"] = patch_apply
+    if save_vertex_pair is not None:
+        params["save_vertex_pair"] = save_vertex_pair
+    if m3z_transform is not None:
+        params["m3z_transform"] = m3z_transform
+    if inv_m3z_transform is not None:
+        params["inv_m3z_transform"] = inv_m3z_transform
+    if src_reg_scale is not None:
+        params["src_reg_scale"] = src_reg_scale
+    if trg_reg_scale is not None:
+        params["trg_reg_scale"] = trg_reg_scale
+    return params
+
+
+def mris_apply_reg_cargs(
+    params: MrisApplyRegParameters,
+    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_apply_reg")
+    cargs.extend([
+        "--src",
+        execution.input_file(params.get("src_input"))
+    ])
+    cargs.extend([
+        "--trg",
+        params.get("trg_output")
+    ])
+    cargs.extend([
+        "--streg",
+        params.get("streg_pair")
+    ])
+    cargs.append("[STREG_ADDITIONAL...]")
+    if params.get("src_label") is not None:
+        cargs.extend([
+            "--src-label",
+            execution.input_file(params.get("src_label"))
+        ])
+    if params.get("src_annotation") is not None:
+        cargs.extend([
+            "--src-annot",
+            execution.input_file(params.get("src_annotation"))
+        ])
+    if params.get("src_xyz") is not None:
+        cargs.extend([
+            "--src-xyz",
+            execution.input_file(params.get("src_xyz"))
+        ])
+    if params.get("jacobian"):
+        cargs.append("--jac")
+    if params.get("no_reverse"):
+        cargs.append("--no-rev")
+    if params.get("rand_noise"):
+        cargs.append("--randn")
+    if params.get("replace_ones"):
+        cargs.append("--ones")
+    if params.get("center_output"):
+        cargs.append("--center")
+    if params.get("curv_format"):
+        cargs.append("--curv")
+    if params.get("lta_transform") is not None:
+        cargs.extend([
+            "--lta",
+            params.get("lta_transform")
+        ])
+    if params.get("lta_patch_transform") is not None:
+        cargs.extend([
+            "--lta-patch",
+            params.get("lta_patch_transform")
+        ])
+    if params.get("reverse_surface") is not None:
+        cargs.extend([
+            "--reverse",
+            params.get("reverse_surface")
+        ])
+    if params.get("patch_apply") is not None:
+        cargs.extend([
+            "--patch",
+            params.get("patch_apply")
+        ])
+    if params.get("save_vertex_pair") is not None:
+        cargs.extend([
+            "--stvpair",
+            execution.input_file(params.get("save_vertex_pair"))
+        ])
+    if params.get("m3z_transform") is not None:
+        cargs.extend([
+            "--m3z",
+            params.get("m3z_transform")
+        ])
+    if params.get("inv_m3z_transform") is not None:
+        cargs.extend([
+            "--inv-m3z",
+            params.get("inv_m3z_transform")
+        ])
+    if params.get("src_reg_scale") is not None:
+        cargs.extend([
+            "--src-reg-scale",
+            str(params.get("src_reg_scale"))
+        ])
+    if params.get("trg_reg_scale") is not None:
+        cargs.extend([
+            "--trg-reg-scale",
+            str(params.get("trg_reg_scale"))
+        ])
+    if params.get("debug_mode"):
+        cargs.append("--debug")
+    if params.get("check_options"):
+        cargs.append("--checkopts")
+    return cargs
+
+
+def mris_apply_reg_outputs(
+    params: MrisApplyRegParameters,
+    execution: Execution,
+) -> MrisApplyRegOutputs:
+    """
+    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 = MrisApplyRegOutputs(
+        root=execution.output_file("."),
+        output_result=execution.output_file(params.get("trg_output")),
+    )
+    return ret
+
+
+def mris_apply_reg_execute(
+    params: MrisApplyRegParameters,
+    execution: Execution,
+) -> MrisApplyRegOutputs:
+    """
+    Apply surface registration in FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisApplyRegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_apply_reg_cargs(params, execution)
+    ret = mris_apply_reg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_apply_reg(
+    src_input: InputPathType,
+    trg_output: str,
+    streg_pair: str,
+    src_label: InputPathType | None = None,
+    src_annotation: InputPathType | None = None,
+    src_xyz: InputPathType | None = None,
+    jacobian: bool = False,
+    no_reverse: bool = False,
+    rand_noise: bool = False,
+    replace_ones: bool = False,
+    center_output: bool = False,
+    curv_format: bool = False,
+    lta_transform: str | None = None,
+    lta_patch_transform: str | None = None,
+    reverse_surface: str | None = None,
+    patch_apply: str | None = None,
+    save_vertex_pair: InputPathType | None = None,
+    m3z_transform: str | None = None,
+    inv_m3z_transform: str | None = None,
+    src_reg_scale: float | None = None,
+    trg_reg_scale: float | None = None,
+    debug_mode: bool = False,
+    check_options: bool = False,
+    runner: Runner | None = None,
+) -> MrisApplyRegOutputs:
+    """
+    Apply surface registration in FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        src_input: Source values (surface overlay).
+        trg_output: Target output file.
+        streg_pair: Source and target registration file pair.
+        src_label: Source label file (implies --no-rev).
+        src_annotation: Source annotation file (implies --no-rev).
+        src_xyz: XYZ coordinates from the given surface file as input.
+        jacobian: Use jacobian correction.
+        no_reverse: Do not do reverse mapping.
+        rand_noise: Replace input with white Gaussian noise.
+        replace_ones: Replace input with ones.
+        center_output: Place the center of the output surface at (0,0,0).
+        curv_format: Save output in curvature file format.
+        lta_transform: Apply LTA transform to the surface.
+        lta_patch_transform: Apply LTA transform to surface patch.
+        reverse_surface: LR reverse surface with optional patch.
+        patch_apply: Apply patch for each --streg.
+        save_vertex_pair: Save vertex pairs from source and target surfaces.
+        m3z_transform: Apply M3Z transform.
+        inv_m3z_transform: Apply inverse M3Z transform.
+        src_reg_scale: Scale the coordinates of the first surface.
+        trg_reg_scale: Scale the coordinates of the last surface.
+        debug_mode: Turn on debugging.
+        check_options: Check options without executing anything.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisApplyRegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_APPLY_REG_METADATA)
+    params = mris_apply_reg_params(
+        src_input=src_input,
+        trg_output=trg_output,
+        streg_pair=streg_pair,
+        src_label=src_label,
+        src_annotation=src_annotation,
+        src_xyz=src_xyz,
+        jacobian=jacobian,
+        no_reverse=no_reverse,
+        rand_noise=rand_noise,
+        replace_ones=replace_ones,
+        center_output=center_output,
+        curv_format=curv_format,
+        lta_transform=lta_transform,
+        lta_patch_transform=lta_patch_transform,
+        reverse_surface=reverse_surface,
+        patch_apply=patch_apply,
+        save_vertex_pair=save_vertex_pair,
+        m3z_transform=m3z_transform,
+        inv_m3z_transform=inv_m3z_transform,
+        src_reg_scale=src_reg_scale,
+        trg_reg_scale=trg_reg_scale,
+        debug_mode=debug_mode,
+        check_options=check_options,
+    )
+    return mris_apply_reg_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_APPLY_REG_METADATA",
+    "MrisApplyRegOutputs",
+    "MrisApplyRegParameters",
+    "mris_apply_reg",
+    "mris_apply_reg_params",
+]