niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_register_label_map.py

@@ -0,0 +1,281 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_REGISTER_LABEL_MAP_METADATA = Metadata(
+    id="da7f5799fccbaa00ae28b92114de5d6ef1a4db4f.boutiques",
+    name="mris_register_label_map",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisRegisterLabelMapParameters = typing.TypedDict('MrisRegisterLabelMapParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_register_label_map"],
+    "subjects_list": str,
+    "target_subject": str,
+    "prior": str,
+    "label": str,
+    "template_volume": InputPathType,
+    "debug": bool,
+    "check_opts": bool,
+    "help": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+    "version": bool,
+    "vno": 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 {
+        "mris_register_label_map": mris_register_label_map_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 MrisRegisterLabelMapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_register_label_map(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_register_label_map_params(
+    subjects_list: str,
+    target_subject: str,
+    prior: str,
+    label: str,
+    template_volume: InputPathType,
+    debug: bool = False,
+    check_opts: bool = False,
+    help_: bool = False,
+    subjects_dir: str | None = None,
+    version: bool = False,
+    vno: float | None = None,
+) -> MrisRegisterLabelMapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjects_list: List of training subjects.
+        target_subject: Name of target subject.
+        prior: Name of prior surface overlay.
+        label: Name of label for each subject.
+        template_volume: Template volume file.
+        debug: Turn on debugging.
+        check_opts: Don't run anything, just check options and exit.
+        help_: Print out information on how to use this program.
+        subjects_dir: SUBJECTS_DIR.
+        version: Print out version and exit.
+        vno: Debug this vertex.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_register_label_map",
+        "subjects_list": subjects_list,
+        "target_subject": target_subject,
+        "prior": prior,
+        "label": label,
+        "template_volume": template_volume,
+        "debug": debug,
+        "check_opts": check_opts,
+        "help": help_,
+        "version": version,
+    }
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if vno is not None:
+        params["vno"] = vno
+    return params
+
+
+def mris_register_label_map_cargs(
+    params: MrisRegisterLabelMapParameters,
+    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_register_label_map")
+    cargs.extend([
+        "--subjects",
+        params.get("subjects_list")
+    ])
+    cargs.extend([
+        "--trgsubject",
+        params.get("target_subject")
+    ])
+    cargs.extend([
+        "--prior",
+        params.get("prior")
+    ])
+    cargs.extend([
+        "--label",
+        params.get("label")
+    ])
+    cargs.extend([
+        "--temp-vol",
+        execution.input_file(params.get("template_volume"))
+    ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("check_opts"):
+        cargs.append("--checkopts")
+    if params.get("help"):
+        cargs.append("--help")
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--sdir",
+            params.get("subjects_dir")
+        ])
+    if params.get("version"):
+        cargs.append("--version")
+    if params.get("vno") is not None:
+        cargs.extend([
+            "--v",
+            str(params.get("vno"))
+        ])
+    return cargs
+
+
+def mris_register_label_map_outputs(
+    params: MrisRegisterLabelMapParameters,
+    execution: Execution,
+) -> MrisRegisterLabelMapOutputs:
+    """
+    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 = MrisRegisterLabelMapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_register_label_map_execute(
+    params: MrisRegisterLabelMapParameters,
+    execution: Execution,
+) -> MrisRegisterLabelMapOutputs:
+    """
+    Tool for registering label maps 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 `MrisRegisterLabelMapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_register_label_map_cargs(params, execution)
+    ret = mris_register_label_map_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_register_label_map(
+    subjects_list: str,
+    target_subject: str,
+    prior: str,
+    label: str,
+    template_volume: InputPathType,
+    debug: bool = False,
+    check_opts: bool = False,
+    help_: bool = False,
+    subjects_dir: str | None = None,
+    version: bool = False,
+    vno: float | None = None,
+    runner: Runner | None = None,
+) -> MrisRegisterLabelMapOutputs:
+    """
+    Tool for registering label maps in Freesurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjects_list: List of training subjects.
+        target_subject: Name of target subject.
+        prior: Name of prior surface overlay.
+        label: Name of label for each subject.
+        template_volume: Template volume file.
+        debug: Turn on debugging.
+        check_opts: Don't run anything, just check options and exit.
+        help_: Print out information on how to use this program.
+        subjects_dir: SUBJECTS_DIR.
+        version: Print out version and exit.
+        vno: Debug this vertex.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisRegisterLabelMapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REGISTER_LABEL_MAP_METADATA)
+    params = mris_register_label_map_params(
+        subjects_list=subjects_list,
+        target_subject=target_subject,
+        prior=prior,
+        label=label,
+        template_volume=template_volume,
+        debug=debug,
+        check_opts=check_opts,
+        help_=help_,
+        subjects_dir=subjects_dir,
+        version=version,
+        vno=vno,
+    )
+    return mris_register_label_map_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_REGISTER_LABEL_MAP_METADATA",
+    "MrisRegisterLabelMapOutputs",
+    "MrisRegisterLabelMapParameters",
+    "mris_register_label_map",
+    "mris_register_label_map_params",
+]

niwrap_freesurfer/freesurfer/mris_register_to_label.py

@@ -0,0 +1,310 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_REGISTER_TO_LABEL_METADATA = Metadata(
+    id="36d8ca89ec62d6d129c91373f3bc303868500379.boutiques",
+    name="mris_register_to_label",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisRegisterToLabelParameters = typing.TypedDict('MrisRegisterToLabelParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_register_to_label"],
+    "surface": InputPathType,
+    "regfile": InputPathType,
+    "mri_reg": InputPathType,
+    "mov_volume": InputPathType,
+    "resolution": float,
+    "max_rot": typing.NotRequired[float | None],
+    "max_trans": typing.NotRequired[float | None],
+    "subject": typing.NotRequired[str | None],
+    "label": typing.NotRequired[str | None],
+    "out_reg": typing.NotRequired[str | None],
+    "downsample": typing.NotRequired[float | None],
+    "cost_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 {
+        "mris_register_to_label": mris_register_to_label_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 MrisRegisterToLabelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_register_to_label(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_register_to_label_params(
+    surface: InputPathType,
+    regfile: InputPathType,
+    mri_reg: InputPathType,
+    mov_volume: InputPathType,
+    resolution: float,
+    max_rot: float | None = None,
+    max_trans: float | None = None,
+    subject: str | None = None,
+    label: str | None = None,
+    out_reg: str | None = None,
+    downsample: float | None = None,
+    cost_file: InputPathType | None = None,
+) -> MrisRegisterToLabelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surface: Surface file for registration.
+        regfile: Registration file.
+        mri_reg: Volume for MRI registration.
+        mov_volume: Volume on which label points are specified.
+        resolution: Resolution for calculations.
+        max_rot: Maximum angle (degrees) to search over for rotation.
+        max_trans: Maximum translation (mm) to search over.
+        subject: Specify name of subject for register.dat file.
+        label: Load label and limit calculations to it.
+        out_reg: Output registration at lowest cost.
+        downsample: Downsample input volume by a factor.
+        cost_file: Cost file for registration.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_register_to_label",
+        "surface": surface,
+        "regfile": regfile,
+        "mri_reg": mri_reg,
+        "mov_volume": mov_volume,
+        "resolution": resolution,
+    }
+    if max_rot is not None:
+        params["max_rot"] = max_rot
+    if max_trans is not None:
+        params["max_trans"] = max_trans
+    if subject is not None:
+        params["subject"] = subject
+    if label is not None:
+        params["label"] = label
+    if out_reg is not None:
+        params["out_reg"] = out_reg
+    if downsample is not None:
+        params["downsample"] = downsample
+    if cost_file is not None:
+        params["cost_file"] = cost_file
+    return params
+
+
+def mris_register_to_label_cargs(
+    params: MrisRegisterToLabelParameters,
+    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_register_to_label")
+    cargs.extend([
+        "--surf",
+        execution.input_file(params.get("surface"))
+    ])
+    cargs.extend([
+        "--reg",
+        execution.input_file(params.get("regfile"))
+    ])
+    cargs.extend([
+        "--mri_reg",
+        execution.input_file(params.get("mri_reg"))
+    ])
+    cargs.extend([
+        "--mov",
+        execution.input_file(params.get("mov_volume"))
+    ])
+    cargs.extend([
+        "--res",
+        str(params.get("resolution"))
+    ])
+    if params.get("max_rot") is not None:
+        cargs.extend([
+            "--max_rot",
+            str(params.get("max_rot"))
+        ])
+    if params.get("max_trans") is not None:
+        cargs.extend([
+            "--max_trans",
+            str(params.get("max_trans"))
+        ])
+    if params.get("subject") is not None:
+        cargs.extend([
+            "--s",
+            params.get("subject")
+        ])
+    if params.get("label") is not None:
+        cargs.extend([
+            "--label",
+            params.get("label")
+        ])
+    if params.get("out_reg") is not None:
+        cargs.extend([
+            "--out-reg",
+            params.get("out_reg")
+        ])
+    if params.get("downsample") is not None:
+        cargs.extend([
+            "--downsample",
+            str(params.get("downsample"))
+        ])
+    if params.get("cost_file") is not None:
+        cargs.extend([
+            "--cost",
+            execution.input_file(params.get("cost_file"))
+        ])
+    return cargs
+
+
+def mris_register_to_label_outputs(
+    params: MrisRegisterToLabelParameters,
+    execution: Execution,
+) -> MrisRegisterToLabelOutputs:
+    """
+    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 = MrisRegisterToLabelOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_register_to_label_execute(
+    params: MrisRegisterToLabelParameters,
+    execution: Execution,
+) -> MrisRegisterToLabelOutputs:
+    """
+    Register a surface to a volume using a label.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisRegisterToLabelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_register_to_label_cargs(params, execution)
+    ret = mris_register_to_label_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_register_to_label(
+    surface: InputPathType,
+    regfile: InputPathType,
+    mri_reg: InputPathType,
+    mov_volume: InputPathType,
+    resolution: float,
+    max_rot: float | None = None,
+    max_trans: float | None = None,
+    subject: str | None = None,
+    label: str | None = None,
+    out_reg: str | None = None,
+    downsample: float | None = None,
+    cost_file: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> MrisRegisterToLabelOutputs:
+    """
+    Register a surface to a volume using a label.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        surface: Surface file for registration.
+        regfile: Registration file.
+        mri_reg: Volume for MRI registration.
+        mov_volume: Volume on which label points are specified.
+        resolution: Resolution for calculations.
+        max_rot: Maximum angle (degrees) to search over for rotation.
+        max_trans: Maximum translation (mm) to search over.
+        subject: Specify name of subject for register.dat file.
+        label: Load label and limit calculations to it.
+        out_reg: Output registration at lowest cost.
+        downsample: Downsample input volume by a factor.
+        cost_file: Cost file for registration.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisRegisterToLabelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REGISTER_TO_LABEL_METADATA)
+    params = mris_register_to_label_params(
+        surface=surface,
+        regfile=regfile,
+        mri_reg=mri_reg,
+        mov_volume=mov_volume,
+        resolution=resolution,
+        max_rot=max_rot,
+        max_trans=max_trans,
+        subject=subject,
+        label=label,
+        out_reg=out_reg,
+        downsample=downsample,
+        cost_file=cost_file,
+    )
+    return mris_register_to_label_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_REGISTER_TO_LABEL_METADATA",
+    "MrisRegisterToLabelOutputs",
+    "MrisRegisterToLabelParameters",
+    "mris_register_to_label",
+    "mris_register_to_label_params",
+]