niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/register_subject_flash.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+REGISTER_SUBJECT_FLASH_METADATA = Metadata(
+    id="9a7a639d778167b266b2e9f5c9a4ba404e0ced41.boutiques",
+    name="register_subject_flash",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+RegisterSubjectFlashParameters = typing.TypedDict('RegisterSubjectFlashParameters', {
+    "__STYX_TYPE__": typing.Literal["register_subject_flash"],
+    "input_volumes": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "register_subject_flash": register_subject_flash_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 {
+        "register_subject_flash": register_subject_flash_outputs,
+    }.get(t)
+
+
+class RegisterSubjectFlashOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `register_subject_flash(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    log_file: OutputPathType
+    """Log file output with registration results."""
+
+
+def register_subject_flash_params(
+    input_volumes: list[InputPathType],
+) -> RegisterSubjectFlashParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volumes: Input volumes to register.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "register_subject_flash",
+        "input_volumes": input_volumes,
+    }
+    return params
+
+
+def register_subject_flash_cargs(
+    params: RegisterSubjectFlashParameters,
+    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("register_subject_flash")
+    cargs.extend([execution.input_file(f) for f in params.get("input_volumes")])
+    return cargs
+
+
+def register_subject_flash_outputs(
+    params: RegisterSubjectFlashParameters,
+    execution: Execution,
+) -> RegisterSubjectFlashOutputs:
+    """
+    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 = RegisterSubjectFlashOutputs(
+        root=execution.output_file("."),
+        log_file=execution.output_file("talairach.log"),
+    )
+    return ret
+
+
+def register_subject_flash_execute(
+    params: RegisterSubjectFlashParameters,
+    execution: Execution,
+) -> RegisterSubjectFlashOutputs:
+    """
+    Register subject using the FLASH forward model to predict intensity values.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `RegisterSubjectFlashOutputs`).
+    """
+    params = execution.params(params)
+    cargs = register_subject_flash_cargs(params, execution)
+    ret = register_subject_flash_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def register_subject_flash(
+    input_volumes: list[InputPathType],
+    runner: Runner | None = None,
+) -> RegisterSubjectFlashOutputs:
+    """
+    Register subject using the FLASH forward model to predict intensity values.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volumes: Input volumes to register.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `RegisterSubjectFlashOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REGISTER_SUBJECT_FLASH_METADATA)
+    params = register_subject_flash_params(
+        input_volumes=input_volumes,
+    )
+    return register_subject_flash_execute(params, execution)
+
+
+__all__ = [
+    "REGISTER_SUBJECT_FLASH_METADATA",
+    "RegisterSubjectFlashOutputs",
+    "RegisterSubjectFlashParameters",
+    "register_subject_flash",
+    "register_subject_flash_params",
+]

niwrap_freesurfer/freesurfer/reinflate_subject.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+REINFLATE_SUBJECT_METADATA = Metadata(
+    id="1e08a83747d403bdb6fd509a84d2ca27a452f873.boutiques",
+    name="reinflate_subject",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+ReinflateSubjectParameters = typing.TypedDict('ReinflateSubjectParameters', {
+    "__STYX_TYPE__": typing.Literal["reinflate_subject"],
+    "args": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "reinflate_subject": reinflate_subject_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 ReinflateSubjectOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `reinflate_subject(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def reinflate_subject_params(
+    args: str | None = None,
+) -> ReinflateSubjectParameters:
+    """
+    Build parameters.
+    
+    Args:
+        args: Arguments for reinflate_subject.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "reinflate_subject",
+    }
+    if args is not None:
+        params["args"] = args
+    return params
+
+
+def reinflate_subject_cargs(
+    params: ReinflateSubjectParameters,
+    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("reinflate_subject")
+    if params.get("args") is not None:
+        cargs.append(params.get("args"))
+    return cargs
+
+
+def reinflate_subject_outputs(
+    params: ReinflateSubjectParameters,
+    execution: Execution,
+) -> ReinflateSubjectOutputs:
+    """
+    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 = ReinflateSubjectOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def reinflate_subject_execute(
+    params: ReinflateSubjectParameters,
+    execution: Execution,
+) -> ReinflateSubjectOutputs:
+    """
+    Tool for reinflating brain surfaces.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ReinflateSubjectOutputs`).
+    """
+    params = execution.params(params)
+    cargs = reinflate_subject_cargs(params, execution)
+    ret = reinflate_subject_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def reinflate_subject(
+    args: str | None = None,
+    runner: Runner | None = None,
+) -> ReinflateSubjectOutputs:
+    """
+    Tool for reinflating brain surfaces.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        args: Arguments for reinflate_subject.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ReinflateSubjectOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REINFLATE_SUBJECT_METADATA)
+    params = reinflate_subject_params(
+        args=args,
+    )
+    return reinflate_subject_execute(params, execution)
+
+
+__all__ = [
+    "REINFLATE_SUBJECT_METADATA",
+    "ReinflateSubjectOutputs",
+    "ReinflateSubjectParameters",
+    "reinflate_subject",
+    "reinflate_subject_params",
+]

niwrap_freesurfer/freesurfer/reinflate_subject_lh.py

@@ -0,0 +1,178 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+REINFLATE_SUBJECT_LH_METADATA = Metadata(
+    id="3a29a9cc35621246bc04494a51e4c6898d34911c.boutiques",
+    name="reinflate_subject-lh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+ReinflateSubjectLhParameters = typing.TypedDict('ReinflateSubjectLhParameters', {
+    "__STYX_TYPE__": typing.Literal["reinflate_subject-lh"],
+    "subject_id": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "reinflate_subject-lh": reinflate_subject_lh_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 {
+        "reinflate_subject-lh": reinflate_subject_lh_outputs,
+    }.get(t)
+
+
+class ReinflateSubjectLhOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `reinflate_subject_lh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    inflated_surface: OutputPathType
+    """Reinflated left hemisphere cortical surface"""
+
+
+def reinflate_subject_lh_params(
+    subject_id: str,
+) -> ReinflateSubjectLhParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_id: Subject identifier.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "reinflate_subject-lh",
+        "subject_id": subject_id,
+    }
+    return params
+
+
+def reinflate_subject_lh_cargs(
+    params: ReinflateSubjectLhParameters,
+    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.extend([
+        "-lh",
+        "reinflate_subject" + params.get("subject_id")
+    ])
+    return cargs
+
+
+def reinflate_subject_lh_outputs(
+    params: ReinflateSubjectLhParameters,
+    execution: Execution,
+) -> ReinflateSubjectLhOutputs:
+    """
+    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 = ReinflateSubjectLhOutputs(
+        root=execution.output_file("."),
+        inflated_surface=execution.output_file(params.get("subject_id") + "/surf/lh.inflated"),
+    )
+    return ret
+
+
+def reinflate_subject_lh_execute(
+    params: ReinflateSubjectLhParameters,
+    execution: Execution,
+) -> ReinflateSubjectLhOutputs:
+    """
+    Utility to reinflate cortical surfaces for left hemisphere 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 `ReinflateSubjectLhOutputs`).
+    """
+    params = execution.params(params)
+    cargs = reinflate_subject_lh_cargs(params, execution)
+    ret = reinflate_subject_lh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def reinflate_subject_lh(
+    subject_id: str,
+    runner: Runner | None = None,
+) -> ReinflateSubjectLhOutputs:
+    """
+    Utility to reinflate cortical surfaces for left hemisphere in FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_id: Subject identifier.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ReinflateSubjectLhOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REINFLATE_SUBJECT_LH_METADATA)
+    params = reinflate_subject_lh_params(
+        subject_id=subject_id,
+    )
+    return reinflate_subject_lh_execute(params, execution)
+
+
+__all__ = [
+    "REINFLATE_SUBJECT_LH_METADATA",
+    "ReinflateSubjectLhOutputs",
+    "ReinflateSubjectLhParameters",
+    "reinflate_subject_lh",
+    "reinflate_subject_lh_params",
+]

niwrap_freesurfer/freesurfer/reinflate_subject_rh.py

@@ -0,0 +1,188 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+REINFLATE_SUBJECT_RH_METADATA = Metadata(
+    id="46c17d80d09536f705ed323c939acc704434405c.boutiques",
+    name="reinflate_subject-rh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+ReinflateSubjectRhParameters = typing.TypedDict('ReinflateSubjectRhParameters', {
+    "__STYX_TYPE__": typing.Literal["reinflate_subject-rh"],
+    "subject_dir": str,
+    "additional_options": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "reinflate_subject-rh": reinflate_subject_rh_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 ReinflateSubjectRhOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `reinflate_subject_rh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def reinflate_subject_rh_params(
+    subject_dir: str,
+    additional_options: str | None = None,
+) -> ReinflateSubjectRhParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_dir: Directory of the subject within FreeSurfer environment.
+        additional_options: Additional options for the reinflate_subject-rh\
+            command.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "reinflate_subject-rh",
+        "subject_dir": subject_dir,
+    }
+    if additional_options is not None:
+        params["additional_options"] = additional_options
+    return params
+
+
+def reinflate_subject_rh_cargs(
+    params: ReinflateSubjectRhParameters,
+    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.extend([
+        "-rh",
+        "reinflate_subject" + params.get("subject_dir")
+    ])
+    if params.get("additional_options") is not None:
+        cargs.append(params.get("additional_options"))
+    return cargs
+
+
+def reinflate_subject_rh_outputs(
+    params: ReinflateSubjectRhParameters,
+    execution: Execution,
+) -> ReinflateSubjectRhOutputs:
+    """
+    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 = ReinflateSubjectRhOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def reinflate_subject_rh_execute(
+    params: ReinflateSubjectRhParameters,
+    execution: Execution,
+) -> ReinflateSubjectRhOutputs:
+    """
+    A tool for reinflating the cortical surfaces for a given subject in FreeSurfer,
+    specifically for the right hemisphere.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ReinflateSubjectRhOutputs`).
+    """
+    params = execution.params(params)
+    cargs = reinflate_subject_rh_cargs(params, execution)
+    ret = reinflate_subject_rh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def reinflate_subject_rh(
+    subject_dir: str,
+    additional_options: str | None = None,
+    runner: Runner | None = None,
+) -> ReinflateSubjectRhOutputs:
+    """
+    A tool for reinflating the cortical surfaces for a given subject in FreeSurfer,
+    specifically for the right hemisphere.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_dir: Directory of the subject within FreeSurfer environment.
+        additional_options: Additional options for the reinflate_subject-rh\
+            command.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ReinflateSubjectRhOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REINFLATE_SUBJECT_RH_METADATA)
+    params = reinflate_subject_rh_params(
+        subject_dir=subject_dir,
+        additional_options=additional_options,
+    )
+    return reinflate_subject_rh_execute(params, execution)
+
+
+__all__ = [
+    "REINFLATE_SUBJECT_RH_METADATA",
+    "ReinflateSubjectRhOutputs",
+    "ReinflateSubjectRhParameters",
+    "reinflate_subject_rh",
+    "reinflate_subject_rh_params",
+]