niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/deface_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 *
+
+DEFACE_SUBJECT_METADATA = Metadata(
+    id="274e5ad239a83bd50707ef1a9dcf8ce7c5e84775.boutiques",
+    name="deface_subject",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+DefaceSubjectParameters = typing.TypedDict('DefaceSubjectParameters', {
+    "__STYX_TYPE__": typing.Literal["deface_subject"],
+    "subjects_dir": str,
+    "subject_id": str,
+    "volume_input": InputPathType,
+    "volume_output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "deface_subject": deface_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 {
+        "deface_subject": deface_subject_outputs,
+    }.get(t)
+
+
+class DefaceSubjectOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `deface_subject(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume: OutputPathType
+    """Defaced output volume."""
+
+
+def deface_subject_params(
+    subjects_dir: str,
+    subject_id: str,
+    volume_input: InputPathType,
+    volume_output: str,
+) -> DefaceSubjectParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjects_dir: Directory containing FreeSurfer subject directories.
+        subject_id: Subject ID that specifies the subject directory.
+        volume_input: Input volume to be defaced.
+        volume_output: Output volume after defacing.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "deface_subject",
+        "subjects_dir": subjects_dir,
+        "subject_id": subject_id,
+        "volume_input": volume_input,
+        "volume_output": volume_output,
+    }
+    return params
+
+
+def deface_subject_cargs(
+    params: DefaceSubjectParameters,
+    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("deface_subject")
+    cargs.extend([
+        "-sdir",
+        params.get("subjects_dir")
+    ])
+    cargs.extend([
+        "-id",
+        params.get("subject_id")
+    ])
+    cargs.extend([
+        "-i",
+        execution.input_file(params.get("volume_input"))
+    ])
+    cargs.extend([
+        "-o",
+        params.get("volume_output")
+    ])
+    return cargs
+
+
+def deface_subject_outputs(
+    params: DefaceSubjectParameters,
+    execution: Execution,
+) -> DefaceSubjectOutputs:
+    """
+    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 = DefaceSubjectOutputs(
+        root=execution.output_file("."),
+        output_volume=execution.output_file(params.get("volume_output")),
+    )
+    return ret
+
+
+def deface_subject_execute(
+    params: DefaceSubjectParameters,
+    execution: Execution,
+) -> DefaceSubjectOutputs:
+    """
+    Tool for defacing MRI images to anonymize patient data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DefaceSubjectOutputs`).
+    """
+    params = execution.params(params)
+    cargs = deface_subject_cargs(params, execution)
+    ret = deface_subject_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def deface_subject(
+    subjects_dir: str,
+    subject_id: str,
+    volume_input: InputPathType,
+    volume_output: str,
+    runner: Runner | None = None,
+) -> DefaceSubjectOutputs:
+    """
+    Tool for defacing MRI images to anonymize patient data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjects_dir: Directory containing FreeSurfer subject directories.
+        subject_id: Subject ID that specifies the subject directory.
+        volume_input: Input volume to be defaced.
+        volume_output: Output volume after defacing.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DefaceSubjectOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DEFACE_SUBJECT_METADATA)
+    params = deface_subject_params(
+        subjects_dir=subjects_dir,
+        subject_id=subject_id,
+        volume_input=volume_input,
+        volume_output=volume_output,
+    )
+    return deface_subject_execute(params, execution)
+
+
+__all__ = [
+    "DEFACE_SUBJECT_METADATA",
+    "DefaceSubjectOutputs",
+    "DefaceSubjectParameters",
+    "deface_subject",
+    "deface_subject_params",
+]

niwrap_freesurfer/freesurfer/defect2seg.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 *
+
+DEFECT2SEG_METADATA = Metadata(
+    id="a0c3f2a6d8ce1bf2e14e38a191f684088ba5acc6.boutiques",
+    name="defect2seg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+Defect2segParameters = typing.TypedDict('Defect2segParameters', {
+    "__STYX_TYPE__": typing.Literal["defect2seg"],
+    "output_seg": str,
+    "template": InputPathType,
+    "left_hemisphere": typing.NotRequired[list[str] | None],
+    "right_hemisphere": typing.NotRequired[list[str] | None],
+    "subject": typing.NotRequired[str | None],
+    "lh_only": bool,
+    "rh_only": bool,
+    "cortex": bool,
+    "no_cortex": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "defect2seg": defect2seg_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 {
+        "defect2seg": defect2seg_outputs,
+    }.get(t)
+
+
+class Defect2segOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `defect2seg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_segmentation: OutputPathType
+    """Resulting defect segmentation volume"""
+
+
+def defect2seg_params(
+    output_seg: str,
+    template: InputPathType,
+    left_hemisphere: list[str] | None = None,
+    right_hemisphere: list[str] | None = None,
+    subject: str | None = None,
+    lh_only: bool = False,
+    rh_only: bool = False,
+    cortex: bool = False,
+    no_cortex: bool = False,
+) -> Defect2segParameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_seg: Output segmentation volume.
+        template: Template for segmentation.
+        left_hemisphere: Left hemisphere inputs: surface, defect labels,\
+            pointset, and offset.
+        right_hemisphere: Right hemisphere inputs: surface, defect labels,\
+            pointset, and offset.
+        subject: Subject identifier, sets default values for other parameters.
+        lh_only: Consider only left hemisphere defects.
+        rh_only: Consider only right hemisphere defects.
+        cortex: Constrain defects to within cortex.
+        no_cortex: Allow defects outside of cortex.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "defect2seg",
+        "output_seg": output_seg,
+        "template": template,
+        "lh_only": lh_only,
+        "rh_only": rh_only,
+        "cortex": cortex,
+        "no_cortex": no_cortex,
+    }
+    if left_hemisphere is not None:
+        params["left_hemisphere"] = left_hemisphere
+    if right_hemisphere is not None:
+        params["right_hemisphere"] = right_hemisphere
+    if subject is not None:
+        params["subject"] = subject
+    return params
+
+
+def defect2seg_cargs(
+    params: Defect2segParameters,
+    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("defect2seg")
+    cargs.extend([
+        "--o",
+        params.get("output_seg")
+    ])
+    cargs.extend([
+        "--t",
+        execution.input_file(params.get("template"))
+    ])
+    if params.get("left_hemisphere") is not None:
+        cargs.extend([
+            "--lh",
+            *params.get("left_hemisphere")
+        ])
+    if params.get("right_hemisphere") is not None:
+        cargs.extend([
+            "--rh",
+            *params.get("right_hemisphere")
+        ])
+    if params.get("subject") is not None:
+        cargs.extend([
+            "--s",
+            params.get("subject")
+        ])
+    if params.get("lh_only"):
+        cargs.append("--lh-only")
+    if params.get("rh_only"):
+        cargs.append("--rh-only")
+    if params.get("cortex"):
+        cargs.append("--cortex")
+    if params.get("no_cortex"):
+        cargs.append("--no-cortex")
+    return cargs
+
+
+def defect2seg_outputs(
+    params: Defect2segParameters,
+    execution: Execution,
+) -> Defect2segOutputs:
+    """
+    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 = Defect2segOutputs(
+        root=execution.output_file("."),
+        output_segmentation=execution.output_file(params.get("output_seg")),
+    )
+    return ret
+
+
+def defect2seg_execute(
+    params: Defect2segParameters,
+    execution: Execution,
+) -> Defect2segOutputs:
+    """
+    Converts surface defect labels into a segmentation volume and pointsets.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Defect2segOutputs`).
+    """
+    params = execution.params(params)
+    cargs = defect2seg_cargs(params, execution)
+    ret = defect2seg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def defect2seg(
+    output_seg: str,
+    template: InputPathType,
+    left_hemisphere: list[str] | None = None,
+    right_hemisphere: list[str] | None = None,
+    subject: str | None = None,
+    lh_only: bool = False,
+    rh_only: bool = False,
+    cortex: bool = False,
+    no_cortex: bool = False,
+    runner: Runner | None = None,
+) -> Defect2segOutputs:
+    """
+    Converts surface defect labels into a segmentation volume and pointsets.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        output_seg: Output segmentation volume.
+        template: Template for segmentation.
+        left_hemisphere: Left hemisphere inputs: surface, defect labels,\
+            pointset, and offset.
+        right_hemisphere: Right hemisphere inputs: surface, defect labels,\
+            pointset, and offset.
+        subject: Subject identifier, sets default values for other parameters.
+        lh_only: Consider only left hemisphere defects.
+        rh_only: Consider only right hemisphere defects.
+        cortex: Constrain defects to within cortex.
+        no_cortex: Allow defects outside of cortex.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Defect2segOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DEFECT2SEG_METADATA)
+    params = defect2seg_params(
+        output_seg=output_seg,
+        template=template,
+        left_hemisphere=left_hemisphere,
+        right_hemisphere=right_hemisphere,
+        subject=subject,
+        lh_only=lh_only,
+        rh_only=rh_only,
+        cortex=cortex,
+        no_cortex=no_cortex,
+    )
+    return defect2seg_execute(params, execution)
+
+
+__all__ = [
+    "DEFECT2SEG_METADATA",
+    "Defect2segOutputs",
+    "Defect2segParameters",
+    "defect2seg",
+    "defect2seg_params",
+]

niwrap_freesurfer/freesurfer/defect_seg.py

@@ -0,0 +1,219 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DEFECT_SEG_METADATA = Metadata(
+    id="0e4a4cf0254a2348ea18fc134e746047a23ee4d4.boutiques",
+    name="defect-seg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+DefectSegParameters = typing.TypedDict('DefectSegParameters', {
+    "__STYX_TYPE__": typing.Literal["defect-seg"],
+    "subject": str,
+    "lh_only": bool,
+    "rh_only": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "defect-seg": defect_seg_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 {
+        "defect-seg": defect_seg_outputs,
+    }.get(t)
+
+
+class DefectSegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `defect_seg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    surface_defects: OutputPathType
+    """Surface defects volume."""
+    defects_summary: OutputPathType
+    """Summary of defects indicating numerical ID and number of vertices."""
+    defect_labels_fix: OutputPathType
+    """Fixed defect labels on the surface."""
+    defect_labels_fix_bin: OutputPathType
+    """Binary labels for fixed defects."""
+    defects_nofix_annot: OutputPathType
+    """Annotation file for defects without fixes."""
+    defects_fix_annot: OutputPathType
+    """Annotation file for defects with fixes."""
+    defects_stats: OutputPathType
+    """Statistics summary of defects indicating area and average thickness."""
+
+
+def defect_seg_params(
+    subject: str,
+    lh_only: bool = False,
+    rh_only: bool = False,
+) -> DefectSegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject: Subject identifier.
+        lh_only: Only process the left hemisphere.
+        rh_only: Only process the right hemisphere.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "defect-seg",
+        "subject": subject,
+        "lh_only": lh_only,
+        "rh_only": rh_only,
+    }
+    return params
+
+
+def defect_seg_cargs(
+    params: DefectSegParameters,
+    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("defect-seg")
+    cargs.extend([
+        "--s",
+        params.get("subject")
+    ])
+    if params.get("lh_only"):
+        cargs.append("--lh-only")
+    if params.get("rh_only"):
+        cargs.append("--rh-only")
+    return cargs
+
+
+def defect_seg_outputs(
+    params: DefectSegParameters,
+    execution: Execution,
+) -> DefectSegOutputs:
+    """
+    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 = DefectSegOutputs(
+        root=execution.output_file("."),
+        surface_defects=execution.output_file("mri/surface.defects.mgz"),
+        defects_summary=execution.output_file("scripts/?h.defects.summary"),
+        defect_labels_fix=execution.output_file("surf/?h.defect_labels.fix.mgz"),
+        defect_labels_fix_bin=execution.output_file("surf/?h.defect_labels.fix.bin.mgz"),
+        defects_nofix_annot=execution.output_file("label/?h.defects.nofix.annot"),
+        defects_fix_annot=execution.output_file("label/?h.defects.fix.annot"),
+        defects_stats=execution.output_file("stats/?h.defects.stats"),
+    )
+    return ret
+
+
+def defect_seg_execute(
+    params: DefectSegParameters,
+    execution: Execution,
+) -> DefectSegOutputs:
+    """
+    This program creates some files that allows the user to visualize and evaluate
+    the surface defects that were automatically detected and fixed by the topology
+    correction program.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DefectSegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = defect_seg_cargs(params, execution)
+    ret = defect_seg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def defect_seg(
+    subject: str,
+    lh_only: bool = False,
+    rh_only: bool = False,
+    runner: Runner | None = None,
+) -> DefectSegOutputs:
+    """
+    This program creates some files that allows the user to visualize and evaluate
+    the surface defects that were automatically detected and fixed by the topology
+    correction program.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject: Subject identifier.
+        lh_only: Only process the left hemisphere.
+        rh_only: Only process the right hemisphere.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DefectSegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DEFECT_SEG_METADATA)
+    params = defect_seg_params(
+        subject=subject,
+        lh_only=lh_only,
+        rh_only=rh_only,
+    )
+    return defect_seg_execute(params, execution)
+
+
+__all__ = [
+    "DEFECT_SEG_METADATA",
+    "DefectSegOutputs",
+    "DefectSegParameters",
+    "defect_seg",
+    "defect_seg_params",
+]