niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_compute_overlap.py

@@ -0,0 +1,239 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_COMPUTE_OVERLAP_METADATA = Metadata(
+    id="a5b5b5d3058860c230b1e6a107208c5201cd453b.boutiques",
+    name="mris_compute_overlap",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisComputeOverlapParameters = typing.TypedDict('MrisComputeOverlapParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_compute_overlap"],
+    "subject": str,
+    "hemi": str,
+    "surface": str,
+    "annotation": str,
+    "labels": list[str],
+    "percentage": bool,
+    "log_file": typing.NotRequired[str | None],
+    "brain_volume": 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_compute_overlap": mris_compute_overlap_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 MrisComputeOverlapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_compute_overlap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_compute_overlap_params(
+    subject: str,
+    hemi: str,
+    surface: str,
+    annotation: str,
+    labels: list[str],
+    percentage: bool = False,
+    log_file: str | None = None,
+    brain_volume: InputPathType | None = None,
+) -> MrisComputeOverlapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject: Subject name.
+        hemi: Hemisphere (e.g. lh or rh).
+        surface: Surface name.
+        annotation: Annotation name.
+        labels: Labels to compute overlap for.
+        percentage: Compute brain area as a percentage of all brain labels.
+        log_file: Log results to file, where %d will include label number.
+        brain_volume: Load brain volume and use it to normalize areas.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_compute_overlap",
+        "subject": subject,
+        "hemi": hemi,
+        "surface": surface,
+        "annotation": annotation,
+        "labels": labels,
+        "percentage": percentage,
+    }
+    if log_file is not None:
+        params["log_file"] = log_file
+    if brain_volume is not None:
+        params["brain_volume"] = brain_volume
+    return params
+
+
+def mris_compute_overlap_cargs(
+    params: MrisComputeOverlapParameters,
+    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_compute_overlap")
+    cargs.append(params.get("subject"))
+    cargs.append(params.get("hemi"))
+    cargs.append(params.get("surface"))
+    cargs.append(params.get("annotation"))
+    cargs.extend(params.get("labels"))
+    if params.get("percentage"):
+        cargs.append("-p")
+    if params.get("log_file") is not None:
+        cargs.extend([
+            "-l",
+            params.get("log_file")
+        ])
+    if params.get("brain_volume") is not None:
+        cargs.extend([
+            "-b",
+            execution.input_file(params.get("brain_volume"))
+        ])
+    return cargs
+
+
+def mris_compute_overlap_outputs(
+    params: MrisComputeOverlapParameters,
+    execution: Execution,
+) -> MrisComputeOverlapOutputs:
+    """
+    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 = MrisComputeOverlapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_compute_overlap_execute(
+    params: MrisComputeOverlapParameters,
+    execution: Execution,
+) -> MrisComputeOverlapOutputs:
+    """
+    Tool to compute the overlap between two or more labels on a cortical surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisComputeOverlapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_compute_overlap_cargs(params, execution)
+    ret = mris_compute_overlap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_compute_overlap(
+    subject: str,
+    hemi: str,
+    surface: str,
+    annotation: str,
+    labels: list[str],
+    percentage: bool = False,
+    log_file: str | None = None,
+    brain_volume: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> MrisComputeOverlapOutputs:
+    """
+    Tool to compute the overlap between two or more labels on a cortical surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject: Subject name.
+        hemi: Hemisphere (e.g. lh or rh).
+        surface: Surface name.
+        annotation: Annotation name.
+        labels: Labels to compute overlap for.
+        percentage: Compute brain area as a percentage of all brain labels.
+        log_file: Log results to file, where %d will include label number.
+        brain_volume: Load brain volume and use it to normalize areas.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisComputeOverlapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_COMPUTE_OVERLAP_METADATA)
+    params = mris_compute_overlap_params(
+        subject=subject,
+        hemi=hemi,
+        surface=surface,
+        annotation=annotation,
+        labels=labels,
+        percentage=percentage,
+        log_file=log_file,
+        brain_volume=brain_volume,
+    )
+    return mris_compute_overlap_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_COMPUTE_OVERLAP_METADATA",
+    "MrisComputeOverlapOutputs",
+    "MrisComputeOverlapParameters",
+    "mris_compute_overlap",
+    "mris_compute_overlap_params",
+]

niwrap_freesurfer/freesurfer/mris_compute_parc_overlap.py

@@ -0,0 +1,346 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_COMPUTE_PARC_OVERLAP_METADATA = Metadata(
+    id="d598ee06b2c8bac2b0e66dc28fd526ceb983bfbd.boutiques",
+    name="mris_compute_parc_overlap",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisComputeParcOverlapParameters = typing.TypedDict('MrisComputeParcOverlapParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_compute_parc_overlap"],
+    "subject": str,
+    "hemi": str,
+    "annot1": typing.NotRequired[InputPathType | None],
+    "annot2": typing.NotRequired[InputPathType | None],
+    "label1": typing.NotRequired[InputPathType | None],
+    "label2": typing.NotRequired[InputPathType | None],
+    "subj_dir": typing.NotRequired[str | None],
+    "log_file": typing.NotRequired[str | None],
+    "label_list": typing.NotRequired[InputPathType | None],
+    "nocheck_label1_xyz": bool,
+    "nocheck_label2_xyz": bool,
+    "nocheck_label_xyz": bool,
+    "use_label1_xyz": bool,
+    "use_label2_xyz": bool,
+    "use_label_xyz": bool,
+    "debug_overlap": 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_compute_parc_overlap": mris_compute_parc_overlap_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 MrisComputeParcOverlapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_compute_parc_overlap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_compute_parc_overlap_params(
+    subject: str,
+    hemi: str,
+    annot1: InputPathType | None = None,
+    annot2: InputPathType | None = None,
+    label1: InputPathType | None = None,
+    label2: InputPathType | None = None,
+    subj_dir: str | None = None,
+    log_file: str | None = None,
+    label_list: InputPathType | None = None,
+    nocheck_label1_xyz: bool = False,
+    nocheck_label2_xyz: bool = False,
+    nocheck_label_xyz: bool = False,
+    use_label1_xyz: bool = False,
+    use_label2_xyz: bool = False,
+    use_label_xyz: bool = False,
+    debug_overlap: bool = False,
+) -> MrisComputeParcOverlapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject: Subject to check.
+        hemi: Hemisphere: rh or lh.
+        annot1: First .annot file.
+        annot2: Second .annot file.
+        label1: First .label file.
+        label2: Second .label file.
+        subj_dir: Set SUBJECTS_DIR.
+        log_file: Output the overall DICE and minimum distance to filename.
+        label_list: File containing labels to check, one per line.
+        nocheck_label1_xyz: When loading label1 file, don't check x,y,z coords\
+            to surface.
+        nocheck_label2_xyz: When loading label2 file, don't check x,y,z coords\
+            to surface.
+        nocheck_label_xyz: Do not check label1 and label2.
+        use_label1_xyz: Replace surface x,y,z coords with those in label1 file.
+        use_label2_xyz: Replace surface x,y,z coords with those in label2 file.
+        use_label_xyz: Use label1 and label2 coords.
+        debug_overlap: Generate ?h.overlap.annot.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_compute_parc_overlap",
+        "subject": subject,
+        "hemi": hemi,
+        "nocheck_label1_xyz": nocheck_label1_xyz,
+        "nocheck_label2_xyz": nocheck_label2_xyz,
+        "nocheck_label_xyz": nocheck_label_xyz,
+        "use_label1_xyz": use_label1_xyz,
+        "use_label2_xyz": use_label2_xyz,
+        "use_label_xyz": use_label_xyz,
+        "debug_overlap": debug_overlap,
+    }
+    if annot1 is not None:
+        params["annot1"] = annot1
+    if annot2 is not None:
+        params["annot2"] = annot2
+    if label1 is not None:
+        params["label1"] = label1
+    if label2 is not None:
+        params["label2"] = label2
+    if subj_dir is not None:
+        params["subj_dir"] = subj_dir
+    if log_file is not None:
+        params["log_file"] = log_file
+    if label_list is not None:
+        params["label_list"] = label_list
+    return params
+
+
+def mris_compute_parc_overlap_cargs(
+    params: MrisComputeParcOverlapParameters,
+    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_compute_parc_overlap")
+    cargs.extend([
+        "--s",
+        params.get("subject")
+    ])
+    cargs.extend([
+        "--hemi",
+        params.get("hemi")
+    ])
+    if params.get("annot1") is not None:
+        cargs.extend([
+            "--annot1",
+            execution.input_file(params.get("annot1"))
+        ])
+    if params.get("annot2") is not None:
+        cargs.extend([
+            "--annot2",
+            execution.input_file(params.get("annot2"))
+        ])
+    if params.get("label1") is not None:
+        cargs.extend([
+            "--label1",
+            execution.input_file(params.get("label1"))
+        ])
+    if params.get("label2") is not None:
+        cargs.extend([
+            "--label2",
+            execution.input_file(params.get("label2"))
+        ])
+    if params.get("subj_dir") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subj_dir")
+        ])
+    if params.get("log_file") is not None:
+        cargs.extend([
+            "--log",
+            params.get("log_file")
+        ])
+    if params.get("label_list") is not None:
+        cargs.extend([
+            "--label-list",
+            execution.input_file(params.get("label_list"))
+        ])
+    if params.get("nocheck_label1_xyz"):
+        cargs.append("--nocheck-label1-xyz")
+    if params.get("nocheck_label2_xyz"):
+        cargs.append("--nocheck-label2-xyz")
+    if params.get("nocheck_label_xyz"):
+        cargs.append("--nocheck-label-xyz")
+    if params.get("use_label1_xyz"):
+        cargs.append("--use-label1-xyz")
+    if params.get("use_label2_xyz"):
+        cargs.append("--use-label2-xyz")
+    if params.get("use_label_xyz"):
+        cargs.append("--use-label-xyz")
+    if params.get("debug_overlap"):
+        cargs.append("--debug-overlap")
+    return cargs
+
+
+def mris_compute_parc_overlap_outputs(
+    params: MrisComputeParcOverlapParameters,
+    execution: Execution,
+) -> MrisComputeParcOverlapOutputs:
+    """
+    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 = MrisComputeParcOverlapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_compute_parc_overlap_execute(
+    params: MrisComputeParcOverlapParameters,
+    execution: Execution,
+) -> MrisComputeParcOverlapOutputs:
+    """
+    Compares two parcellated (annotated or labeled) surfaces and computes an overall
+    Dice coefficient and mean minimum distances (mm).
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisComputeParcOverlapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_compute_parc_overlap_cargs(params, execution)
+    ret = mris_compute_parc_overlap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_compute_parc_overlap(
+    subject: str,
+    hemi: str,
+    annot1: InputPathType | None = None,
+    annot2: InputPathType | None = None,
+    label1: InputPathType | None = None,
+    label2: InputPathType | None = None,
+    subj_dir: str | None = None,
+    log_file: str | None = None,
+    label_list: InputPathType | None = None,
+    nocheck_label1_xyz: bool = False,
+    nocheck_label2_xyz: bool = False,
+    nocheck_label_xyz: bool = False,
+    use_label1_xyz: bool = False,
+    use_label2_xyz: bool = False,
+    use_label_xyz: bool = False,
+    debug_overlap: bool = False,
+    runner: Runner | None = None,
+) -> MrisComputeParcOverlapOutputs:
+    """
+    Compares two parcellated (annotated or labeled) surfaces and computes an overall
+    Dice coefficient and mean minimum distances (mm).
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject: Subject to check.
+        hemi: Hemisphere: rh or lh.
+        annot1: First .annot file.
+        annot2: Second .annot file.
+        label1: First .label file.
+        label2: Second .label file.
+        subj_dir: Set SUBJECTS_DIR.
+        log_file: Output the overall DICE and minimum distance to filename.
+        label_list: File containing labels to check, one per line.
+        nocheck_label1_xyz: When loading label1 file, don't check x,y,z coords\
+            to surface.
+        nocheck_label2_xyz: When loading label2 file, don't check x,y,z coords\
+            to surface.
+        nocheck_label_xyz: Do not check label1 and label2.
+        use_label1_xyz: Replace surface x,y,z coords with those in label1 file.
+        use_label2_xyz: Replace surface x,y,z coords with those in label2 file.
+        use_label_xyz: Use label1 and label2 coords.
+        debug_overlap: Generate ?h.overlap.annot.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisComputeParcOverlapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_COMPUTE_PARC_OVERLAP_METADATA)
+    params = mris_compute_parc_overlap_params(
+        subject=subject,
+        hemi=hemi,
+        annot1=annot1,
+        annot2=annot2,
+        label1=label1,
+        label2=label2,
+        subj_dir=subj_dir,
+        log_file=log_file,
+        label_list=label_list,
+        nocheck_label1_xyz=nocheck_label1_xyz,
+        nocheck_label2_xyz=nocheck_label2_xyz,
+        nocheck_label_xyz=nocheck_label_xyz,
+        use_label1_xyz=use_label1_xyz,
+        use_label2_xyz=use_label2_xyz,
+        use_label_xyz=use_label_xyz,
+        debug_overlap=debug_overlap,
+    )
+    return mris_compute_parc_overlap_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_COMPUTE_PARC_OVERLAP_METADATA",
+    "MrisComputeParcOverlapOutputs",
+    "MrisComputeParcOverlapParameters",
+    "mris_compute_parc_overlap",
+    "mris_compute_parc_overlap_params",
+]