niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_compute_layer_fractions.py

@@ -0,0 +1,324 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_COMPUTE_LAYER_FRACTIONS_METADATA = Metadata(
+    id="4b975414209d034dddfda14c61a9efcc219f17d0.boutiques",
+    name="mri_compute_layer_fractions",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriComputeLayerFractionsParameters = typing.TypedDict('MriComputeLayerFractionsParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_compute_layer_fractions"],
+    "reg_file": InputPathType,
+    "input_volume": InputPathType,
+    "output_stem": str,
+    "output_directory": typing.NotRequired[str | None],
+    "aseg_file": typing.NotRequired[InputPathType | None],
+    "target_volume": typing.NotRequired[InputPathType | None],
+    "hemi_flag": bool,
+    "fs_names_flag": bool,
+    "subject_id": typing.NotRequired[str | None],
+    "n_layers": typing.NotRequired[float | None],
+    "synth_flag": bool,
+    "thickness": typing.NotRequired[float | None],
+    "random_file": typing.NotRequired[InputPathType | None],
+    "identity_file": 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 {
+        "mri_compute_layer_fractions": mri_compute_layer_fractions_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 {
+        "mri_compute_layer_fractions": mri_compute_layer_fractions_outputs,
+    }.get(t)
+
+
+class MriComputeLayerFractionsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_compute_layer_fractions(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    layer_fractions_output: OutputPathType
+    """Output file for layer fractions computation"""
+    synth_output: OutputPathType
+    """Synthesized output volume combining layers and aseg"""
+
+
+def mri_compute_layer_fractions_params(
+    reg_file: InputPathType,
+    input_volume: InputPathType,
+    output_stem: str,
+    output_directory: str | None = None,
+    aseg_file: InputPathType | None = None,
+    target_volume: InputPathType | None = None,
+    hemi_flag: bool = False,
+    fs_names_flag: bool = False,
+    subject_id: str | None = None,
+    n_layers: float | None = None,
+    synth_flag: bool = False,
+    thickness: float | None = None,
+    random_file: InputPathType | None = None,
+    identity_file: str | None = None,
+) -> MriComputeLayerFractionsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        reg_file: Input registration file.
+        input_volume: Input volume file.
+        output_stem: Output stem for generated files.
+        output_directory: Output directory specified by SUBJECTS_DIR.
+        aseg_file: Input ASEG file for synthesis.
+        target_volume: Target volume for analysis.
+        hemi_flag: Specify hemisphere processing.
+        fs_names_flag: Flag to use FreeSurfer names.
+        subject_id: Subject ID for processing.
+        n_layers: Number of layers for volume fraction computation.
+        synth_flag: Flag to combine with the ASEG for a single segmentation\
+            volume.
+        thickness: Specify cortical thickness fraction.
+        random_file: Specify random volume file.
+        identity_file: Specify identity file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_compute_layer_fractions",
+        "reg_file": reg_file,
+        "input_volume": input_volume,
+        "output_stem": output_stem,
+        "hemi_flag": hemi_flag,
+        "fs_names_flag": fs_names_flag,
+        "synth_flag": synth_flag,
+    }
+    if output_directory is not None:
+        params["output_directory"] = output_directory
+    if aseg_file is not None:
+        params["aseg_file"] = aseg_file
+    if target_volume is not None:
+        params["target_volume"] = target_volume
+    if subject_id is not None:
+        params["subject_id"] = subject_id
+    if n_layers is not None:
+        params["n_layers"] = n_layers
+    if thickness is not None:
+        params["thickness"] = thickness
+    if random_file is not None:
+        params["random_file"] = random_file
+    if identity_file is not None:
+        params["identity_file"] = identity_file
+    return params
+
+
+def mri_compute_layer_fractions_cargs(
+    params: MriComputeLayerFractionsParameters,
+    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("mri_compute_layer_fractions")
+    cargs.append(execution.input_file(params.get("reg_file")))
+    cargs.append(execution.input_file(params.get("input_volume")))
+    cargs.append(params.get("output_stem"))
+    if params.get("output_directory") is not None:
+        cargs.extend([
+            "-SDIR",
+            params.get("output_directory")
+        ])
+    if params.get("aseg_file") is not None:
+        cargs.extend([
+            "-a",
+            execution.input_file(params.get("aseg_file"))
+        ])
+    if params.get("target_volume") is not None:
+        cargs.append(execution.input_file(params.get("target_volume")))
+    if params.get("hemi_flag"):
+        cargs.append("-hemi")
+    if params.get("fs_names_flag"):
+        cargs.append("-FS_names")
+    if params.get("subject_id") is not None:
+        cargs.extend([
+            "-s",
+            params.get("subject_id")
+        ])
+    if params.get("n_layers") is not None:
+        cargs.extend([
+            "-nlayers",
+            str(params.get("n_layers"))
+        ])
+    if params.get("synth_flag"):
+        cargs.append("-synth")
+    if params.get("thickness") is not None:
+        cargs.extend([
+            "-r",
+            str(params.get("thickness"))
+        ])
+    if params.get("random_file") is not None:
+        cargs.extend([
+            "-n",
+            execution.input_file(params.get("random_file"))
+        ])
+    if params.get("identity_file") is not None:
+        cargs.append(params.get("identity_file"))
+    return cargs
+
+
+def mri_compute_layer_fractions_outputs(
+    params: MriComputeLayerFractionsParameters,
+    execution: Execution,
+) -> MriComputeLayerFractionsOutputs:
+    """
+    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 = MriComputeLayerFractionsOutputs(
+        root=execution.output_file("."),
+        layer_fractions_output=execution.output_file(params.get("output_stem") + "_layer_fractions.mgz"),
+        synth_output=execution.output_file(params.get("output_stem") + "_synth.mgz"),
+    )
+    return ret
+
+
+def mri_compute_layer_fractions_execute(
+    params: MriComputeLayerFractionsParameters,
+    execution: Execution,
+) -> MriComputeLayerFractionsOutputs:
+    """
+    This program computes volumetric partial volume fractions from laminar surfaces
+    using FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriComputeLayerFractionsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_compute_layer_fractions_cargs(params, execution)
+    ret = mri_compute_layer_fractions_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_compute_layer_fractions(
+    reg_file: InputPathType,
+    input_volume: InputPathType,
+    output_stem: str,
+    output_directory: str | None = None,
+    aseg_file: InputPathType | None = None,
+    target_volume: InputPathType | None = None,
+    hemi_flag: bool = False,
+    fs_names_flag: bool = False,
+    subject_id: str | None = None,
+    n_layers: float | None = None,
+    synth_flag: bool = False,
+    thickness: float | None = None,
+    random_file: InputPathType | None = None,
+    identity_file: str | None = None,
+    runner: Runner | None = None,
+) -> MriComputeLayerFractionsOutputs:
+    """
+    This program computes volumetric partial volume fractions from laminar surfaces
+    using FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        reg_file: Input registration file.
+        input_volume: Input volume file.
+        output_stem: Output stem for generated files.
+        output_directory: Output directory specified by SUBJECTS_DIR.
+        aseg_file: Input ASEG file for synthesis.
+        target_volume: Target volume for analysis.
+        hemi_flag: Specify hemisphere processing.
+        fs_names_flag: Flag to use FreeSurfer names.
+        subject_id: Subject ID for processing.
+        n_layers: Number of layers for volume fraction computation.
+        synth_flag: Flag to combine with the ASEG for a single segmentation\
+            volume.
+        thickness: Specify cortical thickness fraction.
+        random_file: Specify random volume file.
+        identity_file: Specify identity file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriComputeLayerFractionsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_LAYER_FRACTIONS_METADATA)
+    params = mri_compute_layer_fractions_params(
+        reg_file=reg_file,
+        input_volume=input_volume,
+        output_stem=output_stem,
+        output_directory=output_directory,
+        aseg_file=aseg_file,
+        target_volume=target_volume,
+        hemi_flag=hemi_flag,
+        fs_names_flag=fs_names_flag,
+        subject_id=subject_id,
+        n_layers=n_layers,
+        synth_flag=synth_flag,
+        thickness=thickness,
+        random_file=random_file,
+        identity_file=identity_file,
+    )
+    return mri_compute_layer_fractions_execute(params, execution)
+
+
+__all__ = [
+    "MRI_COMPUTE_LAYER_FRACTIONS_METADATA",
+    "MriComputeLayerFractionsOutputs",
+    "MriComputeLayerFractionsParameters",
+    "mri_compute_layer_fractions",
+    "mri_compute_layer_fractions_params",
+]

niwrap_freesurfer/freesurfer/mri_compute_overlap.py

@@ -0,0 +1,285 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_COMPUTE_OVERLAP_METADATA = Metadata(
+    id="97d8d567d0e1c761a649f9ba5d647b7d4352a61b.boutiques",
+    name="mri_compute_overlap",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriComputeOverlapParameters = typing.TypedDict('MriComputeOverlapParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_compute_overlap"],
+    "volumes": list[InputPathType],
+    "label_numbers": typing.NotRequired[list[str] | None],
+    "all_labels": bool,
+    "show_label": bool,
+    "total_overlap": bool,
+    "no_summary": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "output_file": typing.NotRequired[str | None],
+    "quiet_mode": bool,
+    "translate_label": typing.NotRequired[list[float] | None],
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_compute_overlap": mri_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 MriComputeOverlapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_compute_overlap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_compute_overlap_params(
+    volumes: list[InputPathType],
+    label_numbers: list[str] | None = None,
+    all_labels: bool = False,
+    show_label: bool = False,
+    total_overlap: bool = False,
+    no_summary: bool = False,
+    mask: InputPathType | None = None,
+    output_file: str | None = None,
+    quiet_mode: bool = False,
+    translate_label: list[float] | None = None,
+    help_: bool = False,
+) -> MriComputeOverlapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        volumes: Input volume files for which overlap measures are computed.
+        label_numbers: List of specific label numbers for which to compute\
+            overlap measures. If not specified, all labels are considered if -a is\
+            provided.
+        all_labels: Compute overlap for all labels.
+        show_label: Show label name for segmentation.
+        total_overlap: Compute the total overlap, which is the number of voxels\
+            that are the same among all labels.
+        no_summary: Do not compute total label summary.
+        mask: Limit the domain of the calculation to the nonzero voxels in\
+            specified volume.
+        output_file: Filename to write results to.
+        quiet_mode: Do not display results on standard display. If -l is\
+            specified, this flag is automatically set.
+        translate_label: Translate label l1 to label l2.
+        help_: Print help.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_compute_overlap",
+        "volumes": volumes,
+        "all_labels": all_labels,
+        "show_label": show_label,
+        "total_overlap": total_overlap,
+        "no_summary": no_summary,
+        "quiet_mode": quiet_mode,
+        "help": help_,
+    }
+    if label_numbers is not None:
+        params["label_numbers"] = label_numbers
+    if mask is not None:
+        params["mask"] = mask
+    if output_file is not None:
+        params["output_file"] = output_file
+    if translate_label is not None:
+        params["translate_label"] = translate_label
+    return params
+
+
+def mri_compute_overlap_cargs(
+    params: MriComputeOverlapParameters,
+    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("mri_compute_overlap")
+    cargs.extend([execution.input_file(f) for f in params.get("volumes")])
+    if params.get("label_numbers") is not None:
+        cargs.extend(params.get("label_numbers"))
+    if params.get("all_labels"):
+        cargs.append("-a")
+    if params.get("show_label"):
+        cargs.append("-s")
+    if params.get("total_overlap"):
+        cargs.append("-total")
+    if params.get("no_summary"):
+        cargs.append("-nosummary")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "-l",
+            params.get("output_file")
+        ])
+    if params.get("quiet_mode"):
+        cargs.append("-q")
+    if params.get("translate_label") is not None:
+        cargs.extend([
+            "-t",
+            *map(str, params.get("translate_label"))
+        ])
+    if params.get("help"):
+        cargs.append("-h")
+    return cargs
+
+
+def mri_compute_overlap_outputs(
+    params: MriComputeOverlapParameters,
+    execution: Execution,
+) -> MriComputeOverlapOutputs:
+    """
+    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 = MriComputeOverlapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_compute_overlap_execute(
+    params: MriComputeOverlapParameters,
+    execution: Execution,
+) -> MriComputeOverlapOutputs:
+    """
+    Computes three different types of overlap measures for labels in input volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriComputeOverlapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_compute_overlap_cargs(params, execution)
+    ret = mri_compute_overlap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_compute_overlap(
+    volumes: list[InputPathType],
+    label_numbers: list[str] | None = None,
+    all_labels: bool = False,
+    show_label: bool = False,
+    total_overlap: bool = False,
+    no_summary: bool = False,
+    mask: InputPathType | None = None,
+    output_file: str | None = None,
+    quiet_mode: bool = False,
+    translate_label: list[float] | None = None,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> MriComputeOverlapOutputs:
+    """
+    Computes three different types of overlap measures for labels in input volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        volumes: Input volume files for which overlap measures are computed.
+        label_numbers: List of specific label numbers for which to compute\
+            overlap measures. If not specified, all labels are considered if -a is\
+            provided.
+        all_labels: Compute overlap for all labels.
+        show_label: Show label name for segmentation.
+        total_overlap: Compute the total overlap, which is the number of voxels\
+            that are the same among all labels.
+        no_summary: Do not compute total label summary.
+        mask: Limit the domain of the calculation to the nonzero voxels in\
+            specified volume.
+        output_file: Filename to write results to.
+        quiet_mode: Do not display results on standard display. If -l is\
+            specified, this flag is automatically set.
+        translate_label: Translate label l1 to label l2.
+        help_: Print help.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriComputeOverlapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_OVERLAP_METADATA)
+    params = mri_compute_overlap_params(
+        volumes=volumes,
+        label_numbers=label_numbers,
+        all_labels=all_labels,
+        show_label=show_label,
+        total_overlap=total_overlap,
+        no_summary=no_summary,
+        mask=mask,
+        output_file=output_file,
+        quiet_mode=quiet_mode,
+        translate_label=translate_label,
+        help_=help_,
+    )
+    return mri_compute_overlap_execute(params, execution)
+
+
+__all__ = [
+    "MRI_COMPUTE_OVERLAP_METADATA",
+    "MriComputeOverlapOutputs",
+    "MriComputeOverlapParameters",
+    "mri_compute_overlap",
+    "mri_compute_overlap_params",
+]