niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_extract.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 *
+
+MRI_EXTRACT_METADATA = Metadata(
+    id="8ea8492114a69493e6fb6d2e1d9f2b2b63d51237.boutiques",
+    name="mri_extract",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriExtractParameters = typing.TypedDict('MriExtractParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_extract"],
+    "like_template": typing.NotRequired[InputPathType | None],
+    "src_volume": InputPathType,
+    "dst_volume": InputPathType,
+    "coordinates": typing.NotRequired[list[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 {
+        "mri_extract": mri_extract_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_extract": mri_extract_outputs,
+    }.get(t)
+
+
+class MriExtractOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_extract(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_extracted_volume: OutputPathType
+    """Output file with extracted MRI data."""
+
+
+def mri_extract_params(
+    src_volume: InputPathType,
+    dst_volume: InputPathType,
+    like_template: InputPathType | None = None,
+    coordinates: list[float] | None = None,
+) -> MriExtractParameters:
+    """
+    Build parameters.
+    
+    Args:
+        src_volume: Source MRI volume file from which data will be extracted.
+        dst_volume: The destination file where the extracted data will be\
+            saved.
+        like_template: Extract region like the given template volume.
+        coordinates: Coordinates and size of the extraction box: x0 y0 z0 dx dy\
+            dz.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_extract",
+        "src_volume": src_volume,
+        "dst_volume": dst_volume,
+    }
+    if like_template is not None:
+        params["like_template"] = like_template
+    if coordinates is not None:
+        params["coordinates"] = coordinates
+    return params
+
+
+def mri_extract_cargs(
+    params: MriExtractParameters,
+    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_extract")
+    if params.get("like_template") is not None:
+        cargs.extend([
+            "-like",
+            execution.input_file(params.get("like_template"))
+        ])
+    cargs.append(execution.input_file(params.get("src_volume")))
+    cargs.append(execution.input_file(params.get("dst_volume")))
+    if params.get("coordinates") is not None:
+        cargs.extend(map(str, params.get("coordinates")))
+    return cargs
+
+
+def mri_extract_outputs(
+    params: MriExtractParameters,
+    execution: Execution,
+) -> MriExtractOutputs:
+    """
+    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 = MriExtractOutputs(
+        root=execution.output_file("."),
+        output_extracted_volume=execution.output_file(pathlib.Path(params.get("dst_volume")).name),
+    )
+    return ret
+
+
+def mri_extract_execute(
+    params: MriExtractParameters,
+    execution: Execution,
+) -> MriExtractOutputs:
+    """
+    MRI data extraction tool for FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriExtractOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_extract_cargs(params, execution)
+    ret = mri_extract_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_extract(
+    src_volume: InputPathType,
+    dst_volume: InputPathType,
+    like_template: InputPathType | None = None,
+    coordinates: list[float] | None = None,
+    runner: Runner | None = None,
+) -> MriExtractOutputs:
+    """
+    MRI data extraction tool for FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        src_volume: Source MRI volume file from which data will be extracted.
+        dst_volume: The destination file where the extracted data will be\
+            saved.
+        like_template: Extract region like the given template volume.
+        coordinates: Coordinates and size of the extraction box: x0 y0 z0 dx dy\
+            dz.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriExtractOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXTRACT_METADATA)
+    params = mri_extract_params(
+        like_template=like_template,
+        src_volume=src_volume,
+        dst_volume=dst_volume,
+        coordinates=coordinates,
+    )
+    return mri_extract_execute(params, execution)
+
+
+__all__ = [
+    "MRI_EXTRACT_METADATA",
+    "MriExtractOutputs",
+    "MriExtractParameters",
+    "mri_extract",
+    "mri_extract_params",
+]

niwrap_freesurfer/freesurfer/mri_extract_fcd_features.py

@@ -0,0 +1,203 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_EXTRACT_FCD_FEATURES_METADATA = Metadata(
+    id="4dc97ce09339ae602c500d2ce62f291dceb53709.boutiques",
+    name="mri_extract_fcd_features",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriExtractFcdFeaturesParameters = typing.TypedDict('MriExtractFcdFeaturesParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_extract_fcd_features"],
+    "subject": str,
+    "hemi": str,
+    "output_file": InputPathType,
+    "subjects_dir": 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_extract_fcd_features": mri_extract_fcd_features_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 MriExtractFcdFeaturesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_extract_fcd_features(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_extract_fcd_features_params(
+    subject: str,
+    hemi: str,
+    output_file: InputPathType,
+    subjects_dir: str | None = None,
+) -> MriExtractFcdFeaturesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject: The subject identifier.
+        hemi: The hemisphere (e.g., lh or rh).
+        output_file: Output file path.
+        subjects_dir: Specify SUBJECTS_DIR on the command line instead of in\
+            the environment.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_extract_fcd_features",
+        "subject": subject,
+        "hemi": hemi,
+        "output_file": output_file,
+    }
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    return params
+
+
+def mri_extract_fcd_features_cargs(
+    params: MriExtractFcdFeaturesParameters,
+    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_extract_fcd_features")
+    cargs.append(params.get("subject"))
+    cargs.append(params.get("hemi"))
+    cargs.append(execution.input_file(params.get("output_file")))
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "sdir",
+            params.get("subjects_dir")
+        ])
+    return cargs
+
+
+def mri_extract_fcd_features_outputs(
+    params: MriExtractFcdFeaturesParameters,
+    execution: Execution,
+) -> MriExtractFcdFeaturesOutputs:
+    """
+    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 = MriExtractFcdFeaturesOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_extract_fcd_features_execute(
+    params: MriExtractFcdFeaturesParameters,
+    execution: Execution,
+) -> MriExtractFcdFeaturesOutputs:
+    """
+    A tool for extracting focal cortical dysplasia features.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriExtractFcdFeaturesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_extract_fcd_features_cargs(params, execution)
+    ret = mri_extract_fcd_features_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_extract_fcd_features(
+    subject: str,
+    hemi: str,
+    output_file: InputPathType,
+    subjects_dir: str | None = None,
+    runner: Runner | None = None,
+) -> MriExtractFcdFeaturesOutputs:
+    """
+    A tool for extracting focal cortical dysplasia features.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject: The subject identifier.
+        hemi: The hemisphere (e.g., lh or rh).
+        output_file: Output file path.
+        subjects_dir: Specify SUBJECTS_DIR on the command line instead of in\
+            the environment.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriExtractFcdFeaturesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXTRACT_FCD_FEATURES_METADATA)
+    params = mri_extract_fcd_features_params(
+        subject=subject,
+        hemi=hemi,
+        output_file=output_file,
+        subjects_dir=subjects_dir,
+    )
+    return mri_extract_fcd_features_execute(params, execution)
+
+
+__all__ = [
+    "MRI_EXTRACT_FCD_FEATURES_METADATA",
+    "MriExtractFcdFeaturesOutputs",
+    "MriExtractFcdFeaturesParameters",
+    "mri_extract_fcd_features",
+    "mri_extract_fcd_features_params",
+]

niwrap_freesurfer/freesurfer/mri_extract_label.py

@@ -0,0 +1,257 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_EXTRACT_LABEL_METADATA = Metadata(
+    id="0b9620a7206508bacb4685ef0d5ac119a68d3dd9.boutiques",
+    name="mri_extract_label",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriExtractLabelParameters = typing.TypedDict('MriExtractLabelParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_extract_label"],
+    "input_volume": InputPathType,
+    "labels": list[str],
+    "output_name": str,
+    "gaussian_smoothing": typing.NotRequired[float | None],
+    "transform_file": typing.NotRequired[InputPathType | None],
+    "exit_none_found": bool,
+    "dilate": typing.NotRequired[float | None],
+    "erode": 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 {
+        "mri_extract_label": mri_extract_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 {
+        "mri_extract_label": mri_extract_label_outputs,
+    }.get(t)
+
+
+class MriExtractLabelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_extract_label(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume: OutputPathType
+    """Extracted labeled voxels output volume."""
+
+
+def mri_extract_label_params(
+    input_volume: InputPathType,
+    labels: list[str],
+    output_name: str,
+    gaussian_smoothing: float | None = None,
+    transform_file: InputPathType | None = None,
+    exit_none_found: bool = False,
+    dilate: float | None = None,
+    erode: float | None = None,
+) -> MriExtractLabelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volume: Input volume from which to extract labels.
+        labels: Labels to extract. Can include one or more labels.
+        output_name: Name of the output file.
+        gaussian_smoothing: Apply a Gaussian smoothing kernel with sigma.
+        transform_file: Apply the transform in xform file to the extracted\
+            volume.
+        exit_none_found: Exit with error if none of the specified labels are\
+            found.
+        dilate: Dilate the output volume n times.
+        erode: Erode the output volume n times.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_extract_label",
+        "input_volume": input_volume,
+        "labels": labels,
+        "output_name": output_name,
+        "exit_none_found": exit_none_found,
+    }
+    if gaussian_smoothing is not None:
+        params["gaussian_smoothing"] = gaussian_smoothing
+    if transform_file is not None:
+        params["transform_file"] = transform_file
+    if dilate is not None:
+        params["dilate"] = dilate
+    if erode is not None:
+        params["erode"] = erode
+    return params
+
+
+def mri_extract_label_cargs(
+    params: MriExtractLabelParameters,
+    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_extract_label")
+    cargs.append(execution.input_file(params.get("input_volume")))
+    cargs.extend(params.get("labels"))
+    cargs.append(params.get("output_name"))
+    if params.get("gaussian_smoothing") is not None:
+        cargs.extend([
+            "-s",
+            str(params.get("gaussian_smoothing"))
+        ])
+    if params.get("transform_file") is not None:
+        cargs.extend([
+            "-t",
+            execution.input_file(params.get("transform_file"))
+        ])
+    if params.get("exit_none_found"):
+        cargs.append("-exit_none_found")
+    if params.get("dilate") is not None:
+        cargs.extend([
+            "-dilate",
+            str(params.get("dilate"))
+        ])
+    if params.get("erode") is not None:
+        cargs.extend([
+            "-erode",
+            str(params.get("erode"))
+        ])
+    return cargs
+
+
+def mri_extract_label_outputs(
+    params: MriExtractLabelParameters,
+    execution: Execution,
+) -> MriExtractLabelOutputs:
+    """
+    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 = MriExtractLabelOutputs(
+        root=execution.output_file("."),
+        output_volume=execution.output_file(params.get("output_name")),
+    )
+    return ret
+
+
+def mri_extract_label_execute(
+    params: MriExtractLabelParameters,
+    execution: Execution,
+) -> MriExtractLabelOutputs:
+    """
+    Extracts a set of labeled voxels from an image.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriExtractLabelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_extract_label_cargs(params, execution)
+    ret = mri_extract_label_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_extract_label(
+    input_volume: InputPathType,
+    labels: list[str],
+    output_name: str,
+    gaussian_smoothing: float | None = None,
+    transform_file: InputPathType | None = None,
+    exit_none_found: bool = False,
+    dilate: float | None = None,
+    erode: float | None = None,
+    runner: Runner | None = None,
+) -> MriExtractLabelOutputs:
+    """
+    Extracts a set of labeled voxels from an image.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volume: Input volume from which to extract labels.
+        labels: Labels to extract. Can include one or more labels.
+        output_name: Name of the output file.
+        gaussian_smoothing: Apply a Gaussian smoothing kernel with sigma.
+        transform_file: Apply the transform in xform file to the extracted\
+            volume.
+        exit_none_found: Exit with error if none of the specified labels are\
+            found.
+        dilate: Dilate the output volume n times.
+        erode: Erode the output volume n times.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriExtractLabelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXTRACT_LABEL_METADATA)
+    params = mri_extract_label_params(
+        input_volume=input_volume,
+        labels=labels,
+        output_name=output_name,
+        gaussian_smoothing=gaussian_smoothing,
+        transform_file=transform_file,
+        exit_none_found=exit_none_found,
+        dilate=dilate,
+        erode=erode,
+    )
+    return mri_extract_label_execute(params, execution)
+
+
+__all__ = [
+    "MRI_EXTRACT_LABEL_METADATA",
+    "MriExtractLabelOutputs",
+    "MriExtractLabelParameters",
+    "mri_extract_label",
+    "mri_extract_label_params",
+]