niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_synthseg.py

@@ -0,0 +1,334 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SYNTHSEG_METADATA = Metadata(
+    id="576c0067650470dbfa8631765aae242b35b3480b.boutiques",
+    name="mri_synthseg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSynthsegParameters = typing.TypedDict('MriSynthsegParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_synthseg"],
+    "input_image": InputPathType,
+    "output_segmentation": str,
+    "cortex_parcellation": bool,
+    "robust_prediction": bool,
+    "fast_prediction": bool,
+    "clip_ct": bool,
+    "output_volume": typing.NotRequired[str | None],
+    "output_qc": typing.NotRequired[str | None],
+    "output_posteriors": typing.NotRequired[str | None],
+    "resampled_images": typing.NotRequired[str | None],
+    "image_patch_size": typing.NotRequired[list[float] | None],
+    "threads": typing.NotRequired[float | None],
+    "cpu": bool,
+    "version_1": bool,
+    "photo_synthseg": 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_synthseg": mri_synthseg_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_synthseg": mri_synthseg_outputs,
+    }.get(t)
+
+
+class MriSynthsegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_synthseg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_segmentation_file: OutputPathType
+    """Segmentation output(s)"""
+    output_volume_csv: OutputPathType | None
+    """CSV file with volumes for all structures and subjects"""
+    output_qc_csv: OutputPathType | None
+    """CSV file with QC scores for all subjects"""
+    output_posteriors_file: OutputPathType | None
+    """Posteriors output(s)"""
+    resampled_images_file: OutputPathType | None
+    """Resampled image(s)"""
+
+
+def mri_synthseg_params(
+    input_image: InputPathType,
+    output_segmentation: str,
+    cortex_parcellation: bool = False,
+    robust_prediction: bool = False,
+    fast_prediction: bool = False,
+    clip_ct: bool = False,
+    output_volume: str | None = None,
+    output_qc: str | None = None,
+    output_posteriors: str | None = None,
+    resampled_images: str | None = None,
+    image_patch_size: list[float] | None = None,
+    threads: float | None = None,
+    cpu: bool = False,
+    version_1: bool = False,
+    photo_synthseg: str | None = None,
+) -> MriSynthsegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: Image(s) to segment. Can be a path to an image or to a\
+            folder.
+        output_segmentation: Segmentation output(s). Must be a folder if --i\
+            designates a folder.
+        cortex_parcellation: Perform cortex parcellation.
+        robust_prediction: Use robust predictions (slower).
+        fast_prediction: Bypass some processing for faster prediction.
+        clip_ct: Clip CT scans in Hounsfield scale to [0, 80].
+        output_volume: Output CSV file with volumes for all structures and\
+            subjects.
+        output_qc: Output CSV file with QC scores for all subjects.
+        output_posteriors: Posteriors output(s). Must be a folder if --i\
+            designates a folder.
+        resampled_images: Resampled image(s). Must be a folder if --i is a\
+            folder.
+        image_patch_size: Only analyse an image patch of the given size.
+        threads: Number of cores to be used. Default is 1.
+        cpu: Enforce running with CPU rather than GPU.
+        version_1: Use SynthSeg 1.0 (updated 25/06/22).
+        photo_synthseg: Photo-SynthSeg: segment 3D reconstructed stack of\
+            coronal dissection photos of the cerebrum; must be left, right, or\
+            both.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_synthseg",
+        "input_image": input_image,
+        "output_segmentation": output_segmentation,
+        "cortex_parcellation": cortex_parcellation,
+        "robust_prediction": robust_prediction,
+        "fast_prediction": fast_prediction,
+        "clip_ct": clip_ct,
+        "cpu": cpu,
+        "version_1": version_1,
+    }
+    if output_volume is not None:
+        params["output_volume"] = output_volume
+    if output_qc is not None:
+        params["output_qc"] = output_qc
+    if output_posteriors is not None:
+        params["output_posteriors"] = output_posteriors
+    if resampled_images is not None:
+        params["resampled_images"] = resampled_images
+    if image_patch_size is not None:
+        params["image_patch_size"] = image_patch_size
+    if threads is not None:
+        params["threads"] = threads
+    if photo_synthseg is not None:
+        params["photo_synthseg"] = photo_synthseg
+    return params
+
+
+def mri_synthseg_cargs(
+    params: MriSynthsegParameters,
+    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_synthseg")
+    cargs.append(execution.input_file(params.get("input_image")))
+    cargs.append(params.get("output_segmentation"))
+    if params.get("cortex_parcellation"):
+        cargs.append("--parc")
+    if params.get("robust_prediction"):
+        cargs.append("--robust")
+    if params.get("fast_prediction"):
+        cargs.append("--fast")
+    if params.get("clip_ct"):
+        cargs.append("--ct")
+    if params.get("output_volume") is not None:
+        cargs.append(params.get("output_volume"))
+    if params.get("output_qc") is not None:
+        cargs.append(params.get("output_qc"))
+    if params.get("output_posteriors") is not None:
+        cargs.append(params.get("output_posteriors"))
+    if params.get("resampled_images") is not None:
+        cargs.append(params.get("resampled_images"))
+    if params.get("image_patch_size") is not None:
+        cargs.extend(map(str, params.get("image_patch_size")))
+    if params.get("threads") is not None:
+        cargs.append(str(params.get("threads")))
+    if params.get("cpu"):
+        cargs.append("--cpu")
+    if params.get("version_1"):
+        cargs.append("--v1")
+    if params.get("photo_synthseg") is not None:
+        cargs.append(params.get("photo_synthseg"))
+    return cargs
+
+
+def mri_synthseg_outputs(
+    params: MriSynthsegParameters,
+    execution: Execution,
+) -> MriSynthsegOutputs:
+    """
+    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 = MriSynthsegOutputs(
+        root=execution.output_file("."),
+        output_segmentation_file=execution.output_file(params.get("output_segmentation")),
+        output_volume_csv=execution.output_file(params.get("output_volume")) if (params.get("output_volume") is not None) else None,
+        output_qc_csv=execution.output_file(params.get("output_qc")) if (params.get("output_qc") is not None) else None,
+        output_posteriors_file=execution.output_file(params.get("output_posteriors")) if (params.get("output_posteriors") is not None) else None,
+        resampled_images_file=execution.output_file(params.get("resampled_images")) if (params.get("resampled_images") is not None) else None,
+    )
+    return ret
+
+
+def mri_synthseg_execute(
+    params: MriSynthsegParameters,
+    execution: Execution,
+) -> MriSynthsegOutputs:
+    """
+    SynthSeg is a tool for brain image segmentation.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSynthsegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_synthseg_cargs(params, execution)
+    ret = mri_synthseg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_synthseg(
+    input_image: InputPathType,
+    output_segmentation: str,
+    cortex_parcellation: bool = False,
+    robust_prediction: bool = False,
+    fast_prediction: bool = False,
+    clip_ct: bool = False,
+    output_volume: str | None = None,
+    output_qc: str | None = None,
+    output_posteriors: str | None = None,
+    resampled_images: str | None = None,
+    image_patch_size: list[float] | None = None,
+    threads: float | None = None,
+    cpu: bool = False,
+    version_1: bool = False,
+    photo_synthseg: str | None = None,
+    runner: Runner | None = None,
+) -> MriSynthsegOutputs:
+    """
+    SynthSeg is a tool for brain image segmentation.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_image: Image(s) to segment. Can be a path to an image or to a\
+            folder.
+        output_segmentation: Segmentation output(s). Must be a folder if --i\
+            designates a folder.
+        cortex_parcellation: Perform cortex parcellation.
+        robust_prediction: Use robust predictions (slower).
+        fast_prediction: Bypass some processing for faster prediction.
+        clip_ct: Clip CT scans in Hounsfield scale to [0, 80].
+        output_volume: Output CSV file with volumes for all structures and\
+            subjects.
+        output_qc: Output CSV file with QC scores for all subjects.
+        output_posteriors: Posteriors output(s). Must be a folder if --i\
+            designates a folder.
+        resampled_images: Resampled image(s). Must be a folder if --i is a\
+            folder.
+        image_patch_size: Only analyse an image patch of the given size.
+        threads: Number of cores to be used. Default is 1.
+        cpu: Enforce running with CPU rather than GPU.
+        version_1: Use SynthSeg 1.0 (updated 25/06/22).
+        photo_synthseg: Photo-SynthSeg: segment 3D reconstructed stack of\
+            coronal dissection photos of the cerebrum; must be left, right, or\
+            both.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSynthsegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SYNTHSEG_METADATA)
+    params = mri_synthseg_params(
+        input_image=input_image,
+        output_segmentation=output_segmentation,
+        cortex_parcellation=cortex_parcellation,
+        robust_prediction=robust_prediction,
+        fast_prediction=fast_prediction,
+        clip_ct=clip_ct,
+        output_volume=output_volume,
+        output_qc=output_qc,
+        output_posteriors=output_posteriors,
+        resampled_images=resampled_images,
+        image_patch_size=image_patch_size,
+        threads=threads,
+        cpu=cpu,
+        version_1=version_1,
+        photo_synthseg=photo_synthseg,
+    )
+    return mri_synthseg_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SYNTHSEG_METADATA",
+    "MriSynthsegOutputs",
+    "MriSynthsegParameters",
+    "mri_synthseg",
+    "mri_synthseg_params",
+]

niwrap_freesurfer/freesurfer/mri_synthsr.py

@@ -0,0 +1,272 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SYNTHSR_METADATA = Metadata(
+    id="eb82e2176f14f70334dc8bcaf770b81e214106e0.boutiques",
+    name="mri_synthsr",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSynthsrParameters = typing.TypedDict('MriSynthsrParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_synthsr"],
+    "input": str,
+    "output": str,
+    "ct": bool,
+    "disable_sharpening": bool,
+    "disable_flipping": bool,
+    "lowfield": bool,
+    "v1": bool,
+    "threads": typing.NotRequired[float | None],
+    "cpu": bool,
+    "model": 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_synthsr": mri_synthsr_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 MriSynthsrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_synthsr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_synthsr_params(
+    input_: str,
+    output: str,
+    ct: bool = False,
+    disable_sharpening: bool = False,
+    disable_flipping: bool = False,
+    lowfield: bool = False,
+    v1: bool = False,
+    threads: float | None = None,
+    cpu: bool = False,
+    model: str | None = None,
+) -> MriSynthsrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Image(s) to super-resolve. Can be a path to an image or to a\
+            folder.
+        output: Output(s), i.e., synthetic 1mm MP-RAGE(s). Must be a folder if\
+            input is a folder.
+        ct: Use this flag for CT scans in Hounsfield scale, it clips\
+            intensities to [0,80].
+        disable_sharpening: Use this flag to disable unsharp masking.
+        disable_flipping: Use this flag to disable flipping augmentation at\
+            test time.
+        lowfield: Use model for low-field scans (e.g., acquired with\
+            Hyperfine's Swoop scanner).
+        v1: Use version 1 model from July 2021.
+        threads: Number of cores to be used. Default is 1.
+        cpu: Enforce running with CPU rather than GPU.
+        model: Use a different model file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_synthsr",
+        "input": input_,
+        "output": output,
+        "ct": ct,
+        "disable_sharpening": disable_sharpening,
+        "disable_flipping": disable_flipping,
+        "lowfield": lowfield,
+        "v1": v1,
+        "cpu": cpu,
+    }
+    if threads is not None:
+        params["threads"] = threads
+    if model is not None:
+        params["model"] = model
+    return params
+
+
+def mri_synthsr_cargs(
+    params: MriSynthsrParameters,
+    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_synthsr")
+    cargs.append(params.get("input"))
+    cargs.append(params.get("output"))
+    if params.get("ct"):
+        cargs.append("--ct")
+    if params.get("disable_sharpening"):
+        cargs.append("--disable_sharpening")
+    if params.get("disable_flipping"):
+        cargs.append("--disable_flipping")
+    if params.get("lowfield"):
+        cargs.append("--lowfield")
+    if params.get("v1"):
+        cargs.append("--v1")
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("cpu"):
+        cargs.append("--cpu")
+    if params.get("model") is not None:
+        cargs.extend([
+            "--model",
+            params.get("model")
+        ])
+    return cargs
+
+
+def mri_synthsr_outputs(
+    params: MriSynthsrParameters,
+    execution: Execution,
+) -> MriSynthsrOutputs:
+    """
+    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 = MriSynthsrOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_synthsr_execute(
+    params: MriSynthsrParameters,
+    execution: Execution,
+) -> MriSynthsrOutputs:
+    """
+    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a scan of
+    any contrast and resolution.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSynthsrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_synthsr_cargs(params, execution)
+    ret = mri_synthsr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_synthsr(
+    input_: str,
+    output: str,
+    ct: bool = False,
+    disable_sharpening: bool = False,
+    disable_flipping: bool = False,
+    lowfield: bool = False,
+    v1: bool = False,
+    threads: float | None = None,
+    cpu: bool = False,
+    model: str | None = None,
+    runner: Runner | None = None,
+) -> MriSynthsrOutputs:
+    """
+    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a scan of
+    any contrast and resolution.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_: Image(s) to super-resolve. Can be a path to an image or to a\
+            folder.
+        output: Output(s), i.e., synthetic 1mm MP-RAGE(s). Must be a folder if\
+            input is a folder.
+        ct: Use this flag for CT scans in Hounsfield scale, it clips\
+            intensities to [0,80].
+        disable_sharpening: Use this flag to disable unsharp masking.
+        disable_flipping: Use this flag to disable flipping augmentation at\
+            test time.
+        lowfield: Use model for low-field scans (e.g., acquired with\
+            Hyperfine's Swoop scanner).
+        v1: Use version 1 model from July 2021.
+        threads: Number of cores to be used. Default is 1.
+        cpu: Enforce running with CPU rather than GPU.
+        model: Use a different model file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSynthsrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SYNTHSR_METADATA)
+    params = mri_synthsr_params(
+        input_=input_,
+        output=output,
+        ct=ct,
+        disable_sharpening=disable_sharpening,
+        disable_flipping=disable_flipping,
+        lowfield=lowfield,
+        v1=v1,
+        threads=threads,
+        cpu=cpu,
+        model=model,
+    )
+    return mri_synthsr_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SYNTHSR_METADATA",
+    "MriSynthsrOutputs",
+    "MriSynthsrParameters",
+    "mri_synthsr",
+    "mri_synthsr_params",
+]