niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_segment_hypothalamic_subunits.py

@@ -0,0 +1,336 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SEGMENT_HYPOTHALAMIC_SUBUNITS_METADATA = Metadata(
+    id="f03ac3b7165171b1e5dc19884858113ebce6c791.boutiques",
+    name="mri_segment_hypothalamic_subunits",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSegmentHypothalamicSubunitsParameters = typing.TypedDict('MriSegmentHypothalamicSubunitsParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_segment_hypothalamic_subunits"],
+    "subjects": typing.NotRequired[list[str] | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "write_posteriors": bool,
+    "image_input": typing.NotRequired[str | None],
+    "output": typing.NotRequired[str | None],
+    "posteriors": typing.NotRequired[str | None],
+    "resample": typing.NotRequired[str | None],
+    "volume_output": typing.NotRequired[str | None],
+    "crop_size": typing.NotRequired[list[float] | None],
+    "threads": typing.NotRequired[float | None],
+    "cpu": 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_segment_hypothalamic_subunits": mri_segment_hypothalamic_subunits_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_segment_hypothalamic_subunits": mri_segment_hypothalamic_subunits_outputs,
+    }.get(t)
+
+
+class MriSegmentHypothalamicSubunitsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_segment_hypothalamic_subunits(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    segmentation_output_files: OutputPathType | None
+    """Segmentation output(s) in T1 mode."""
+    posteriors_output: OutputPathType | None
+    """Posteriors output(s)."""
+    resampled_output: OutputPathType | None
+    """Resampled image(s) output."""
+    volume_output_csv: OutputPathType | None
+    """CSV file with volumes for all structures and subjects."""
+
+
+def mri_segment_hypothalamic_subunits_params(
+    subjects: list[str] | None = None,
+    subjects_dir: str | None = None,
+    write_posteriors: bool = False,
+    image_input: str | None = None,
+    output: str | None = None,
+    posteriors: str | None = None,
+    resample: str | None = None,
+    volume_output: str | None = None,
+    crop_size: list[float] | None = None,
+    threads: float | None = None,
+    cpu: bool = False,
+) -> MriSegmentHypothalamicSubunitsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjects: (required in FS mode) Name of one or several subjects in\
+            $SUBJECTS_DIR on which to run the module, assuming recon-all has been\
+            run on the specified subjects.
+        subjects_dir: (FS mode, optional) Override current $SUBJECTS_DIR.
+        write_posteriors: (FS mode, optional) Save posteriors; default is\
+            False.
+        image_input: (required in T1 mode) Image(s) to segment. Can be a path\
+            to a single image or to a folder.
+        output: (required in T1 mode) Segmentation output(s). Must be a folder\
+            if --i designates a folder.
+        posteriors: (T1 mode, optional) Posteriors output(s). Must be a folder\
+            if --i designates a folder.
+        resample: (T1 mode, optional) Resampled image(s). Must be a folder if\
+            --i designates a folder.
+        volume_output: (T1 mode, optional) Output CSV file with volumes for all\
+            structures and subjects.
+        crop_size: (both modes, optional) Size of the central patch to analyse\
+            (must be divisible by 8). The whole image is analysed by default.
+        threads: (both modes, optional) Number of cores to be used. Default\
+            uses 1 core.
+        cpu: (both modes, optional) Enforce running with CPU rather than GPU.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_segment_hypothalamic_subunits",
+        "write_posteriors": write_posteriors,
+        "cpu": cpu,
+    }
+    if subjects is not None:
+        params["subjects"] = subjects
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if image_input is not None:
+        params["image_input"] = image_input
+    if output is not None:
+        params["output"] = output
+    if posteriors is not None:
+        params["posteriors"] = posteriors
+    if resample is not None:
+        params["resample"] = resample
+    if volume_output is not None:
+        params["volume_output"] = volume_output
+    if crop_size is not None:
+        params["crop_size"] = crop_size
+    if threads is not None:
+        params["threads"] = threads
+    return params
+
+
+def mri_segment_hypothalamic_subunits_cargs(
+    params: MriSegmentHypothalamicSubunitsParameters,
+    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_segment_hypothalamic_subunits")
+    if params.get("subjects") is not None:
+        cargs.extend([
+            "--s",
+            *params.get("subjects")
+        ])
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subjects_dir")
+        ])
+    if params.get("write_posteriors"):
+        cargs.append("--write_posteriors")
+    if params.get("image_input") is not None:
+        cargs.extend([
+            "--i",
+            params.get("image_input")
+        ])
+    if params.get("output") is not None:
+        cargs.extend([
+            "--o",
+            params.get("output")
+        ])
+    if params.get("posteriors") is not None:
+        cargs.extend([
+            "--post",
+            params.get("posteriors")
+        ])
+    if params.get("resample") is not None:
+        cargs.extend([
+            "--resample",
+            params.get("resample")
+        ])
+    if params.get("volume_output") is not None:
+        cargs.extend([
+            "--vol",
+            params.get("volume_output")
+        ])
+    if params.get("crop_size") is not None:
+        cargs.extend([
+            "--crop",
+            *map(str, params.get("crop_size"))
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("cpu"):
+        cargs.append("--cpu")
+    return cargs
+
+
+def mri_segment_hypothalamic_subunits_outputs(
+    params: MriSegmentHypothalamicSubunitsParameters,
+    execution: Execution,
+) -> MriSegmentHypothalamicSubunitsOutputs:
+    """
+    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 = MriSegmentHypothalamicSubunitsOutputs(
+        root=execution.output_file("."),
+        segmentation_output_files=execution.output_file(params.get("output")) if (params.get("output") is not None) else None,
+        posteriors_output=execution.output_file(params.get("posteriors")) if (params.get("posteriors") is not None) else None,
+        resampled_output=execution.output_file(params.get("resample")) if (params.get("resample") is not None) else None,
+        volume_output_csv=execution.output_file(params.get("volume_output")) if (params.get("volume_output") is not None) else None,
+    )
+    return ret
+
+
+def mri_segment_hypothalamic_subunits_execute(
+    params: MriSegmentHypothalamicSubunitsParameters,
+    execution: Execution,
+) -> MriSegmentHypothalamicSubunitsOutputs:
+    """
+    This module segments hypothalamic subunits and can be run in two modes: on
+    FreeSurfer subjects or on any T1-weighted scan(s) of approximately 1mm
+    resolution.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSegmentHypothalamicSubunitsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_segment_hypothalamic_subunits_cargs(params, execution)
+    ret = mri_segment_hypothalamic_subunits_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_segment_hypothalamic_subunits(
+    subjects: list[str] | None = None,
+    subjects_dir: str | None = None,
+    write_posteriors: bool = False,
+    image_input: str | None = None,
+    output: str | None = None,
+    posteriors: str | None = None,
+    resample: str | None = None,
+    volume_output: str | None = None,
+    crop_size: list[float] | None = None,
+    threads: float | None = None,
+    cpu: bool = False,
+    runner: Runner | None = None,
+) -> MriSegmentHypothalamicSubunitsOutputs:
+    """
+    This module segments hypothalamic subunits and can be run in two modes: on
+    FreeSurfer subjects or on any T1-weighted scan(s) of approximately 1mm
+    resolution.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjects: (required in FS mode) Name of one or several subjects in\
+            $SUBJECTS_DIR on which to run the module, assuming recon-all has been\
+            run on the specified subjects.
+        subjects_dir: (FS mode, optional) Override current $SUBJECTS_DIR.
+        write_posteriors: (FS mode, optional) Save posteriors; default is\
+            False.
+        image_input: (required in T1 mode) Image(s) to segment. Can be a path\
+            to a single image or to a folder.
+        output: (required in T1 mode) Segmentation output(s). Must be a folder\
+            if --i designates a folder.
+        posteriors: (T1 mode, optional) Posteriors output(s). Must be a folder\
+            if --i designates a folder.
+        resample: (T1 mode, optional) Resampled image(s). Must be a folder if\
+            --i designates a folder.
+        volume_output: (T1 mode, optional) Output CSV file with volumes for all\
+            structures and subjects.
+        crop_size: (both modes, optional) Size of the central patch to analyse\
+            (must be divisible by 8). The whole image is analysed by default.
+        threads: (both modes, optional) Number of cores to be used. Default\
+            uses 1 core.
+        cpu: (both modes, optional) Enforce running with CPU rather than GPU.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSegmentHypothalamicSubunitsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SEGMENT_HYPOTHALAMIC_SUBUNITS_METADATA)
+    params = mri_segment_hypothalamic_subunits_params(
+        subjects=subjects,
+        subjects_dir=subjects_dir,
+        write_posteriors=write_posteriors,
+        image_input=image_input,
+        output=output,
+        posteriors=posteriors,
+        resample=resample,
+        volume_output=volume_output,
+        crop_size=crop_size,
+        threads=threads,
+        cpu=cpu,
+    )
+    return mri_segment_hypothalamic_subunits_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SEGMENT_HYPOTHALAMIC_SUBUNITS_METADATA",
+    "MriSegmentHypothalamicSubunitsOutputs",
+    "MriSegmentHypothalamicSubunitsParameters",
+    "mri_segment_hypothalamic_subunits",
+    "mri_segment_hypothalamic_subunits_params",
+]

niwrap_freesurfer/freesurfer/mri_segment_thalamic_nuclei_dti_cnn.py

@@ -0,0 +1,298 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SEGMENT_THALAMIC_NUCLEI_DTI_CNN_METADATA = Metadata(
+    id="f630b8f89597694e7e554e66b7fcc460b26de43a.boutiques",
+    name="mri_segment_thalamic_nuclei_dti_cnn",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSegmentThalamicNucleiDtiCnnParameters = typing.TypedDict('MriSegmentThalamicNucleiDtiCnnParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_segment_thalamic_nuclei_dti_cnn"],
+    "t1_images": InputPathType,
+    "aseg": typing.NotRequired[InputPathType | None],
+    "fa": InputPathType,
+    "v1": InputPathType,
+    "output": str,
+    "volume_output": typing.NotRequired[str | None],
+    "posteriors_output": typing.NotRequired[str | None],
+    "threads": typing.NotRequired[float | None],
+    "force_cpu": bool,
+    "model": 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 {
+        "mri_segment_thalamic_nuclei_dti_cnn": mri_segment_thalamic_nuclei_dti_cnn_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_segment_thalamic_nuclei_dti_cnn": mri_segment_thalamic_nuclei_dti_cnn_outputs,
+    }.get(t)
+
+
+class MriSegmentThalamicNucleiDtiCnnOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_segment_thalamic_nuclei_dti_cnn(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    segmentation_output: OutputPathType
+    """Path to the segmentation output."""
+    volume_csv: OutputPathType | None
+    """CSV file with volumes for all structures."""
+    posteriors: OutputPathType | None
+    """Path to the posteriors output."""
+
+
+def mri_segment_thalamic_nuclei_dti_cnn_params(
+    t1_images: InputPathType,
+    fa: InputPathType,
+    v1: InputPathType,
+    output: str,
+    aseg: InputPathType | None = None,
+    volume_output: str | None = None,
+    posteriors_output: str | None = None,
+    threads: float | None = None,
+    force_cpu: bool = False,
+    model: InputPathType | None = None,
+) -> MriSegmentThalamicNucleiDtiCnnParameters:
+    """
+    Build parameters.
+    
+    Args:
+        t1_images: Path to the T1 image(s) or folder containing images. These\
+            must be registered to the FAs in physical coordinates.
+        fa: Path to the FA image(s) or folder.
+        v1: Path to the V1 image(s) or folder.
+        output: Path to the segmentation output(s) or folder.
+        aseg: Path to the ASEG segmentation(s) or folder. These must be\
+            registered to the FAs in physical coordinates.
+        volume_output: CSV file for volumes of all structures and subjects.
+        posteriors_output: Path to the posteriors output(s) or folder.
+        threads: Number of cores to be used. Default is 1.
+        force_cpu: Enforce running with CPU rather than GPU.
+        model: Path to an alternative model file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_segment_thalamic_nuclei_dti_cnn",
+        "t1_images": t1_images,
+        "fa": fa,
+        "v1": v1,
+        "output": output,
+        "force_cpu": force_cpu,
+    }
+    if aseg is not None:
+        params["aseg"] = aseg
+    if volume_output is not None:
+        params["volume_output"] = volume_output
+    if posteriors_output is not None:
+        params["posteriors_output"] = posteriors_output
+    if threads is not None:
+        params["threads"] = threads
+    if model is not None:
+        params["model"] = model
+    return params
+
+
+def mri_segment_thalamic_nuclei_dti_cnn_cargs(
+    params: MriSegmentThalamicNucleiDtiCnnParameters,
+    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_segment_thalamic_nuclei_dti_cnn")
+    cargs.extend([
+        "--t1",
+        execution.input_file(params.get("t1_images"))
+    ])
+    if params.get("aseg") is not None:
+        cargs.extend([
+            "--aseg",
+            execution.input_file(params.get("aseg"))
+        ])
+    cargs.extend([
+        "--fa",
+        execution.input_file(params.get("fa"))
+    ])
+    cargs.extend([
+        "--v1",
+        execution.input_file(params.get("v1"))
+    ])
+    cargs.extend([
+        "--o",
+        params.get("output")
+    ])
+    if params.get("volume_output") is not None:
+        cargs.extend([
+            "--vol",
+            params.get("volume_output")
+        ])
+    if params.get("posteriors_output") is not None:
+        cargs.extend([
+            "--post",
+            params.get("posteriors_output")
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("force_cpu"):
+        cargs.append("--cpu")
+    if params.get("model") is not None:
+        cargs.extend([
+            "--model",
+            execution.input_file(params.get("model"))
+        ])
+    return cargs
+
+
+def mri_segment_thalamic_nuclei_dti_cnn_outputs(
+    params: MriSegmentThalamicNucleiDtiCnnParameters,
+    execution: Execution,
+) -> MriSegmentThalamicNucleiDtiCnnOutputs:
+    """
+    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 = MriSegmentThalamicNucleiDtiCnnOutputs(
+        root=execution.output_file("."),
+        segmentation_output=execution.output_file(params.get("output")),
+        volume_csv=execution.output_file(params.get("volume_output")) if (params.get("volume_output") is not None) else None,
+        posteriors=execution.output_file(params.get("posteriors_output")) if (params.get("posteriors_output") is not None) else None,
+    )
+    return ret
+
+
+def mri_segment_thalamic_nuclei_dti_cnn_execute(
+    params: MriSegmentThalamicNucleiDtiCnnParameters,
+    execution: Execution,
+) -> MriSegmentThalamicNucleiDtiCnnOutputs:
+    """
+    Thalamic segmentation tool providing 0.7mm isotropic thalamus segmentation from
+    registered T1, FA, and V1 volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSegmentThalamicNucleiDtiCnnOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_segment_thalamic_nuclei_dti_cnn_cargs(params, execution)
+    ret = mri_segment_thalamic_nuclei_dti_cnn_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_segment_thalamic_nuclei_dti_cnn(
+    t1_images: InputPathType,
+    fa: InputPathType,
+    v1: InputPathType,
+    output: str,
+    aseg: InputPathType | None = None,
+    volume_output: str | None = None,
+    posteriors_output: str | None = None,
+    threads: float | None = None,
+    force_cpu: bool = False,
+    model: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> MriSegmentThalamicNucleiDtiCnnOutputs:
+    """
+    Thalamic segmentation tool providing 0.7mm isotropic thalamus segmentation from
+    registered T1, FA, and V1 volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        t1_images: Path to the T1 image(s) or folder containing images. These\
+            must be registered to the FAs in physical coordinates.
+        fa: Path to the FA image(s) or folder.
+        v1: Path to the V1 image(s) or folder.
+        output: Path to the segmentation output(s) or folder.
+        aseg: Path to the ASEG segmentation(s) or folder. These must be\
+            registered to the FAs in physical coordinates.
+        volume_output: CSV file for volumes of all structures and subjects.
+        posteriors_output: Path to the posteriors output(s) or folder.
+        threads: Number of cores to be used. Default is 1.
+        force_cpu: Enforce running with CPU rather than GPU.
+        model: Path to an alternative model file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSegmentThalamicNucleiDtiCnnOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SEGMENT_THALAMIC_NUCLEI_DTI_CNN_METADATA)
+    params = mri_segment_thalamic_nuclei_dti_cnn_params(
+        t1_images=t1_images,
+        aseg=aseg,
+        fa=fa,
+        v1=v1,
+        output=output,
+        volume_output=volume_output,
+        posteriors_output=posteriors_output,
+        threads=threads,
+        force_cpu=force_cpu,
+        model=model,
+    )
+    return mri_segment_thalamic_nuclei_dti_cnn_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SEGMENT_THALAMIC_NUCLEI_DTI_CNN_METADATA",
+    "MriSegmentThalamicNucleiDtiCnnOutputs",
+    "MriSegmentThalamicNucleiDtiCnnParameters",
+    "mri_segment_thalamic_nuclei_dti_cnn",
+    "mri_segment_thalamic_nuclei_dti_cnn_params",
+]