niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_synthsr_hyperfine.py

@@ -0,0 +1,235 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SYNTHSR_HYPERFINE_METADATA = Metadata(
+    id="8af5c94607ef31a7bceecdbe213a0b0e78928e27.boutiques",
+    name="mri_synthsr_hyperfine",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSynthsrHyperfineParameters = typing.TypedDict('MriSynthsrHyperfineParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_synthsr_hyperfine"],
+    "t1_image": InputPathType,
+    "t2_image": InputPathType,
+    "output": str,
+    "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_synthsr_hyperfine": mri_synthsr_hyperfine_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_synthsr_hyperfine": mri_synthsr_hyperfine_outputs,
+    }.get(t)
+
+
+class MriSynthsrHyperfineOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_synthsr_hyperfine(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    synthetic_mprage: OutputPathType
+    """Synthetic 1mm MP-RAGE(s) generated from T1 and T2 inputs"""
+
+
+def mri_synthsr_hyperfine_params(
+    t1_image: InputPathType,
+    t2_image: InputPathType,
+    output: str,
+    threads: float | None = 1,
+    cpu: bool = False,
+) -> MriSynthsrHyperfineParameters:
+    """
+    Build parameters.
+    
+    Args:
+        t1_image: T1 image(s) to super-resolve, at native 1.5x1.5x5 axial\
+            resolution. Can be a path to an image or to a folder.
+        t2_image: T2 image(s). Must be a folder if --t1 designates a folder.\
+            These must be registered to the T1s, in physical coordinates (i.e.,\
+            with the headers, do NOT resample when registering; see instructions on\
+            FreeSurfer wiki).
+        output: Output(s), i.e. synthetic 1mm MP-RAGE(s). Must be a folder if\
+            --t1 designates a folder.
+        threads: (optional) Number of cores to be used. Default is 1.
+        cpu: (optional) Enforce running with CPU rather than GPU.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_synthsr_hyperfine",
+        "t1_image": t1_image,
+        "t2_image": t2_image,
+        "output": output,
+        "cpu": cpu,
+    }
+    if threads is not None:
+        params["threads"] = threads
+    return params
+
+
+def mri_synthsr_hyperfine_cargs(
+    params: MriSynthsrHyperfineParameters,
+    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_hyperfine")
+    cargs.extend([
+        "--t1",
+        execution.input_file(params.get("t1_image"))
+    ])
+    cargs.extend([
+        "--t2",
+        execution.input_file(params.get("t2_image"))
+    ])
+    cargs.extend([
+        "--o",
+        params.get("output")
+    ])
+    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_synthsr_hyperfine_outputs(
+    params: MriSynthsrHyperfineParameters,
+    execution: Execution,
+) -> MriSynthsrHyperfineOutputs:
+    """
+    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 = MriSynthsrHyperfineOutputs(
+        root=execution.output_file("."),
+        synthetic_mprage=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def mri_synthsr_hyperfine_execute(
+    params: MriSynthsrHyperfineParameters,
+    execution: Execution,
+) -> MriSynthsrHyperfineOutputs:
+    """
+    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a pair of
+    T1-T2 standard Hyperfine scans (1.5x1.5x5mm axial).
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSynthsrHyperfineOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_synthsr_hyperfine_cargs(params, execution)
+    ret = mri_synthsr_hyperfine_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_synthsr_hyperfine(
+    t1_image: InputPathType,
+    t2_image: InputPathType,
+    output: str,
+    threads: float | None = 1,
+    cpu: bool = False,
+    runner: Runner | None = None,
+) -> MriSynthsrHyperfineOutputs:
+    """
+    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a pair of
+    T1-T2 standard Hyperfine scans (1.5x1.5x5mm axial).
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        t1_image: T1 image(s) to super-resolve, at native 1.5x1.5x5 axial\
+            resolution. Can be a path to an image or to a folder.
+        t2_image: T2 image(s). Must be a folder if --t1 designates a folder.\
+            These must be registered to the T1s, in physical coordinates (i.e.,\
+            with the headers, do NOT resample when registering; see instructions on\
+            FreeSurfer wiki).
+        output: Output(s), i.e. synthetic 1mm MP-RAGE(s). Must be a folder if\
+            --t1 designates a folder.
+        threads: (optional) Number of cores to be used. Default is 1.
+        cpu: (optional) Enforce running with CPU rather than GPU.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSynthsrHyperfineOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SYNTHSR_HYPERFINE_METADATA)
+    params = mri_synthsr_hyperfine_params(
+        t1_image=t1_image,
+        t2_image=t2_image,
+        output=output,
+        threads=threads,
+        cpu=cpu,
+    )
+    return mri_synthsr_hyperfine_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SYNTHSR_HYPERFINE_METADATA",
+    "MriSynthsrHyperfineOutputs",
+    "MriSynthsrHyperfineParameters",
+    "mri_synthsr_hyperfine",
+    "mri_synthsr_hyperfine_params",
+]

niwrap_freesurfer/freesurfer/mri_synthstrip.py

@@ -0,0 +1,252 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SYNTHSTRIP_METADATA = Metadata(
+    id="b76a61f5aba0de9ca4cafed66778de7469902685.boutiques",
+    name="mri_synthstrip",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSynthstripParameters = typing.TypedDict('MriSynthstripParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_synthstrip"],
+    "image": InputPathType,
+    "output_image": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "gpu": bool,
+    "border": typing.NotRequired[float | None],
+    "exclude_csf": bool,
+    "model_weights": 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_synthstrip": mri_synthstrip_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_synthstrip": mri_synthstrip_outputs,
+    }.get(t)
+
+
+class MriSynthstripOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_synthstrip(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_image_file: OutputPathType | None
+    """Stripped brain image output."""
+    output_mask_file: OutputPathType | None
+    """Binary brain mask output."""
+
+
+def mri_synthstrip_params(
+    image: InputPathType,
+    output_image: str | None = None,
+    mask: InputPathType | None = None,
+    gpu: bool = False,
+    border: float | None = 1,
+    exclude_csf: bool = False,
+    model_weights: InputPathType | None = None,
+) -> MriSynthstripParameters:
+    """
+    Build parameters.
+    
+    Args:
+        image: Input image to skullstrip.
+        output_image: Save stripped image to path.
+        mask: Save binary brain mask to path.
+        gpu: Use the GPU.
+        border: Mask border threshold in mm. Default is 1.
+        exclude_csf: Exclude CSF from brain border.
+        model_weights: Alternative model weights.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_synthstrip",
+        "image": image,
+        "gpu": gpu,
+        "exclude_csf": exclude_csf,
+    }
+    if output_image is not None:
+        params["output_image"] = output_image
+    if mask is not None:
+        params["mask"] = mask
+    if border is not None:
+        params["border"] = border
+    if model_weights is not None:
+        params["model_weights"] = model_weights
+    return params
+
+
+def mri_synthstrip_cargs(
+    params: MriSynthstripParameters,
+    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_synthstrip")
+    cargs.extend([
+        "-i",
+        execution.input_file(params.get("image"))
+    ])
+    if params.get("output_image") is not None:
+        cargs.extend([
+            "-o",
+            "[" + params.get("output_image") + "]"
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-m",
+            "[" + execution.input_file(params.get("mask")) + "]"
+        ])
+    if params.get("gpu"):
+        cargs.append("[" + "-g" + "]")
+    if params.get("border") is not None:
+        cargs.extend([
+            "-b",
+            "[" + str(params.get("border")) + "]"
+        ])
+    if params.get("exclude_csf"):
+        cargs.append("[" + "--no-csf" + "]")
+    if params.get("model_weights") is not None:
+        cargs.extend([
+            "--model",
+            "[" + execution.input_file(params.get("model_weights")) + "]"
+        ])
+    return cargs
+
+
+def mri_synthstrip_outputs(
+    params: MriSynthstripParameters,
+    execution: Execution,
+) -> MriSynthstripOutputs:
+    """
+    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 = MriSynthstripOutputs(
+        root=execution.output_file("."),
+        output_image_file=execution.output_file(params.get("output_image")) if (params.get("output_image") is not None) else None,
+        output_mask_file=execution.output_file(pathlib.Path(params.get("mask")).name) if (params.get("mask") is not None) else None,
+    )
+    return ret
+
+
+def mri_synthstrip_execute(
+    params: MriSynthstripParameters,
+    execution: Execution,
+) -> MriSynthstripOutputs:
+    """
+    Robust, universal skull-stripping for brain images of any type.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSynthstripOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_synthstrip_cargs(params, execution)
+    ret = mri_synthstrip_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_synthstrip(
+    image: InputPathType,
+    output_image: str | None = None,
+    mask: InputPathType | None = None,
+    gpu: bool = False,
+    border: float | None = 1,
+    exclude_csf: bool = False,
+    model_weights: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> MriSynthstripOutputs:
+    """
+    Robust, universal skull-stripping for brain images of any type.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        image: Input image to skullstrip.
+        output_image: Save stripped image to path.
+        mask: Save binary brain mask to path.
+        gpu: Use the GPU.
+        border: Mask border threshold in mm. Default is 1.
+        exclude_csf: Exclude CSF from brain border.
+        model_weights: Alternative model weights.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSynthstripOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SYNTHSTRIP_METADATA)
+    params = mri_synthstrip_params(
+        image=image,
+        output_image=output_image,
+        mask=mask,
+        gpu=gpu,
+        border=border,
+        exclude_csf=exclude_csf,
+        model_weights=model_weights,
+    )
+    return mri_synthstrip_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SYNTHSTRIP_METADATA",
+    "MriSynthstripOutputs",
+    "MriSynthstripParameters",
+    "mri_synthstrip",
+    "mri_synthstrip_params",
+]

niwrap_freesurfer/freesurfer/mri_tessellate.py

@@ -0,0 +1,229 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_TESSELLATE_METADATA = Metadata(
+    id="9dcf92c1d5089255feba7b2627ab0237e0be1c67.boutiques",
+    name="mri_tessellate",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriTessellateParameters = typing.TypedDict('MriTessellateParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_tessellate"],
+    "input_volume": InputPathType,
+    "label_value": int,
+    "output_surf": str,
+    "different_labels": bool,
+    "max_vertices": typing.NotRequired[int | None],
+    "real_ras": 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_tessellate": mri_tessellate_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_tessellate": mri_tessellate_outputs,
+    }.get(t)
+
+
+class MriTessellateOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_tessellate(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_surface_file: OutputPathType
+    """Output file of the tessellation surface, typically ?h.orig."""
+
+
+def mri_tessellate_params(
+    input_volume: InputPathType,
+    label_value: int,
+    output_surf: str,
+    different_labels: bool = False,
+    max_vertices: int | None = None,
+    real_ras: bool = False,
+) -> MriTessellateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volume: Input volume (e.g., a filled MRI image).
+        label_value: Label value for the tessellation. Integer value, if input\
+            is filled volume, 127 is rh, 255 is lh.
+        output_surf: Binary surface of the tessellation, output file.
+        different_labels: Tessellate the surface of all voxels with different\
+            labels.
+        max_vertices: Set the max number of vertices to nvertices, and the max\
+            number of faces to (2 * nvertices).
+        real_ras: Save surface with real RAS coordinates where c_(r,a,s) != 0.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_tessellate",
+        "input_volume": input_volume,
+        "label_value": label_value,
+        "output_surf": output_surf,
+        "different_labels": different_labels,
+        "real_ras": real_ras,
+    }
+    if max_vertices is not None:
+        params["max_vertices"] = max_vertices
+    return params
+
+
+def mri_tessellate_cargs(
+    params: MriTessellateParameters,
+    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_tessellate")
+    cargs.append(execution.input_file(params.get("input_volume")))
+    cargs.append(str(params.get("label_value")))
+    cargs.append(params.get("output_surf"))
+    if params.get("different_labels"):
+        cargs.append("-a")
+    if params.get("max_vertices") is not None:
+        cargs.extend([
+            "-maxv",
+            str(params.get("max_vertices"))
+        ])
+    if params.get("real_ras"):
+        cargs.append("-n")
+    return cargs
+
+
+def mri_tessellate_outputs(
+    params: MriTessellateParameters,
+    execution: Execution,
+) -> MriTessellateOutputs:
+    """
+    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 = MriTessellateOutputs(
+        root=execution.output_file("."),
+        output_surface_file=execution.output_file(params.get("output_surf")),
+    )
+    return ret
+
+
+def mri_tessellate_execute(
+    params: MriTessellateParameters,
+    execution: Execution,
+) -> MriTessellateOutputs:
+    """
+    This program creates a surface by tessellating a given input volume.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriTessellateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_tessellate_cargs(params, execution)
+    ret = mri_tessellate_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_tessellate(
+    input_volume: InputPathType,
+    label_value: int,
+    output_surf: str,
+    different_labels: bool = False,
+    max_vertices: int | None = None,
+    real_ras: bool = False,
+    runner: Runner | None = None,
+) -> MriTessellateOutputs:
+    """
+    This program creates a surface by tessellating a given input volume.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volume: Input volume (e.g., a filled MRI image).
+        label_value: Label value for the tessellation. Integer value, if input\
+            is filled volume, 127 is rh, 255 is lh.
+        output_surf: Binary surface of the tessellation, output file.
+        different_labels: Tessellate the surface of all voxels with different\
+            labels.
+        max_vertices: Set the max number of vertices to nvertices, and the max\
+            number of faces to (2 * nvertices).
+        real_ras: Save surface with real RAS coordinates where c_(r,a,s) != 0.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriTessellateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_TESSELLATE_METADATA)
+    params = mri_tessellate_params(
+        input_volume=input_volume,
+        label_value=label_value,
+        output_surf=output_surf,
+        different_labels=different_labels,
+        max_vertices=max_vertices,
+        real_ras=real_ras,
+    )
+    return mri_tessellate_execute(params, execution)
+
+
+__all__ = [
+    "MRI_TESSELLATE_METADATA",
+    "MriTessellateOutputs",
+    "MriTessellateParameters",
+    "mri_tessellate",
+    "mri_tessellate_params",
+]