niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_warp.py

@@ -0,0 +1,262 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_WARP_METADATA = Metadata(
+    id="a60346ae5a51f63c7f32e60f45dc20db2e519c51.boutiques",
+    name="mris_warp",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisWarpParameters = typing.TypedDict('MrisWarpParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_warp"],
+    "deformvol": typing.NotRequired[str | None],
+    "m3z": typing.NotRequired[str | None],
+    "regfile": typing.NotRequired[str | None],
+    "surf": typing.NotRequired[str | None],
+    "out": typing.NotRequired[str | None],
+    "abs": bool,
+    "help": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_warp": mris_warp_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 {
+        "mris_warp": mris_warp_outputs,
+    }.get(t)
+
+
+class MrisWarpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_warp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_surface: OutputPathType | None
+    """Output surface file"""
+
+
+def mris_warp_params(
+    deformvol: str | None = None,
+    m3z: str | None = None,
+    regfile: str | None = None,
+    surf: str | None = None,
+    out: str | None = None,
+    abs_: bool = False,
+    help_: bool = False,
+    version: bool = False,
+) -> MrisWarpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        deformvol: Volume containing deformation.
+        m3z: M3Z file containing deformation.
+        regfile: register.dat file between surface and volume.
+        surf: Surface file to warp.
+        out: Name for output surface (if does not contain '/', outputs to same\
+            directory as input surface).
+        abs_: Absolute coordinate displacement convention (default).
+        help_: Print out information on how to use this program.
+        version: Print out version and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_warp",
+        "abs": abs_,
+        "help": help_,
+        "version": version,
+    }
+    if deformvol is not None:
+        params["deformvol"] = deformvol
+    if m3z is not None:
+        params["m3z"] = m3z
+    if regfile is not None:
+        params["regfile"] = regfile
+    if surf is not None:
+        params["surf"] = surf
+    if out is not None:
+        params["out"] = out
+    return params
+
+
+def mris_warp_cargs(
+    params: MrisWarpParameters,
+    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("mris_warp")
+    if params.get("deformvol") is not None:
+        cargs.extend([
+            "--deformvol",
+            params.get("deformvol")
+        ])
+    if params.get("m3z") is not None:
+        cargs.extend([
+            "--m3z",
+            params.get("m3z")
+        ])
+    if params.get("regfile") is not None:
+        cargs.extend([
+            "--reg",
+            params.get("regfile")
+        ])
+    if params.get("surf") is not None:
+        cargs.extend([
+            "--surf",
+            params.get("surf")
+        ])
+    if params.get("out") is not None:
+        cargs.extend([
+            "--out",
+            params.get("out")
+        ])
+    if params.get("abs"):
+        cargs.append("--abs")
+    if params.get("help"):
+        cargs.append("--help")
+    if params.get("version"):
+        cargs.append("--version")
+    return cargs
+
+
+def mris_warp_outputs(
+    params: MrisWarpParameters,
+    execution: Execution,
+) -> MrisWarpOutputs:
+    """
+    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 = MrisWarpOutputs(
+        root=execution.output_file("."),
+        output_surface=execution.output_file(params.get("out")) if (params.get("out") is not None) else None,
+    )
+    return ret
+
+
+def mris_warp_execute(
+    params: MrisWarpParameters,
+    execution: Execution,
+) -> MrisWarpOutputs:
+    """
+    This program will warp a surface using a specified deformation field.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisWarpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_warp_cargs(params, execution)
+    ret = mris_warp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_warp(
+    deformvol: str | None = None,
+    m3z: str | None = None,
+    regfile: str | None = None,
+    surf: str | None = None,
+    out: str | None = None,
+    abs_: bool = False,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrisWarpOutputs:
+    """
+    This program will warp a surface using a specified deformation field.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        deformvol: Volume containing deformation.
+        m3z: M3Z file containing deformation.
+        regfile: register.dat file between surface and volume.
+        surf: Surface file to warp.
+        out: Name for output surface (if does not contain '/', outputs to same\
+            directory as input surface).
+        abs_: Absolute coordinate displacement convention (default).
+        help_: Print out information on how to use this program.
+        version: Print out version and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisWarpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_WARP_METADATA)
+    params = mris_warp_params(
+        deformvol=deformvol,
+        m3z=m3z,
+        regfile=regfile,
+        surf=surf,
+        out=out,
+        abs_=abs_,
+        help_=help_,
+        version=version,
+    )
+    return mris_warp_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_WARP_METADATA",
+    "MrisWarpOutputs",
+    "MrisWarpParameters",
+    "mris_warp",
+    "mris_warp_params",
+]

niwrap_freesurfer/freesurfer/mris_watershed.py

@@ -0,0 +1,222 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_WATERSHED_METADATA = Metadata(
+    id="9a2bd956b5f350b8c0603b62d7b760dba26dc82d.boutiques",
+    name="mris_watershed",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisWatershedParameters = typing.TypedDict('MrisWatershedParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_watershed"],
+    "input_surface": InputPathType,
+    "input_gradient_field": InputPathType,
+    "output_annotation": str,
+    "max_clusters": typing.NotRequired[float | None],
+    "mask_label": 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 {
+        "mris_watershed": mris_watershed_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 {
+        "mris_watershed": mris_watershed_outputs,
+    }.get(t)
+
+
+class MrisWatershedOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_watershed(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_annotation_file: OutputPathType
+    """The resulting annotation file from the watershed transform"""
+
+
+def mris_watershed_params(
+    input_surface: InputPathType,
+    input_gradient_field: InputPathType,
+    output_annotation: str,
+    max_clusters: float | None = None,
+    mask_label: str | None = None,
+) -> MrisWatershedParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_surface: Input surface file.
+        input_gradient_field: Input gradient field file.
+        output_annotation: Output annotation file.
+        max_clusters: Set the number of maximum clusters.
+        mask_label: Read in and mask the input volume that is not in the\
+            specified label.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_watershed",
+        "input_surface": input_surface,
+        "input_gradient_field": input_gradient_field,
+        "output_annotation": output_annotation,
+    }
+    if max_clusters is not None:
+        params["max_clusters"] = max_clusters
+    if mask_label is not None:
+        params["mask_label"] = mask_label
+    return params
+
+
+def mris_watershed_cargs(
+    params: MrisWatershedParameters,
+    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("mris_watershed")
+    cargs.append(execution.input_file(params.get("input_surface")))
+    cargs.append(execution.input_file(params.get("input_gradient_field")))
+    cargs.append(params.get("output_annotation"))
+    if params.get("max_clusters") is not None:
+        cargs.extend([
+            "-M",
+            str(params.get("max_clusters"))
+        ])
+    if params.get("mask_label") is not None:
+        cargs.extend([
+            "-mask_label",
+            params.get("mask_label")
+        ])
+    return cargs
+
+
+def mris_watershed_outputs(
+    params: MrisWatershedParameters,
+    execution: Execution,
+) -> MrisWatershedOutputs:
+    """
+    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 = MrisWatershedOutputs(
+        root=execution.output_file("."),
+        output_annotation_file=execution.output_file(params.get("output_annotation")),
+    )
+    return ret
+
+
+def mris_watershed_execute(
+    params: MrisWatershedParameters,
+    execution: Execution,
+) -> MrisWatershedOutputs:
+    """
+    This program computes the watershed transform on the surface of an intensity
+    gradient and writes the resulting measurement into a .annot file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisWatershedOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_watershed_cargs(params, execution)
+    ret = mris_watershed_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_watershed(
+    input_surface: InputPathType,
+    input_gradient_field: InputPathType,
+    output_annotation: str,
+    max_clusters: float | None = None,
+    mask_label: str | None = None,
+    runner: Runner | None = None,
+) -> MrisWatershedOutputs:
+    """
+    This program computes the watershed transform on the surface of an intensity
+    gradient and writes the resulting measurement into a .annot file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_surface: Input surface file.
+        input_gradient_field: Input gradient field file.
+        output_annotation: Output annotation file.
+        max_clusters: Set the number of maximum clusters.
+        mask_label: Read in and mask the input volume that is not in the\
+            specified label.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisWatershedOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_WATERSHED_METADATA)
+    params = mris_watershed_params(
+        input_surface=input_surface,
+        input_gradient_field=input_gradient_field,
+        output_annotation=output_annotation,
+        max_clusters=max_clusters,
+        mask_label=mask_label,
+    )
+    return mris_watershed_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_WATERSHED_METADATA",
+    "MrisWatershedOutputs",
+    "MrisWatershedParameters",
+    "mris_watershed",
+    "mris_watershed_params",
+]

niwrap_freesurfer/freesurfer/mris_wm_volume.py

@@ -0,0 +1,230 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_WM_VOLUME_METADATA = Metadata(
+    id="9ae7b77a7d1b48992bd6d203bed29f888cde6271.boutiques",
+    name="mris_wm_volume",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisWmVolumeParameters = typing.TypedDict('MrisWmVolumeParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_wm_volume"],
+    "subject": str,
+    "hemi": str,
+    "subjects_dir": typing.NotRequired[str | None],
+    "whitesurfname": typing.NotRequired[str | None],
+    "asegname": typing.NotRequired[str | None],
+    "verbose": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_wm_volume": mris_wm_volume_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 MrisWmVolumeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_wm_volume(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_wm_volume_params(
+    subject: str,
+    hemi: str,
+    subjects_dir: str | None = None,
+    whitesurfname: str | None = None,
+    asegname: str | None = None,
+    verbose: bool = False,
+) -> MrisWmVolumeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject: Subject identifier.
+        hemi: Hemisphere to compute volume for (e.g., lh or rh).
+        subjects_dir: The SUBJECTS_DIR where the subject data is stored.
+        whitesurfname: Name of the white surface file.
+        asegname: Name of the aseg file.
+        verbose: Output more messages.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_wm_volume",
+        "subject": subject,
+        "hemi": hemi,
+        "verbose": verbose,
+    }
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    if whitesurfname is not None:
+        params["whitesurfname"] = whitesurfname
+    if asegname is not None:
+        params["asegname"] = asegname
+    return params
+
+
+def mris_wm_volume_cargs(
+    params: MrisWmVolumeParameters,
+    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("mris_wm_volume")
+    cargs.append(params.get("subject"))
+    cargs.append(params.get("hemi"))
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "-SDIR",
+            params.get("subjects_dir")
+        ])
+    if params.get("whitesurfname") is not None:
+        cargs.extend([
+            "-white",
+            params.get("whitesurfname")
+        ])
+    if params.get("asegname") is not None:
+        cargs.extend([
+            "-aseg",
+            params.get("asegname")
+        ])
+    if params.get("verbose"):
+        cargs.append("-v")
+    return cargs
+
+
+def mris_wm_volume_outputs(
+    params: MrisWmVolumeParameters,
+    execution: Execution,
+) -> MrisWmVolumeOutputs:
+    """
+    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 = MrisWmVolumeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_wm_volume_execute(
+    params: MrisWmVolumeParameters,
+    execution: Execution,
+) -> MrisWmVolumeOutputs:
+    """
+    Computes the volume of the enclosed hemisphere white matter surface, ignoring
+    non-white matter voxels in the aseg.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisWmVolumeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_wm_volume_cargs(params, execution)
+    ret = mris_wm_volume_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_wm_volume(
+    subject: str,
+    hemi: str,
+    subjects_dir: str | None = None,
+    whitesurfname: str | None = None,
+    asegname: str | None = None,
+    verbose: bool = False,
+    runner: Runner | None = None,
+) -> MrisWmVolumeOutputs:
+    """
+    Computes the volume of the enclosed hemisphere white matter surface, ignoring
+    non-white matter voxels in the aseg.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject: Subject identifier.
+        hemi: Hemisphere to compute volume for (e.g., lh or rh).
+        subjects_dir: The SUBJECTS_DIR where the subject data is stored.
+        whitesurfname: Name of the white surface file.
+        asegname: Name of the aseg file.
+        verbose: Output more messages.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisWmVolumeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_WM_VOLUME_METADATA)
+    params = mris_wm_volume_params(
+        subject=subject,
+        hemi=hemi,
+        subjects_dir=subjects_dir,
+        whitesurfname=whitesurfname,
+        asegname=asegname,
+        verbose=verbose,
+    )
+    return mris_wm_volume_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_WM_VOLUME_METADATA",
+    "MrisWmVolumeOutputs",
+    "MrisWmVolumeParameters",
+    "mris_wm_volume",
+    "mris_wm_volume_params",
+]