niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_morphology.py

@@ -0,0 +1,221 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_MORPHOLOGY_METADATA = Metadata(
+    id="d08cdae88f7fdc7545935fe63ed76b00861cc7e6.boutiques",
+    name="mri_morphology",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriMorphologyParameters = typing.TypedDict('MriMorphologyParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_morphology"],
+    "input_volume": InputPathType,
+    "operation": typing.Literal["open", "close", "dilate", "erode", "mode", "fill_holes", "erode_bottom", "dilate_thresh", "erode_thresh"],
+    "number_iter": int,
+    "output_volume": str,
+    "label_option": 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_morphology": mri_morphology_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_morphology": mri_morphology_outputs,
+    }.get(t)
+
+
+class MriMorphologyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_morphology(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """The result of the morphological operation applied to the input volume."""
+
+
+def mri_morphology_params(
+    input_volume: InputPathType,
+    operation: typing.Literal["open", "close", "dilate", "erode", "mode", "fill_holes", "erode_bottom", "dilate_thresh", "erode_thresh"],
+    number_iter: int,
+    output_volume: str,
+    label_option: float | None = None,
+) -> MriMorphologyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volume: Input volume file on which operations are to be applied.
+        operation: Morphological operation to be performed. Options include:\
+            open, close, dilate, erode, mode, fill_holes, erode_bottom,\
+            dilate_thresh, erode_thresh.
+        number_iter: Number of iterations to apply the operation.
+        output_volume: Output volume file to store the results of the\
+            operation.
+        label_option: Only apply operations to the specified label instead of\
+            all nonzero voxels.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_morphology",
+        "input_volume": input_volume,
+        "operation": operation,
+        "number_iter": number_iter,
+        "output_volume": output_volume,
+    }
+    if label_option is not None:
+        params["label_option"] = label_option
+    return params
+
+
+def mri_morphology_cargs(
+    params: MriMorphologyParameters,
+    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_morphology")
+    cargs.append(execution.input_file(params.get("input_volume")))
+    cargs.append(params.get("operation"))
+    cargs.append(str(params.get("number_iter")))
+    cargs.append(params.get("output_volume"))
+    if params.get("label_option") is not None:
+        cargs.extend([
+            "-l",
+            str(params.get("label_option"))
+        ])
+    return cargs
+
+
+def mri_morphology_outputs(
+    params: MriMorphologyParameters,
+    execution: Execution,
+) -> MriMorphologyOutputs:
+    """
+    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 = MriMorphologyOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_volume")),
+    )
+    return ret
+
+
+def mri_morphology_execute(
+    params: MriMorphologyParameters,
+    execution: Execution,
+) -> MriMorphologyOutputs:
+    """
+    MRI Morphology Tool - performs various morphological operations on a volume.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriMorphologyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_morphology_cargs(params, execution)
+    ret = mri_morphology_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_morphology(
+    input_volume: InputPathType,
+    operation: typing.Literal["open", "close", "dilate", "erode", "mode", "fill_holes", "erode_bottom", "dilate_thresh", "erode_thresh"],
+    number_iter: int,
+    output_volume: str,
+    label_option: float | None = None,
+    runner: Runner | None = None,
+) -> MriMorphologyOutputs:
+    """
+    MRI Morphology Tool - performs various morphological operations on a volume.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volume: Input volume file on which operations are to be applied.
+        operation: Morphological operation to be performed. Options include:\
+            open, close, dilate, erode, mode, fill_holes, erode_bottom,\
+            dilate_thresh, erode_thresh.
+        number_iter: Number of iterations to apply the operation.
+        output_volume: Output volume file to store the results of the\
+            operation.
+        label_option: Only apply operations to the specified label instead of\
+            all nonzero voxels.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriMorphologyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MORPHOLOGY_METADATA)
+    params = mri_morphology_params(
+        input_volume=input_volume,
+        operation=operation,
+        number_iter=number_iter,
+        output_volume=output_volume,
+        label_option=label_option,
+    )
+    return mri_morphology_execute(params, execution)
+
+
+__all__ = [
+    "MRI_MORPHOLOGY_METADATA",
+    "MriMorphologyOutputs",
+    "MriMorphologyParameters",
+    "mri_morphology",
+    "mri_morphology_params",
+]

niwrap_freesurfer/freesurfer/mri_motion_correct.py

@@ -0,0 +1,184 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_MOTION_CORRECT_METADATA = Metadata(
+    id="3cfbb0cc88f7a83298127f974e5ce214fa8cdbf7.boutiques",
+    name="mri_motion_correct",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriMotionCorrectParameters = typing.TypedDict('MriMotionCorrectParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_motion_correct"],
+    "outfile": str,
+    "infiles": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_motion_correct": mri_motion_correct_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_motion_correct": mri_motion_correct_outputs,
+    }.get(t)
+
+
+class MriMotionCorrectOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_motion_correct(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    corrected_outfile: OutputPathType
+    """Corrected MRI image output file."""
+
+
+def mri_motion_correct_params(
+    outfile: str,
+    infiles: list[InputPathType],
+) -> MriMotionCorrectParameters:
+    """
+    Build parameters.
+    
+    Args:
+        outfile: Output file where the corrected MRI image(s) will be stored.
+        infiles: Input MRI image files to be corrected.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_motion_correct",
+        "outfile": outfile,
+        "infiles": infiles,
+    }
+    return params
+
+
+def mri_motion_correct_cargs(
+    params: MriMotionCorrectParameters,
+    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_motion_correct")
+    cargs.append(params.get("outfile"))
+    cargs.extend([execution.input_file(f) for f in params.get("infiles")])
+    return cargs
+
+
+def mri_motion_correct_outputs(
+    params: MriMotionCorrectParameters,
+    execution: Execution,
+) -> MriMotionCorrectOutputs:
+    """
+    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 = MriMotionCorrectOutputs(
+        root=execution.output_file("."),
+        corrected_outfile=execution.output_file(params.get("outfile")),
+    )
+    return ret
+
+
+def mri_motion_correct_execute(
+    params: MriMotionCorrectParameters,
+    execution: Execution,
+) -> MriMotionCorrectOutputs:
+    """
+    Tool for correcting motion in MRI scans.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriMotionCorrectOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_motion_correct_cargs(params, execution)
+    ret = mri_motion_correct_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_motion_correct(
+    outfile: str,
+    infiles: list[InputPathType],
+    runner: Runner | None = None,
+) -> MriMotionCorrectOutputs:
+    """
+    Tool for correcting motion in MRI scans.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        outfile: Output file where the corrected MRI image(s) will be stored.
+        infiles: Input MRI image files to be corrected.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriMotionCorrectOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MOTION_CORRECT_METADATA)
+    params = mri_motion_correct_params(
+        outfile=outfile,
+        infiles=infiles,
+    )
+    return mri_motion_correct_execute(params, execution)
+
+
+__all__ = [
+    "MRI_MOTION_CORRECT_METADATA",
+    "MriMotionCorrectOutputs",
+    "MriMotionCorrectParameters",
+    "mri_motion_correct",
+    "mri_motion_correct_params",
+]

niwrap_freesurfer/freesurfer/mri_motion_correct2.py

@@ -0,0 +1,278 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_MOTION_CORRECT2_METADATA = Metadata(
+    id="a581289aa8203d417a44a5b02cbe1c9a50b8b234.boutiques",
+    name="mri_motion_correct2",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriMotionCorrect2Parameters = typing.TypedDict('MriMotionCorrect2Parameters', {
+    "__STYX_TYPE__": typing.Literal["mri_motion_correct2"],
+    "output_spec": str,
+    "input_files": list[InputPathType],
+    "target": typing.NotRequired[InputPathType | None],
+    "wild": bool,
+    "tmp_dir": typing.NotRequired[str | None],
+    "nocleanup": bool,
+    "umask": typing.NotRequired[str | None],
+    "cm": bool,
+    "version": bool,
+    "debug": 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_motion_correct2": mri_motion_correct2_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_motion_correct2": mri_motion_correct2_outputs,
+    }.get(t)
+
+
+class MriMotionCorrect2Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_motion_correct2(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """The aligned and averaged output file or directory"""
+
+
+def mri_motion_correct2_params(
+    output_spec: str,
+    input_files: list[InputPathType],
+    target: InputPathType | None = None,
+    wild: bool = False,
+    tmp_dir: str | None = None,
+    nocleanup: bool = False,
+    umask: str | None = None,
+    cm: bool = False,
+    version: bool = False,
+    debug: bool = False,
+) -> MriMotionCorrect2Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_spec: Output file or directory (for COR format).
+        input_files: Input volume files, specified multiple times for multiple\
+            files.
+        target: Use the specified target instead of the first input file.
+        wild: Assume unmatched arguments are input files.
+        tmp_dir: Directory for temporary files.
+        nocleanup: Do not delete temporary files.
+        umask: Set UNIX file permission mask.
+        cm: Make COR volumes conform to minimum voxel size.
+        version: Print version information and exit.
+        debug: Print detailed debug information to screen.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_motion_correct2",
+        "output_spec": output_spec,
+        "input_files": input_files,
+        "wild": wild,
+        "nocleanup": nocleanup,
+        "cm": cm,
+        "version": version,
+        "debug": debug,
+    }
+    if target is not None:
+        params["target"] = target
+    if tmp_dir is not None:
+        params["tmp_dir"] = tmp_dir
+    if umask is not None:
+        params["umask"] = umask
+    return params
+
+
+def mri_motion_correct2_cargs(
+    params: MriMotionCorrect2Parameters,
+    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_motion_correct2")
+    cargs.extend([
+        "-o",
+        params.get("output_spec")
+    ])
+    cargs.extend([
+        "-i",
+        *[execution.input_file(f) for f in params.get("input_files")]
+    ])
+    if params.get("target") is not None:
+        cargs.extend([
+            "-t",
+            execution.input_file(params.get("target"))
+        ])
+    if params.get("wild"):
+        cargs.append("-wild")
+    if params.get("tmp_dir") is not None:
+        cargs.extend([
+            "-tmpdir",
+            params.get("tmp_dir")
+        ])
+    if params.get("nocleanup"):
+        cargs.append("-nocleanup")
+    if params.get("umask") is not None:
+        cargs.extend([
+            "-umask",
+            params.get("umask")
+        ])
+    if params.get("cm"):
+        cargs.append("-cm")
+    if params.get("version"):
+        cargs.append("-version")
+    if params.get("debug"):
+        cargs.append("-debug")
+    return cargs
+
+
+def mri_motion_correct2_outputs(
+    params: MriMotionCorrect2Parameters,
+    execution: Execution,
+) -> MriMotionCorrect2Outputs:
+    """
+    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 = MriMotionCorrect2Outputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_spec")),
+    )
+    return ret
+
+
+def mri_motion_correct2_execute(
+    params: MriMotionCorrect2Parameters,
+    execution: Execution,
+) -> MriMotionCorrect2Outputs:
+    """
+    Aligns and averages two or more volumes using minctracc for alignment and
+    mincresample and mincaverage for resampling.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriMotionCorrect2Outputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_motion_correct2_cargs(params, execution)
+    ret = mri_motion_correct2_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_motion_correct2(
+    output_spec: str,
+    input_files: list[InputPathType],
+    target: InputPathType | None = None,
+    wild: bool = False,
+    tmp_dir: str | None = None,
+    nocleanup: bool = False,
+    umask: str | None = None,
+    cm: bool = False,
+    version: bool = False,
+    debug: bool = False,
+    runner: Runner | None = None,
+) -> MriMotionCorrect2Outputs:
+    """
+    Aligns and averages two or more volumes using minctracc for alignment and
+    mincresample and mincaverage for resampling.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        output_spec: Output file or directory (for COR format).
+        input_files: Input volume files, specified multiple times for multiple\
+            files.
+        target: Use the specified target instead of the first input file.
+        wild: Assume unmatched arguments are input files.
+        tmp_dir: Directory for temporary files.
+        nocleanup: Do not delete temporary files.
+        umask: Set UNIX file permission mask.
+        cm: Make COR volumes conform to minimum voxel size.
+        version: Print version information and exit.
+        debug: Print detailed debug information to screen.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriMotionCorrect2Outputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MOTION_CORRECT2_METADATA)
+    params = mri_motion_correct2_params(
+        output_spec=output_spec,
+        input_files=input_files,
+        target=target,
+        wild=wild,
+        tmp_dir=tmp_dir,
+        nocleanup=nocleanup,
+        umask=umask,
+        cm=cm,
+        version=version,
+        debug=debug,
+    )
+    return mri_motion_correct2_execute(params, execution)
+
+
+__all__ = [
+    "MRI_MOTION_CORRECT2_METADATA",
+    "MriMotionCorrect2Outputs",
+    "MriMotionCorrect2Parameters",
+    "mri_motion_correct2",
+    "mri_motion_correct2_params",
+]