niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_mc.py

@@ -0,0 +1,205 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_MC_METADATA = Metadata(
+    id="60a4e6264f565573c6fbb9368b3b82aa19a0f230.boutiques",
+    name="mri_mc",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriMcParameters = typing.TypedDict('MriMcParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_mc"],
+    "input_volume": InputPathType,
+    "label_value": float,
+    "output_surface": str,
+    "connectivity": 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_mc": mri_mc_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_mc": mri_mc_outputs,
+    }.get(t)
+
+
+class MriMcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_mc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    extracted_surface: OutputPathType
+    """The extracted surface output file."""
+
+
+def mri_mc_params(
+    input_volume: InputPathType,
+    label_value: float,
+    output_surface: str,
+    connectivity: float | None = 1,
+) -> MriMcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volume: The input volume from which to extract the surface.
+        label_value: The label value of the structure to extract.
+        output_surface: The file where the extracted surface mesh will be\
+            saved.
+        connectivity: The connectivity used for Marching Cubes. Options are:\
+            1=6+, 2=18, 3=6, 4=26.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_mc",
+        "input_volume": input_volume,
+        "label_value": label_value,
+        "output_surface": output_surface,
+    }
+    if connectivity is not None:
+        params["connectivity"] = connectivity
+    return params
+
+
+def mri_mc_cargs(
+    params: MriMcParameters,
+    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_mc")
+    cargs.append(execution.input_file(params.get("input_volume")))
+    cargs.append(str(params.get("label_value")))
+    if params.get("connectivity") is not None:
+        cargs.append(params.get("output_surface") + str(params.get("connectivity")))
+    return cargs
+
+
+def mri_mc_outputs(
+    params: MriMcParameters,
+    execution: Execution,
+) -> MriMcOutputs:
+    """
+    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 = MriMcOutputs(
+        root=execution.output_file("."),
+        extracted_surface=execution.output_file(params.get("output_surface")),
+    )
+    return ret
+
+
+def mri_mc_execute(
+    params: MriMcParameters,
+    execution: Execution,
+) -> MriMcOutputs:
+    """
+    Extract a surface from a label volume using Marching Cubes algorithm.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriMcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_mc_cargs(params, execution)
+    ret = mri_mc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_mc(
+    input_volume: InputPathType,
+    label_value: float,
+    output_surface: str,
+    connectivity: float | None = 1,
+    runner: Runner | None = None,
+) -> MriMcOutputs:
+    """
+    Extract a surface from a label volume using Marching Cubes algorithm.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volume: The input volume from which to extract the surface.
+        label_value: The label value of the structure to extract.
+        output_surface: The file where the extracted surface mesh will be\
+            saved.
+        connectivity: The connectivity used for Marching Cubes. Options are:\
+            1=6+, 2=18, 3=6, 4=26.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriMcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MC_METADATA)
+    params = mri_mc_params(
+        input_volume=input_volume,
+        label_value=label_value,
+        output_surface=output_surface,
+        connectivity=connectivity,
+    )
+    return mri_mc_execute(params, execution)
+
+
+__all__ = [
+    "MRI_MC_METADATA",
+    "MriMcOutputs",
+    "MriMcParameters",
+    "mri_mc",
+    "mri_mc_params",
+]

niwrap_freesurfer/freesurfer/mri_mcsim.py

@@ -0,0 +1,438 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_MCSIM_METADATA = Metadata(
+    id="c93d6e308a5345c3826d6a5f805dbcd44a658fe1.boutiques",
+    name="mri_mcsim",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriMcsimParameters = typing.TypedDict('MriMcsimParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_mcsim"],
+    "top_output_dir": str,
+    "base_name": str,
+    "surface": list[str],
+    "num_repetitions": float,
+    "fwhm_values": typing.NotRequired[list[float] | None],
+    "fwhm_max": typing.NotRequired[float | None],
+    "avg_vertex_area": bool,
+    "random_seed": typing.NotRequired[float | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "no_label": bool,
+    "no_save_mask": bool,
+    "surface_name": typing.NotRequired[str | None],
+    "log_file": typing.NotRequired[str | None],
+    "done_file": typing.NotRequired[str | None],
+    "stop_file": typing.NotRequired[str | None],
+    "save_file": typing.NotRequired[str | None],
+    "save_iter": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+    "debug": bool,
+    "check_opts": 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 {
+        "mri_mcsim": mri_mcsim_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_mcsim": mri_mcsim_outputs,
+    }.get(t)
+
+
+class MriMcsimOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_mcsim(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    csd_output: OutputPathType
+    """Output CSD files based on the base name"""
+    done_output: OutputPathType | None
+    """Done file created upon completion"""
+    iteration_save: OutputPathType | None
+    """Iteration save file"""
+    log_output: OutputPathType | None
+    """Log file generated during execution"""
+
+
+def mri_mcsim_params(
+    top_output_dir: str,
+    base_name: str,
+    surface: list[str],
+    num_repetitions: float,
+    fwhm_values: list[float] | None = None,
+    fwhm_max: float | None = None,
+    avg_vertex_area: bool = False,
+    random_seed: float | None = None,
+    label_file: InputPathType | None = None,
+    mask_file: InputPathType | None = None,
+    no_label: bool = False,
+    no_save_mask: bool = False,
+    surface_name: str | None = None,
+    log_file: str | None = None,
+    done_file: str | None = None,
+    stop_file: str | None = None,
+    save_file: str | None = None,
+    save_iter: bool = False,
+    subjects_dir: str | None = None,
+    debug: bool = False,
+    check_opts: bool = False,
+    help_: bool = False,
+    version: bool = False,
+) -> MriMcsimParameters:
+    """
+    Build parameters.
+    
+    Args:
+        top_output_dir: Top output directory.
+        base_name: Base name for CSD files.
+        surface: Subject name and hemisphere for the surface (e.g., subjectname\
+            lh).
+        num_repetitions: Number of repetitions for the simulation.
+        fwhm_values: Full Width at Half Maximum values for smoothing.
+        fwhm_max: Maximum FWHM for simulation (default 30).
+        avg_vertex_area: Report cluster area based on average vertex area.
+        random_seed: Random seed value (default is based on Time of Day).
+        label_file: Label file for masking (default is ?h.cortex.label).
+        mask_file: Mask file instead of label.
+        no_label: Do not use a label to mask.
+        no_save_mask: Do not save mask to output.
+        surface_name: Surface name (default is white).
+        log_file: Log file for the output.
+        done_file: Done file to create when finished.
+        stop_file: Stop file (default is ourdir/mri_mcsim.stop).
+        save_file: Save file (default is ourdir/mri_mcsim.save).
+        save_iter: Save output after each iteration.
+        subjects_dir: Subjects directory.
+        debug: Turn on debugging.
+        check_opts: Check options do not run.
+        help_: Display help message.
+        version: Display version and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_mcsim",
+        "top_output_dir": top_output_dir,
+        "base_name": base_name,
+        "surface": surface,
+        "num_repetitions": num_repetitions,
+        "avg_vertex_area": avg_vertex_area,
+        "no_label": no_label,
+        "no_save_mask": no_save_mask,
+        "save_iter": save_iter,
+        "debug": debug,
+        "check_opts": check_opts,
+        "help": help_,
+        "version": version,
+    }
+    if fwhm_values is not None:
+        params["fwhm_values"] = fwhm_values
+    if fwhm_max is not None:
+        params["fwhm_max"] = fwhm_max
+    if random_seed is not None:
+        params["random_seed"] = random_seed
+    if label_file is not None:
+        params["label_file"] = label_file
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if surface_name is not None:
+        params["surface_name"] = surface_name
+    if log_file is not None:
+        params["log_file"] = log_file
+    if done_file is not None:
+        params["done_file"] = done_file
+    if stop_file is not None:
+        params["stop_file"] = stop_file
+    if save_file is not None:
+        params["save_file"] = save_file
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
+    return params
+
+
+def mri_mcsim_cargs(
+    params: MriMcsimParameters,
+    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_mcsim")
+    cargs.extend([
+        "--o",
+        params.get("top_output_dir")
+    ])
+    cargs.extend([
+        "--base",
+        params.get("base_name")
+    ])
+    cargs.extend([
+        "--surface",
+        *params.get("surface")
+    ])
+    cargs.extend([
+        "--nreps",
+        str(params.get("num_repetitions"))
+    ])
+    if params.get("fwhm_values") is not None:
+        cargs.extend([
+            "--fwhm",
+            *map(str, params.get("fwhm_values"))
+        ])
+    if params.get("fwhm_max") is not None:
+        cargs.extend([
+            "--fwhm-max",
+            str(params.get("fwhm_max"))
+        ])
+    if params.get("avg_vertex_area"):
+        cargs.append("--avgvtxarea")
+    if params.get("random_seed") is not None:
+        cargs.extend([
+            "--seed",
+            str(params.get("random_seed"))
+        ])
+    if params.get("label_file") is not None:
+        cargs.extend([
+            "--label",
+            execution.input_file(params.get("label_file"))
+        ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("no_label"):
+        cargs.append("--no-label")
+    if params.get("no_save_mask"):
+        cargs.append("--no-save-mask")
+    if params.get("surface_name") is not None:
+        cargs.extend([
+            "--surfname",
+            params.get("surface_name")
+        ])
+    if params.get("log_file") is not None:
+        cargs.extend([
+            "--log",
+            params.get("log_file")
+        ])
+    if params.get("done_file") is not None:
+        cargs.extend([
+            "--done",
+            params.get("done_file")
+        ])
+    if params.get("stop_file") is not None:
+        cargs.extend([
+            "--stop",
+            params.get("stop_file")
+        ])
+    if params.get("save_file") is not None:
+        cargs.extend([
+            "--save",
+            params.get("save_file")
+        ])
+    if params.get("save_iter"):
+        cargs.append("--save-iter")
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("subjects_dir")
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("check_opts"):
+        cargs.append("--checkopts")
+    if params.get("help"):
+        cargs.append("--help")
+    if params.get("version"):
+        cargs.append("--version")
+    return cargs
+
+
+def mri_mcsim_outputs(
+    params: MriMcsimParameters,
+    execution: Execution,
+) -> MriMcsimOutputs:
+    """
+    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 = MriMcsimOutputs(
+        root=execution.output_file("."),
+        csd_output=execution.output_file(params.get("top_output_dir") + "/" + params.get("base_name") + ".csd"),
+        done_output=execution.output_file(params.get("top_output_dir") + "/done/" + params.get("done_file")) if (params.get("done_file") is not None) else None,
+        iteration_save=execution.output_file(params.get("top_output_dir") + "/" + params.get("save_file")) if (params.get("save_file") is not None) else None,
+        log_output=execution.output_file(params.get("top_output_dir") + "/log/" + params.get("log_file")) if (params.get("log_file") is not None) else None,
+    )
+    return ret
+
+
+def mri_mcsim_execute(
+    params: MriMcsimParameters,
+    execution: Execution,
+) -> MriMcsimOutputs:
+    """
+    Monte Carlo simulation tool for surface-based multiple comparisons.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriMcsimOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_mcsim_cargs(params, execution)
+    ret = mri_mcsim_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_mcsim(
+    top_output_dir: str,
+    base_name: str,
+    surface: list[str],
+    num_repetitions: float,
+    fwhm_values: list[float] | None = None,
+    fwhm_max: float | None = None,
+    avg_vertex_area: bool = False,
+    random_seed: float | None = None,
+    label_file: InputPathType | None = None,
+    mask_file: InputPathType | None = None,
+    no_label: bool = False,
+    no_save_mask: bool = False,
+    surface_name: str | None = None,
+    log_file: str | None = None,
+    done_file: str | None = None,
+    stop_file: str | None = None,
+    save_file: str | None = None,
+    save_iter: bool = False,
+    subjects_dir: str | None = None,
+    debug: bool = False,
+    check_opts: bool = False,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MriMcsimOutputs:
+    """
+    Monte Carlo simulation tool for surface-based multiple comparisons.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        top_output_dir: Top output directory.
+        base_name: Base name for CSD files.
+        surface: Subject name and hemisphere for the surface (e.g., subjectname\
+            lh).
+        num_repetitions: Number of repetitions for the simulation.
+        fwhm_values: Full Width at Half Maximum values for smoothing.
+        fwhm_max: Maximum FWHM for simulation (default 30).
+        avg_vertex_area: Report cluster area based on average vertex area.
+        random_seed: Random seed value (default is based on Time of Day).
+        label_file: Label file for masking (default is ?h.cortex.label).
+        mask_file: Mask file instead of label.
+        no_label: Do not use a label to mask.
+        no_save_mask: Do not save mask to output.
+        surface_name: Surface name (default is white).
+        log_file: Log file for the output.
+        done_file: Done file to create when finished.
+        stop_file: Stop file (default is ourdir/mri_mcsim.stop).
+        save_file: Save file (default is ourdir/mri_mcsim.save).
+        save_iter: Save output after each iteration.
+        subjects_dir: Subjects directory.
+        debug: Turn on debugging.
+        check_opts: Check options do not run.
+        help_: Display help message.
+        version: Display version and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriMcsimOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MCSIM_METADATA)
+    params = mri_mcsim_params(
+        top_output_dir=top_output_dir,
+        base_name=base_name,
+        surface=surface,
+        num_repetitions=num_repetitions,
+        fwhm_values=fwhm_values,
+        fwhm_max=fwhm_max,
+        avg_vertex_area=avg_vertex_area,
+        random_seed=random_seed,
+        label_file=label_file,
+        mask_file=mask_file,
+        no_label=no_label,
+        no_save_mask=no_save_mask,
+        surface_name=surface_name,
+        log_file=log_file,
+        done_file=done_file,
+        stop_file=stop_file,
+        save_file=save_file,
+        save_iter=save_iter,
+        subjects_dir=subjects_dir,
+        debug=debug,
+        check_opts=check_opts,
+        help_=help_,
+        version=version,
+    )
+    return mri_mcsim_execute(params, execution)
+
+
+__all__ = [
+    "MRI_MCSIM_METADATA",
+    "MriMcsimOutputs",
+    "MriMcsimParameters",
+    "mri_mcsim",
+    "mri_mcsim_params",
+]