niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_fwhm.py

@@ -0,0 +1,603 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_FWHM_METADATA = Metadata(
+    id="d03adb51c2f77acaf364735a5ea7ff81b4be91ea.boutiques",
+    name="mri_fwhm",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriFwhmParameters = typing.TypedDict('MriFwhmParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_fwhm"],
+    "inputvol": InputPathType,
+    "outputvol": str,
+    "save_detrended": bool,
+    "save_unmasked": bool,
+    "smooth_only": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_thresh": typing.NotRequired[float | None],
+    "auto_mask": typing.NotRequired[float | None],
+    "nerode": typing.NotRequired[float | None],
+    "mask_inv": bool,
+    "out_mask": typing.NotRequired[str | None],
+    "detrend_matrix": typing.NotRequired[InputPathType | None],
+    "detrend_order": typing.NotRequired[float | None],
+    "square_input": bool,
+    "smooth_by_fwhm": typing.NotRequired[float | None],
+    "smooth_by_gstd": typing.NotRequired[float | None],
+    "median_filter": typing.NotRequired[float | None],
+    "smooth_to_fwhm": typing.NotRequired[float | None],
+    "to_fwhm_tol": typing.NotRequired[float | None],
+    "to_fwhm_nmax": typing.NotRequired[float | None],
+    "to_fwhm_file": typing.NotRequired[str | None],
+    "summary_file": typing.NotRequired[str | None],
+    "dat_file": typing.NotRequired[str | None],
+    "fwhm_dat_file": typing.NotRequired[str | None],
+    "fwhm_vol_mean_file": typing.NotRequired[str | None],
+    "fwhm_vol": typing.NotRequired[str | None],
+    "synth": bool,
+    "synth_frames": typing.NotRequired[float | None],
+    "nframes_min": typing.NotRequired[float | None],
+    "ispm": bool,
+    "nspm_zero_padding": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": 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_fwhm": mri_fwhm_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_fwhm": mri_fwhm_outputs,
+    }.get(t)
+
+
+class MriFwhmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_fwhm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume_file: OutputPathType
+    """Output volume after smoothing."""
+    final_mask_output_file: OutputPathType | None
+    """Final mask volume."""
+    summary_log_file: OutputPathType | None
+    """Summary log file."""
+    final_fwhm_estimate_file: OutputPathType | None
+    """Final FWHM estimate file."""
+    fwhm_of_each_dimension_file: OutputPathType | None
+    """File containing the FWHM of each dimension."""
+    mean_fwhm_volume_file: OutputPathType | None
+    """Mean FWHM from volume file."""
+    fwhm_volume_file: OutputPathType | None
+    """FWHM volume file."""
+
+
+def mri_fwhm_params(
+    inputvol: InputPathType,
+    outputvol: str,
+    save_detrended: bool = False,
+    save_unmasked: bool = False,
+    smooth_only: bool = False,
+    mask: InputPathType | None = None,
+    mask_thresh: float | None = None,
+    auto_mask: float | None = None,
+    nerode: float | None = None,
+    mask_inv: bool = False,
+    out_mask: str | None = None,
+    detrend_matrix: InputPathType | None = None,
+    detrend_order: float | None = None,
+    square_input: bool = False,
+    smooth_by_fwhm: float | None = None,
+    smooth_by_gstd: float | None = None,
+    median_filter: float | None = None,
+    smooth_to_fwhm: float | None = None,
+    to_fwhm_tol: float | None = None,
+    to_fwhm_nmax: float | None = None,
+    to_fwhm_file: str | None = None,
+    summary_file: str | None = None,
+    dat_file: str | None = None,
+    fwhm_dat_file: str | None = None,
+    fwhm_vol_mean_file: str | None = None,
+    fwhm_vol: str | None = None,
+    synth: bool = False,
+    synth_frames: float | None = None,
+    nframes_min: float | None = None,
+    ispm: bool = False,
+    nspm_zero_padding: float | None = None,
+    threads: float | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    version: bool = False,
+) -> MriFwhmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inputvol: Input volume file. Format must be something readable by\
+            mri_convert (e.g., mgh, mgz, img, nii, nii.gz).
+        outputvol: Output volume file: save input after smoothing.
+        save_detrended: Save input after smoothing and detrending.
+        save_unmasked: Do not mask output volume.
+        smooth_only: Smooth and save, do not compute fwhm.
+        mask: Binary mask file.
+        mask_thresh: Threshold for mask (default is 0.5).
+        auto_mask: Auto compute mask based on global mean threshold.
+        nerode: Erode mask n times prior to FWHM computation.
+        mask_inv: Invert mask.
+        out_mask: Save final mask to outmaskvol.
+        detrend_matrix: Detrending matrix file in MATLAB4 format.
+        detrend_order: Polynomial detrending order (default 0).
+        square_input: Compute square of input before smoothing.
+        smooth_by_fwhm: Smooth BY fwhm before measuring.
+        smooth_by_gstd: Smooth using gstd (equivalent to --fwhm).
+        median_filter: Perform median filtering instead of Gaussian.
+        smooth_to_fwhm: Smooth TO this FWHM.
+        to_fwhm_tol: Tolerance for smoothing to FWHM (default 0.5mm).
+        to_fwhm_nmax: Maximum iterations for smoothing to FWHM (default 20).
+        to_fwhm_file: Save smoothing to FWHM parameters to file.
+        summary_file: Summary/log file.
+        dat_file: Prints only the final FWHM estimate into this file.
+        fwhm_dat_file: Compute and save the FWHM of each dimension.
+        fwhm_vol_mean_file: Compute and save the FWHM of each dimension based\
+            on fwhmvol.
+        fwhm_vol: Save FWHM volume.
+        synth: Synthesize input with white Gaussian noise.
+        synth_frames: Number of frames for synthesized input (default is 10).
+        nframes_min: Require at least this many frames.
+        ispm: Input is SPM-analyze.
+        nspm_zero_padding: Zero-padding for SPM-analyze.
+        threads: Set OPEN MP threads.
+        debug: Turn on debugging.
+        checkopts: Check options and exit without running.
+        version: Print version and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_fwhm",
+        "inputvol": inputvol,
+        "outputvol": outputvol,
+        "save_detrended": save_detrended,
+        "save_unmasked": save_unmasked,
+        "smooth_only": smooth_only,
+        "mask_inv": mask_inv,
+        "square_input": square_input,
+        "synth": synth,
+        "ispm": ispm,
+        "debug": debug,
+        "checkopts": checkopts,
+        "version": version,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if mask_thresh is not None:
+        params["mask_thresh"] = mask_thresh
+    if auto_mask is not None:
+        params["auto_mask"] = auto_mask
+    if nerode is not None:
+        params["nerode"] = nerode
+    if out_mask is not None:
+        params["out_mask"] = out_mask
+    if detrend_matrix is not None:
+        params["detrend_matrix"] = detrend_matrix
+    if detrend_order is not None:
+        params["detrend_order"] = detrend_order
+    if smooth_by_fwhm is not None:
+        params["smooth_by_fwhm"] = smooth_by_fwhm
+    if smooth_by_gstd is not None:
+        params["smooth_by_gstd"] = smooth_by_gstd
+    if median_filter is not None:
+        params["median_filter"] = median_filter
+    if smooth_to_fwhm is not None:
+        params["smooth_to_fwhm"] = smooth_to_fwhm
+    if to_fwhm_tol is not None:
+        params["to_fwhm_tol"] = to_fwhm_tol
+    if to_fwhm_nmax is not None:
+        params["to_fwhm_nmax"] = to_fwhm_nmax
+    if to_fwhm_file is not None:
+        params["to_fwhm_file"] = to_fwhm_file
+    if summary_file is not None:
+        params["summary_file"] = summary_file
+    if dat_file is not None:
+        params["dat_file"] = dat_file
+    if fwhm_dat_file is not None:
+        params["fwhm_dat_file"] = fwhm_dat_file
+    if fwhm_vol_mean_file is not None:
+        params["fwhm_vol_mean_file"] = fwhm_vol_mean_file
+    if fwhm_vol is not None:
+        params["fwhm_vol"] = fwhm_vol
+    if synth_frames is not None:
+        params["synth_frames"] = synth_frames
+    if nframes_min is not None:
+        params["nframes_min"] = nframes_min
+    if nspm_zero_padding is not None:
+        params["nspm_zero_padding"] = nspm_zero_padding
+    if threads is not None:
+        params["threads"] = threads
+    return params
+
+
+def mri_fwhm_cargs(
+    params: MriFwhmParameters,
+    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_fwhm")
+    cargs.extend([
+        "--i",
+        execution.input_file(params.get("inputvol"))
+    ])
+    cargs.extend([
+        "--o",
+        params.get("outputvol")
+    ])
+    if params.get("save_detrended"):
+        cargs.append("--save-detrended")
+    if params.get("save_unmasked"):
+        cargs.append("--save-unmasked")
+    if params.get("smooth_only"):
+        cargs.append("--smooth-only")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("mask_thresh") is not None:
+        cargs.extend([
+            "--mask-thresh",
+            str(params.get("mask_thresh"))
+        ])
+    if params.get("auto_mask") is not None:
+        cargs.extend([
+            "--auto-mask",
+            str(params.get("auto_mask"))
+        ])
+    if params.get("nerode") is not None:
+        cargs.extend([
+            "--nerode",
+            str(params.get("nerode"))
+        ])
+    if params.get("mask_inv"):
+        cargs.append("--mask-inv")
+    if params.get("out_mask") is not None:
+        cargs.extend([
+            "--out-mask",
+            params.get("out_mask")
+        ])
+    if params.get("detrend_matrix") is not None:
+        cargs.extend([
+            "--X",
+            execution.input_file(params.get("detrend_matrix"))
+        ])
+    if params.get("detrend_order") is not None:
+        cargs.extend([
+            "--detrend",
+            str(params.get("detrend_order"))
+        ])
+    if params.get("square_input"):
+        cargs.append("--sqr")
+    if params.get("smooth_by_fwhm") is not None:
+        cargs.extend([
+            "--fwhm",
+            str(params.get("smooth_by_fwhm"))
+        ])
+    if params.get("smooth_by_gstd") is not None:
+        cargs.extend([
+            "--gstd",
+            str(params.get("smooth_by_gstd"))
+        ])
+    if params.get("median_filter") is not None:
+        cargs.extend([
+            "--median",
+            str(params.get("median_filter"))
+        ])
+    if params.get("smooth_to_fwhm") is not None:
+        cargs.extend([
+            "--to-fwhm",
+            str(params.get("smooth_to_fwhm"))
+        ])
+    if params.get("to_fwhm_tol") is not None:
+        cargs.extend([
+            "--to-fwhm-tol",
+            str(params.get("to_fwhm_tol"))
+        ])
+    if params.get("to_fwhm_nmax") is not None:
+        cargs.extend([
+            "--to-fwhm-nmax",
+            str(params.get("to_fwhm_nmax"))
+        ])
+    if params.get("to_fwhm_file") is not None:
+        cargs.extend([
+            "--to-fwhm-file",
+            params.get("to_fwhm_file")
+        ])
+    if params.get("summary_file") is not None:
+        cargs.extend([
+            "--sum",
+            params.get("summary_file")
+        ])
+    if params.get("dat_file") is not None:
+        cargs.extend([
+            "--dat",
+            params.get("dat_file")
+        ])
+    if params.get("fwhm_dat_file") is not None:
+        cargs.extend([
+            "--fwhmdat",
+            params.get("fwhm_dat_file")
+        ])
+    if params.get("fwhm_vol_mean_file") is not None:
+        cargs.extend([
+            "--fwhmvolmn",
+            params.get("fwhm_vol_mean_file")
+        ])
+    if params.get("fwhm_vol") is not None:
+        cargs.extend([
+            "--fwhmvol",
+            params.get("fwhm_vol")
+        ])
+    if params.get("synth"):
+        cargs.append("--synth")
+    if params.get("synth_frames") is not None:
+        cargs.extend([
+            "--synth-frames",
+            str(params.get("synth_frames"))
+        ])
+    if params.get("nframes_min") is not None:
+        cargs.extend([
+            "--nframesmin",
+            str(params.get("nframes_min"))
+        ])
+    if params.get("ispm"):
+        cargs.append("--ispm")
+    if params.get("nspm_zero_padding") is not None:
+        cargs.extend([
+            "--in_nspmzeropad",
+            str(params.get("nspm_zero_padding"))
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--nthreads",
+            str(params.get("threads"))
+        ])
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("checkopts"):
+        cargs.append("--checkopts")
+    if params.get("version"):
+        cargs.append("--version")
+    return cargs
+
+
+def mri_fwhm_outputs(
+    params: MriFwhmParameters,
+    execution: Execution,
+) -> MriFwhmOutputs:
+    """
+    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 = MriFwhmOutputs(
+        root=execution.output_file("."),
+        output_volume_file=execution.output_file(params.get("outputvol")),
+        final_mask_output_file=execution.output_file(params.get("out_mask")) if (params.get("out_mask") is not None) else None,
+        summary_log_file=execution.output_file(params.get("summary_file")) if (params.get("summary_file") is not None) else None,
+        final_fwhm_estimate_file=execution.output_file(params.get("dat_file")) if (params.get("dat_file") is not None) else None,
+        fwhm_of_each_dimension_file=execution.output_file(params.get("fwhm_dat_file")) if (params.get("fwhm_dat_file") is not None) else None,
+        mean_fwhm_volume_file=execution.output_file(params.get("fwhm_vol_mean_file")) if (params.get("fwhm_vol_mean_file") is not None) else None,
+        fwhm_volume_file=execution.output_file(params.get("fwhm_vol")) if (params.get("fwhm_vol") is not None) else None,
+    )
+    return ret
+
+
+def mri_fwhm_execute(
+    params: MriFwhmParameters,
+    execution: Execution,
+) -> MriFwhmOutputs:
+    """
+    FreeSurfer program to estimate the global Gaussian smoothness of a multi-frame,
+    volume-based data set.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriFwhmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_fwhm_cargs(params, execution)
+    ret = mri_fwhm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_fwhm(
+    inputvol: InputPathType,
+    outputvol: str,
+    save_detrended: bool = False,
+    save_unmasked: bool = False,
+    smooth_only: bool = False,
+    mask: InputPathType | None = None,
+    mask_thresh: float | None = None,
+    auto_mask: float | None = None,
+    nerode: float | None = None,
+    mask_inv: bool = False,
+    out_mask: str | None = None,
+    detrend_matrix: InputPathType | None = None,
+    detrend_order: float | None = None,
+    square_input: bool = False,
+    smooth_by_fwhm: float | None = None,
+    smooth_by_gstd: float | None = None,
+    median_filter: float | None = None,
+    smooth_to_fwhm: float | None = None,
+    to_fwhm_tol: float | None = None,
+    to_fwhm_nmax: float | None = None,
+    to_fwhm_file: str | None = None,
+    summary_file: str | None = None,
+    dat_file: str | None = None,
+    fwhm_dat_file: str | None = None,
+    fwhm_vol_mean_file: str | None = None,
+    fwhm_vol: str | None = None,
+    synth: bool = False,
+    synth_frames: float | None = None,
+    nframes_min: float | None = None,
+    ispm: bool = False,
+    nspm_zero_padding: float | None = None,
+    threads: float | None = None,
+    debug: bool = False,
+    checkopts: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MriFwhmOutputs:
+    """
+    FreeSurfer program to estimate the global Gaussian smoothness of a multi-frame,
+    volume-based data set.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        inputvol: Input volume file. Format must be something readable by\
+            mri_convert (e.g., mgh, mgz, img, nii, nii.gz).
+        outputvol: Output volume file: save input after smoothing.
+        save_detrended: Save input after smoothing and detrending.
+        save_unmasked: Do not mask output volume.
+        smooth_only: Smooth and save, do not compute fwhm.
+        mask: Binary mask file.
+        mask_thresh: Threshold for mask (default is 0.5).
+        auto_mask: Auto compute mask based on global mean threshold.
+        nerode: Erode mask n times prior to FWHM computation.
+        mask_inv: Invert mask.
+        out_mask: Save final mask to outmaskvol.
+        detrend_matrix: Detrending matrix file in MATLAB4 format.
+        detrend_order: Polynomial detrending order (default 0).
+        square_input: Compute square of input before smoothing.
+        smooth_by_fwhm: Smooth BY fwhm before measuring.
+        smooth_by_gstd: Smooth using gstd (equivalent to --fwhm).
+        median_filter: Perform median filtering instead of Gaussian.
+        smooth_to_fwhm: Smooth TO this FWHM.
+        to_fwhm_tol: Tolerance for smoothing to FWHM (default 0.5mm).
+        to_fwhm_nmax: Maximum iterations for smoothing to FWHM (default 20).
+        to_fwhm_file: Save smoothing to FWHM parameters to file.
+        summary_file: Summary/log file.
+        dat_file: Prints only the final FWHM estimate into this file.
+        fwhm_dat_file: Compute and save the FWHM of each dimension.
+        fwhm_vol_mean_file: Compute and save the FWHM of each dimension based\
+            on fwhmvol.
+        fwhm_vol: Save FWHM volume.
+        synth: Synthesize input with white Gaussian noise.
+        synth_frames: Number of frames for synthesized input (default is 10).
+        nframes_min: Require at least this many frames.
+        ispm: Input is SPM-analyze.
+        nspm_zero_padding: Zero-padding for SPM-analyze.
+        threads: Set OPEN MP threads.
+        debug: Turn on debugging.
+        checkopts: Check options and exit without running.
+        version: Print version and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriFwhmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FWHM_METADATA)
+    params = mri_fwhm_params(
+        inputvol=inputvol,
+        outputvol=outputvol,
+        save_detrended=save_detrended,
+        save_unmasked=save_unmasked,
+        smooth_only=smooth_only,
+        mask=mask,
+        mask_thresh=mask_thresh,
+        auto_mask=auto_mask,
+        nerode=nerode,
+        mask_inv=mask_inv,
+        out_mask=out_mask,
+        detrend_matrix=detrend_matrix,
+        detrend_order=detrend_order,
+        square_input=square_input,
+        smooth_by_fwhm=smooth_by_fwhm,
+        smooth_by_gstd=smooth_by_gstd,
+        median_filter=median_filter,
+        smooth_to_fwhm=smooth_to_fwhm,
+        to_fwhm_tol=to_fwhm_tol,
+        to_fwhm_nmax=to_fwhm_nmax,
+        to_fwhm_file=to_fwhm_file,
+        summary_file=summary_file,
+        dat_file=dat_file,
+        fwhm_dat_file=fwhm_dat_file,
+        fwhm_vol_mean_file=fwhm_vol_mean_file,
+        fwhm_vol=fwhm_vol,
+        synth=synth,
+        synth_frames=synth_frames,
+        nframes_min=nframes_min,
+        ispm=ispm,
+        nspm_zero_padding=nspm_zero_padding,
+        threads=threads,
+        debug=debug,
+        checkopts=checkopts,
+        version=version,
+    )
+    return mri_fwhm_execute(params, execution)
+
+
+__all__ = [
+    "MRI_FWHM_METADATA",
+    "MriFwhmOutputs",
+    "MriFwhmParameters",
+    "mri_fwhm",
+    "mri_fwhm_params",
+]