niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_fwhm.py

@@ -0,0 +1,521 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_FWHM_METADATA = Metadata(
+    id="3df5d08538916b5e720d481edb2f9270d2c60c51.boutiques",
+    name="mris_fwhm",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisFwhmParameters = typing.TypedDict('MrisFwhmParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_fwhm"],
+    "input_file": InputPathType,
+    "subject": str,
+    "hemi": str,
+    "surf": typing.NotRequired[str | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "cortex_flag": bool,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "x_matrix": typing.NotRequired[InputPathType | None],
+    "detrend_order": typing.NotRequired[float | None],
+    "smooth_only_flag": bool,
+    "no_detrend_flag": bool,
+    "sqr_flag": bool,
+    "sum_file": typing.NotRequired[str | None],
+    "dat_file": typing.NotRequired[str | None],
+    "ar1dat_file": typing.NotRequired[str | None],
+    "ar1vol": typing.NotRequired[str | None],
+    "fwhmmap": typing.NotRequired[str | None],
+    "prune_flag": bool,
+    "no_prune_flag": bool,
+    "out_mask": typing.NotRequired[str | None],
+    "varnorm_flag": bool,
+    "fwhm": typing.NotRequired[float | None],
+    "niters_only": typing.NotRequired[str | None],
+    "output_file": str,
+    "sd": typing.NotRequired[str | None],
+    "synth_flag": bool,
+    "synth_frames": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "debug_flag": bool,
+    "checkopts_flag": bool,
+    "version_flag": 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_fwhm": mris_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 {
+    }.get(t)
+
+
+class MrisFwhmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_fwhm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_fwhm_params(
+    input_file: InputPathType,
+    subject: str,
+    hemi: str,
+    output_file: str,
+    surf: str | None = None,
+    label_file: InputPathType | None = None,
+    cortex_flag: bool = False,
+    mask_file: InputPathType | None = None,
+    x_matrix: InputPathType | None = None,
+    detrend_order: float | None = None,
+    smooth_only_flag: bool = False,
+    no_detrend_flag: bool = False,
+    sqr_flag: bool = False,
+    sum_file: str | None = None,
+    dat_file: str | None = None,
+    ar1dat_file: str | None = None,
+    ar1vol: str | None = None,
+    fwhmmap: str | None = None,
+    prune_flag: bool = False,
+    no_prune_flag: bool = False,
+    out_mask: str | None = None,
+    varnorm_flag: bool = False,
+    fwhm: float | None = None,
+    niters_only: str | None = None,
+    sd: str | None = None,
+    synth_flag: bool = False,
+    synth_frames: float | None = None,
+    threads: float | None = None,
+    debug_flag: bool = False,
+    checkopts_flag: bool = False,
+    version_flag: bool = False,
+) -> MrisFwhmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input data file.
+        subject: Subject whose surface the input is defined on.
+        hemi: Hemifield that the input is defined on. Legal values are lh and\
+            rh.
+        output_file: Output file to save the processed data.
+        surf: Surface name to compute AR1 on. Default is white.
+        label_file: Label file to be used as a mask.
+        cortex_flag: Use hemi.cortex.label as a mask.
+        mask_file: Mask file. Compute AR1 only over voxels in the given mask.
+        x_matrix: Detrend data with the matrix in x.mat.
+        detrend_order: Order of polynomial detrending.
+        smooth_only_flag: Only smooth the data, implies --no-detrend.
+        no_detrend_flag: Turn off polynomial detrending.
+        sqr_flag: Compute square of input before smoothing.
+        sum_file: Prints ascii summary to sumfile.
+        dat_file: File for FWHM data.
+        ar1dat_file: File containing ar1mean and ar1std.
+        ar1vol: Save spatial AR1 as an overlay.
+        fwhmmap: Save vertex-wise spatial FWHM as an overlay.
+        prune_flag: Remove any voxel that is zero in any subject (after any\
+            inversion).
+        no_prune_flag: Do not prune (default).
+        out_mask: File to save the final mask.
+        varnorm_flag: Normalize the variance across space within any mask.
+        fwhm: Smooth input by the specified FWHM in mm.
+        niters_only: File that reports the number of iterations needed to\
+            achieve the specified FWHM.
+        sd: Subjects directory.
+        synth_flag: Synthesize input with white gaussian noise.
+        synth_frames: Number of frames for synthesized input.
+        threads: Number of threads to use.
+        debug_flag: Turn on debugging.
+        checkopts_flag: Don't run anything, just check options and exit.
+        version_flag: Print out version and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_fwhm",
+        "input_file": input_file,
+        "subject": subject,
+        "hemi": hemi,
+        "cortex_flag": cortex_flag,
+        "smooth_only_flag": smooth_only_flag,
+        "no_detrend_flag": no_detrend_flag,
+        "sqr_flag": sqr_flag,
+        "prune_flag": prune_flag,
+        "no_prune_flag": no_prune_flag,
+        "varnorm_flag": varnorm_flag,
+        "output_file": output_file,
+        "synth_flag": synth_flag,
+        "debug_flag": debug_flag,
+        "checkopts_flag": checkopts_flag,
+        "version_flag": version_flag,
+    }
+    if surf is not None:
+        params["surf"] = surf
+    if label_file is not None:
+        params["label_file"] = label_file
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if x_matrix is not None:
+        params["x_matrix"] = x_matrix
+    if detrend_order is not None:
+        params["detrend_order"] = detrend_order
+    if sum_file is not None:
+        params["sum_file"] = sum_file
+    if dat_file is not None:
+        params["dat_file"] = dat_file
+    if ar1dat_file is not None:
+        params["ar1dat_file"] = ar1dat_file
+    if ar1vol is not None:
+        params["ar1vol"] = ar1vol
+    if fwhmmap is not None:
+        params["fwhmmap"] = fwhmmap
+    if out_mask is not None:
+        params["out_mask"] = out_mask
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if niters_only is not None:
+        params["niters_only"] = niters_only
+    if sd is not None:
+        params["sd"] = sd
+    if synth_frames is not None:
+        params["synth_frames"] = synth_frames
+    if threads is not None:
+        params["threads"] = threads
+    return params
+
+
+def mris_fwhm_cargs(
+    params: MrisFwhmParameters,
+    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_fwhm")
+    cargs.extend([
+        "--i",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "--subject",
+        params.get("subject")
+    ])
+    cargs.extend([
+        "--hemi",
+        params.get("hemi")
+    ])
+    if params.get("surf") is not None:
+        cargs.extend([
+            "--surf",
+            params.get("surf")
+        ])
+    if params.get("label_file") is not None:
+        cargs.extend([
+            "--label",
+            execution.input_file(params.get("label_file"))
+        ])
+    if params.get("cortex_flag"):
+        cargs.append("--cortex")
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("x_matrix") is not None:
+        cargs.extend([
+            "--X",
+            execution.input_file(params.get("x_matrix"))
+        ])
+    if params.get("detrend_order") is not None:
+        cargs.extend([
+            "--detrend",
+            str(params.get("detrend_order"))
+        ])
+    if params.get("smooth_only_flag"):
+        cargs.append("--smooth-only")
+    if params.get("no_detrend_flag"):
+        cargs.append("--no-detrend")
+    if params.get("sqr_flag"):
+        cargs.append("--sqr")
+    if params.get("sum_file") is not None:
+        cargs.extend([
+            "--sum",
+            params.get("sum_file")
+        ])
+    if params.get("dat_file") is not None:
+        cargs.extend([
+            "--dat",
+            params.get("dat_file")
+        ])
+    if params.get("ar1dat_file") is not None:
+        cargs.extend([
+            "--ar1dat",
+            params.get("ar1dat_file")
+        ])
+    if params.get("ar1vol") is not None:
+        cargs.extend([
+            "--ar1",
+            params.get("ar1vol")
+        ])
+    if params.get("fwhmmap") is not None:
+        cargs.extend([
+            "--fwhm-map",
+            params.get("fwhmmap")
+        ])
+    if params.get("prune_flag"):
+        cargs.append("--prune")
+    if params.get("no_prune_flag"):
+        cargs.append("--no-prune")
+    if params.get("out_mask") is not None:
+        cargs.extend([
+            "--out-mask",
+            params.get("out_mask")
+        ])
+    if params.get("varnorm_flag"):
+        cargs.append("--varnorm")
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "--fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("niters_only") is not None:
+        cargs.extend([
+            "--niters-only",
+            params.get("niters_only")
+        ])
+    cargs.extend([
+        "--o",
+        params.get("output_file")
+    ])
+    if params.get("sd") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("sd")
+        ])
+    if params.get("synth_flag"):
+        cargs.append("--synth")
+    if params.get("synth_frames") is not None:
+        cargs.extend([
+            "--synth-frames",
+            str(params.get("synth_frames"))
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("debug_flag"):
+        cargs.append("--debug")
+    if params.get("checkopts_flag"):
+        cargs.append("--checkopts")
+    if params.get("version_flag"):
+        cargs.append("--version")
+    return cargs
+
+
+def mris_fwhm_outputs(
+    params: MrisFwhmParameters,
+    execution: Execution,
+) -> MrisFwhmOutputs:
+    """
+    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 = MrisFwhmOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_fwhm_execute(
+    params: MrisFwhmParameters,
+    execution: Execution,
+) -> MrisFwhmOutputs:
+    """
+    Smooths surface data and/or estimates FWHM.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisFwhmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_fwhm_cargs(params, execution)
+    ret = mris_fwhm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_fwhm(
+    input_file: InputPathType,
+    subject: str,
+    hemi: str,
+    output_file: str,
+    surf: str | None = None,
+    label_file: InputPathType | None = None,
+    cortex_flag: bool = False,
+    mask_file: InputPathType | None = None,
+    x_matrix: InputPathType | None = None,
+    detrend_order: float | None = None,
+    smooth_only_flag: bool = False,
+    no_detrend_flag: bool = False,
+    sqr_flag: bool = False,
+    sum_file: str | None = None,
+    dat_file: str | None = None,
+    ar1dat_file: str | None = None,
+    ar1vol: str | None = None,
+    fwhmmap: str | None = None,
+    prune_flag: bool = False,
+    no_prune_flag: bool = False,
+    out_mask: str | None = None,
+    varnorm_flag: bool = False,
+    fwhm: float | None = None,
+    niters_only: str | None = None,
+    sd: str | None = None,
+    synth_flag: bool = False,
+    synth_frames: float | None = None,
+    threads: float | None = None,
+    debug_flag: bool = False,
+    checkopts_flag: bool = False,
+    version_flag: bool = False,
+    runner: Runner | None = None,
+) -> MrisFwhmOutputs:
+    """
+    Smooths surface data and/or estimates FWHM.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_file: Input data file.
+        subject: Subject whose surface the input is defined on.
+        hemi: Hemifield that the input is defined on. Legal values are lh and\
+            rh.
+        output_file: Output file to save the processed data.
+        surf: Surface name to compute AR1 on. Default is white.
+        label_file: Label file to be used as a mask.
+        cortex_flag: Use hemi.cortex.label as a mask.
+        mask_file: Mask file. Compute AR1 only over voxels in the given mask.
+        x_matrix: Detrend data with the matrix in x.mat.
+        detrend_order: Order of polynomial detrending.
+        smooth_only_flag: Only smooth the data, implies --no-detrend.
+        no_detrend_flag: Turn off polynomial detrending.
+        sqr_flag: Compute square of input before smoothing.
+        sum_file: Prints ascii summary to sumfile.
+        dat_file: File for FWHM data.
+        ar1dat_file: File containing ar1mean and ar1std.
+        ar1vol: Save spatial AR1 as an overlay.
+        fwhmmap: Save vertex-wise spatial FWHM as an overlay.
+        prune_flag: Remove any voxel that is zero in any subject (after any\
+            inversion).
+        no_prune_flag: Do not prune (default).
+        out_mask: File to save the final mask.
+        varnorm_flag: Normalize the variance across space within any mask.
+        fwhm: Smooth input by the specified FWHM in mm.
+        niters_only: File that reports the number of iterations needed to\
+            achieve the specified FWHM.
+        sd: Subjects directory.
+        synth_flag: Synthesize input with white gaussian noise.
+        synth_frames: Number of frames for synthesized input.
+        threads: Number of threads to use.
+        debug_flag: Turn on debugging.
+        checkopts_flag: Don't run anything, just check options and exit.
+        version_flag: Print out version and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisFwhmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_FWHM_METADATA)
+    params = mris_fwhm_params(
+        input_file=input_file,
+        subject=subject,
+        hemi=hemi,
+        surf=surf,
+        label_file=label_file,
+        cortex_flag=cortex_flag,
+        mask_file=mask_file,
+        x_matrix=x_matrix,
+        detrend_order=detrend_order,
+        smooth_only_flag=smooth_only_flag,
+        no_detrend_flag=no_detrend_flag,
+        sqr_flag=sqr_flag,
+        sum_file=sum_file,
+        dat_file=dat_file,
+        ar1dat_file=ar1dat_file,
+        ar1vol=ar1vol,
+        fwhmmap=fwhmmap,
+        prune_flag=prune_flag,
+        no_prune_flag=no_prune_flag,
+        out_mask=out_mask,
+        varnorm_flag=varnorm_flag,
+        fwhm=fwhm,
+        niters_only=niters_only,
+        output_file=output_file,
+        sd=sd,
+        synth_flag=synth_flag,
+        synth_frames=synth_frames,
+        threads=threads,
+        debug_flag=debug_flag,
+        checkopts_flag=checkopts_flag,
+        version_flag=version_flag,
+    )
+    return mris_fwhm_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_FWHM_METADATA",
+    "MrisFwhmOutputs",
+    "MrisFwhmParameters",
+    "mris_fwhm",
+    "mris_fwhm_params",
+]

niwrap_freesurfer/freesurfer/mris_gradient.py

@@ -0,0 +1,196 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_GRADIENT_METADATA = Metadata(
+    id="4e76ee59424b712977309da37bac35a8195a7230.boutiques",
+    name="mris_gradient",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisGradientParameters = typing.TypedDict('MrisGradientParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_gradient"],
+    "input_surface": InputPathType,
+    "input_vector_field": InputPathType,
+    "output_gradient_file": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_gradient": mris_gradient_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_gradient": mris_gradient_outputs,
+    }.get(t)
+
+
+class MrisGradientOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_gradient(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_gradient: OutputPathType
+    """The resulting gradient measurement written into a .mgz file."""
+
+
+def mris_gradient_params(
+    input_surface: InputPathType,
+    input_vector_field: InputPathType,
+    output_gradient_file: str,
+) -> MrisGradientParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_surface: Path to the input surface file.
+        input_vector_field: Path to the input vector field file.
+        output_gradient_file: Path to the output gradient file ending with\
+            .mgz.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_gradient",
+        "input_surface": input_surface,
+        "input_vector_field": input_vector_field,
+        "output_gradient_file": output_gradient_file,
+    }
+    return params
+
+
+def mris_gradient_cargs(
+    params: MrisGradientParameters,
+    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_gradient")
+    cargs.append(execution.input_file(params.get("input_surface")))
+    cargs.append(execution.input_file(params.get("input_vector_field")))
+    cargs.append(params.get("output_gradient_file"))
+    return cargs
+
+
+def mris_gradient_outputs(
+    params: MrisGradientParameters,
+    execution: Execution,
+) -> MrisGradientOutputs:
+    """
+    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 = MrisGradientOutputs(
+        root=execution.output_file("."),
+        output_gradient=execution.output_file(params.get("output_gradient_file")),
+    )
+    return ret
+
+
+def mris_gradient_execute(
+    params: MrisGradientParameters,
+    execution: Execution,
+) -> MrisGradientOutputs:
+    """
+    This program computes the gradient of an intensity profile of the cortical
+    ribbon and writes the resulting measurement into a .mgz file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisGradientOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_gradient_cargs(params, execution)
+    ret = mris_gradient_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_gradient(
+    input_surface: InputPathType,
+    input_vector_field: InputPathType,
+    output_gradient_file: str,
+    runner: Runner | None = None,
+) -> MrisGradientOutputs:
+    """
+    This program computes the gradient of an intensity profile of the cortical
+    ribbon and writes the resulting measurement into a .mgz file.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_surface: Path to the input surface file.
+        input_vector_field: Path to the input vector field file.
+        output_gradient_file: Path to the output gradient file ending with\
+            .mgz.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisGradientOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_GRADIENT_METADATA)
+    params = mris_gradient_params(
+        input_surface=input_surface,
+        input_vector_field=input_vector_field,
+        output_gradient_file=output_gradient_file,
+    )
+    return mris_gradient_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_GRADIENT_METADATA",
+    "MrisGradientOutputs",
+    "MrisGradientParameters",
+    "mris_gradient",
+    "mris_gradient_params",
+]